Index (magpie API)

A B C D E F G H I J K L M N O P Q R S T U V W Y Z

A

about() - Method in class magpie.attributes.selectors.BaseAttributeSelector
about() - Method in class magpie.cluster.BaseClusterer
about() - Method in class magpie.csp.CSPEngine
about() - Method in class magpie.csp.CSPPerformanceStats
about() - Method in class magpie.data.Dataset
about() - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
about() - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
about() - Method in class magpie.models.BaseModel
about() - Method in class magpie.statistics.performance.BaseStatistics
about() - Method in class magpie.statistics.performance.ClustererStatistics
about() - Method in interface magpie.utility.interfaces.Printable: Prints a simple status message about this object
about() - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
AbstractClassifier - Interface in magpie.models.classification: Interface that defines what operations a Classifier must fulfill
AbstractNonlinearRegression - Class in magpie.models.regression: Abstract class for models that fit terms using non-linear regression.
AbstractNonlinearRegression() - Constructor for class magpie.models.regression.AbstractNonlinearRegression
AbstractParsedNonlinearRegression - Class in magpie.models.regression: Superclass of AbstractNonlinearRegression-based models which parse the equation of interest from text input.
AbstractParsedNonlinearRegression() - Constructor for class magpie.models.regression.AbstractParsedNonlinearRegression
AbstractRegressionModel - Interface in magpie.models.regression: Interface for all regression models.
Accuracy - Variable in class magpie.statistics.performance.ClassificationStatistics: Accuracy
actuallyPrintEntries(Collection<BaseEntry>, OutputStream) - Method in class magpie.data.utilities.output.SimpleOutput: Hidden method to print entries.
AdaptiveScalarizingEntryRanker - Class in magpie.optimization.rankers: Transforms the values of multiple objectives to a single variable using automatically-determined weights.
AdaptiveScalarizingEntryRanker() - Constructor for class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
addAllElementsInDataset(CompositionDataset) - Method in class magpie.data.utilities.output.CompositionOutput: Add all elements present in a dataset to the list of elements being printed.
addAlloyElement(int, double, double, double) - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator: Add alloying element
addAlloyElement(String, double, double, double) - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator: Add alloying element
addAlloyingElement(String) - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator: Add element to list of potential alloying elements
addAlloyingElements(Collection<String>) - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator: Add elements to list of potential alloying elements
addAttribute(double) - Method in class magpie.data.BaseEntry: Adds attribute value to the end of the list of current attributes
addAttribute(String, double[]) - Method in class magpie.data.Dataset: Add in a new attribute.
addAttributeExpander(BaseAttributeExpander) - Method in class magpie.data.Dataset: Add a new tool to expand the number of attributes for this dataset.
addAttributeGenerator(BaseAttributeGenerator) - Method in class magpie.data.Dataset: Add a new tool to generate additional attributes
addAttributes(Dataset) - Method in class magpie.attributes.generators.BaseAttributeGenerator: Generate new attributes for a dataset.
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.APEAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.ChargeDependentAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.ElementalPropertyAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.ElementFractionAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.ElementPairPropertyAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.GCLPAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.IonicCompoundProximityAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.IonicityAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.MeredigAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.ValenceShellAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.YangOmegaAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.crystal.APRDFAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.crystal.ChemicalOrderingAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.crystal.CoordinationNumberAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.crystal.CoulombMatrixAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.crystal.EffectiveCoordinationNumberAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.crystal.LatticeSimilarityAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.crystal.PackingEfficiencyAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.crystal.PRDFAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.crystal.StructuralHeterogeneityAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.element.ElementalPropertyAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.LookupTableAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.ModelPredictionAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.PropertyAsAttributeGenerator
addAttributes(Dataset) - Method in class magpie.attributes.generators.prototype.SingleSiteAttributeGenerator
addAttributes(double[]) - Method in class magpie.data.BaseEntry: Adds several attributes to the end of the attribute list.
addAttributes(List<String>) - Method in class magpie.data.Dataset: Add new attributes.
addAttributeSpecification(String) - Method in class magpie.attributes.selectors.UserSpecifiedAttributeSelector: Add an attribute to the list of attributes to be selected
addCoefficient(String) - Method in class magpie.models.regression.AbstractNonlinearRegression: Adds a new fitting parameter to function (if not already defined).
addCoefficient(String, Double) - Method in class magpie.models.regression.AbstractNonlinearRegression: Adds a new fitting parameter to function (if not already defined)
addComposition(CompositionEntry) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter: Add a new composition to the dataset.
addComposition(CompositionEntry) - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier: Add a new composition to the dataset.
addComposition(CompositionEntry) - Method in class magpie.optimization.rankers.CompositionDistanceRanker: Add a new composition to the dataset.
addCompositionBin(double[], List<String>) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Adds all permutations (i.e.
addCompositions(Collection<CompositionEntry>) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter: Add a list of compositions to the set
addCompositions(Collection<CompositionEntry>) - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier: Add a list of compositions to the set
addCompositions(Collection<CompositionEntry>) - Method in class magpie.optimization.rankers.CompositionDistanceRanker: Add a list of compositions to the set
addElement(int) - Method in class magpie.attributes.generators.crystal.PRDFAttributeGenerator: Add element to list used when computing PRDF
addElement(String) - Method in class magpie.attributes.generators.crystal.PRDFAttributeGenerator: Add element to list used when computing PRDF
addElement(String) - Method in class magpie.data.utilities.generators.FixedStoichiometryCompositionEntryGenerator: Add an element to the list of those used when generating entries
addElement(int) - Method in class magpie.data.utilities.output.CompositionOutput: Add element to the list of elements being printed.
addElement(String) - Method in class magpie.data.utilities.output.CompositionOutput: Add element to the list of elements being printed
addElementalProperty(String) - Method in class magpie.attributes.generators.crystal.APRDFAttributeGenerator: Add elemental property to set of those used for generating attributes
addElementalProperty(String) - Method in class magpie.data.materials.CompositionDataset: Define a new elemental property to use when generating attributes.
addElementalProperty(String) - Method in class magpie.data.materials.ElementDataset: Add an elemental property to the list of those used when computing attributes.
addElementalPropertySet(String) - Method in class magpie.data.materials.CompositionDataset: Add a set of elemental properties to the list of those used when computing attributes.
addElementalPropertySet(String) - Method in class magpie.data.materials.ElementDataset: Add a set of elemental properties to the list of those used when computing attributes.
addElementGroup(String) - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter: Add a list of elements to be defined as the same group.
addElementGroup(Collection<String>) - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter: Add a list of elements to be treated as a single group.
addElementPairProperty(String) - Method in class magpie.data.materials.CompositionDataset: Add a property of a pair of elements that will be used when generating attributes
addElements(Collection<Integer>) - Method in class magpie.data.utilities.output.CompositionOutput: Add several elements to the list of elements being printed.
addElementsByName(Collection<String>) - Method in class magpie.data.utilities.output.CompositionOutput: Add several elements to the list of elements being printed.
addEntries(Collection<? extends BaseEntry>) - Method in class magpie.data.Dataset: Add many entries to a the data set
addEntries(Dataset, boolean) - Method in class magpie.data.Dataset: Add entries from another dataset.
addEntries(Dataset, boolean) - Method in class magpie.data.MultiPropertyDataset: Add entries from another dataset.
addEntries(Collection<? extends BaseEntry>) - Method in class magpie.data.MultiPropertyDataset
addEntriesToDataset(Dataset) - Method in class magpie.data.utilities.generators.BaseEntryGenerator: Generate entries, and add them new a dataset.
addEntriesToDataset(Dataset) - Method in class magpie.data.utilities.generators.IonicCompoundGenerator
addEntry(BaseEntry) - Method in class magpie.data.Dataset: Add an entry.
addEntry(String) - Method in class magpie.data.Dataset: A new entry by parsing an input string.
addEntry(String) - Method in class magpie.data.materials.CompositionDataset
addEntry(String) - Method in class magpie.data.materials.CrystalStructureDataset
addEntry(String) - Method in class magpie.data.materials.ElementDataset
addEntry(String) - Method in class magpie.data.materials.PrototypeDataset
addEntry(BaseEntry) - Method in class magpie.data.MultiPropertyDataset
addFilter(BaseDatasetFilter) - Method in class magpie.data.utilities.filters.MultiFilter: Append filter to the current list of filters in use
addGeneratedElementPairProperty(String, String) - Method in class magpie.data.materials.CompositionDataset: Generate a new lookup table for properties of pairs of elements from properties of single elements
addNewFunction(String) - Method in class magpie.attributes.expanders.FunctionExpander: Add a new function to be used for expansion
addNormalizer(BaseDatasetNormalizer) - Method in class magpie.data.utilities.normalizers.MultiNormalizer: Add a new normalizer to this multi normalizer.
addObjectiveFunction(String, BaseEntryRanker) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker: Define a new objective function.
addPhase(CompositionEntry, double) - Method in class magpie.data.materials.util.GCLPCalculator: Add new phase to the list of phases to consider.
addPhases(CompositionDataset) - Method in class magpie.data.materials.util.GCLPCalculator: Set many phase energies.
addPNorm(int) - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator: Add a p norm to be computed
addPNorms(Collection<Integer>) - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator: Add several norms to be computed
addProperty(String) - Method in class magpie.attributes.generators.PropertyAsAttributeGenerator: Add property to list of properties used as attributes.
addProperty(String) - Method in class magpie.data.MultiPropertyDataset: Add a new property to dataset.
addProperty(String, String[]) - Method in class magpie.data.MultiPropertyDataset: Add a new property to dataset.
addProperty() - Method in class magpie.data.MultiPropertyEntry: Add a new property to this entry.
addProperty(double) - Method in class magpie.data.MultiPropertyEntry: Add a new property and define measured property.
addProperty(double, double) - Method in class magpie.data.MultiPropertyEntry: Add a new property to this entry, set measured and predicted values
AddPropertyModifier - Class in magpie.data.utilities.modifiers: Adds properties to a MultiPropertyDataset.
AddPropertyModifier() - Constructor for class magpie.data.utilities.modifiers.AddPropertyModifier
addResult(String, List<Pair<String, Double>>) - Method in class magpie.csp.CSPPerformanceStats: Add results of a prediction to performance dataset.
addSelector(BaseAttributeSelector) - Method in class magpie.attributes.selectors.StagedAttributeSelector: Add new selector to list, will be run last
addShell(int) - Method in class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator: Add shell to list of used when computing attributes
addShells(Collection<Integer>) - Method in class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator: Add several shells to list of used when computing attributes
addSite(double, boolean, List<Integer>) - Method in class magpie.data.materials.util.PrototypeSiteInformation: Add a new crystallographic site.
addStoichiometry(String) - Method in class magpie.data.utilities.generators.FixedStoichiometryCompositionEntryGenerator: Add a stoichiometry to the list of those to generate
addVariable(String) - Method in class magpie.models.regression.AbstractNonlinearRegression: Define a variable to be used in the user function (if not already defined)
addVariable(String, Object) - Method in class magpie.user.Workspace: Adds a variable to the workspace.
AllMetalsFilter - Class in magpie.data.utilities.filters: Filter entries based on whether all constituents are metals.
AllMetalsFilter() - Constructor for class magpie.data.utilities.filters.AllMetalsFilter
AllMetalsSplitter - Class in magpie.data.utilities.splitters: Splits CompositionDataset based on whether entries contain all metals.
AllMetalsSplitter() - Constructor for class magpie.data.utilities.splitters.AllMetalsSplitter
AllowedMixing - Variable in class magpie.data.utilities.generators.PrototypeEntryGenerator: Allowed mixing on each site.
AlloyingCompositionEntryGenerator - Class in magpie.data.utilities.generators: Generate entries by adding alloying elements into a set composition.
AlloyingCompositionEntryGenerator() - Constructor for class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
AlloyingElements - Variable in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator: Set of elements to add into alloy
AlloyStep - Variable in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator: Step size.
APEAttributeGenerator - Class in magpie.attributes.generators.composition: Compute attributes using Atomic Packing Efficiency (APE) of nearby clusters.
APEAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.APEAttributeGenerator: Create generator with default settings.
applyAttributeSelection(List<Integer>, Dataset) - Static method in class magpie.attributes.selectors.BaseAttributeSelector: Given a list of attribute IDs, adjust a dataset so that it only has the specified attributes.
applyDataset(Dataset, int) - Method in class magpie.data.utilities.modifiers.DiscreteToContinuousModifier: Run modification on Datasets
applyMultiPropertyDataset(MultiPropertyDataset, int) - Method in class magpie.data.utilities.modifiers.DiscreteToContinuousModifier: Run modification on MultiPropertyDatasets
APRDFAttributeGenerator - Class in magpie.attributes.generators.crystal: Attributes based on the Atomic Property Weighted Radial Distribution Function (AP-RDF) approach of Fernandez et al..
APRDFAttributeGenerator() - Constructor for class magpie.attributes.generators.crystal.APRDFAttributeGenerator
AreaUnderROCEvaluator - Class in magpie.attributes.evaluators: Ranks entries based on the area under the Receiver Operating Characteristic Curve.
AreaUnderROCEvaluator() - Constructor for class magpie.attributes.evaluators.AreaUnderROCEvaluator
ARFFOutput - Class in magpie.data.utilities.output: Write dataset to Weka's ARFF Format.
ARFFOutput() - Constructor for class magpie.data.utilities.output.ARFFOutput
assembleDataset(List<String>) - Method in class magpie.user.server.operations.ModelOperator: Given a list of entry names, parse them to make a dataset
assembleSystemCall(File, Dataset) - Method in class magpie.attributes.selectors.LassoAttributeSelector: Prepare the system call with all command-line arguments
assembleSystemCall(File, Dataset) - Method in class magpie.attributes.selectors.PythonBasedAttributeSelector: Prepare the system call with all command-line arguments
assembleSystemCall(File, Dataset) - Method in class magpie.attributes.selectors.RandomForestAttributeSelector
assignment(List<String>) - Method in class magpie.user.CommandHandler: Handle variable assignment
AttrDescription - Variable in class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator: Property description (used in description output)
AttributeComputer - Variable in class magpie.utility.tools.BatchAttributeGenerator: Dataset used to generate attributes
AttributeFilter - Class in magpie.data.utilities.filters: Filter entries based on value of a single attribute.
AttributeFilter() - Constructor for class magpie.data.utilities.filters.AttributeFilter
AttributeID - Variable in class magpie.data.utilities.splitters.AttributeIntervalSplitter: ID of attribute used for split
AttributeIntervalSplitter - Class in magpie.data.utilities.splitters: This class splits data into multiple properties based on the attributes of each entry.
AttributeIntervalSplitter() - Constructor for class magpie.data.utilities.splitters.AttributeIntervalSplitter
AttributeMean - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter: Means of attributes
AttributeName - Variable in class magpie.data.Dataset: Names of attributes that describe each entry
AttributeName - Variable in class magpie.data.utilities.splitters.AttributeIntervalSplitter: Name of attribute used for split
AttributeNames - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter: Names of attributes.
AttributeSelector - Variable in class magpie.models.BaseModel: BaseAttributeSelector used to screen attributes during training
AttributeStdDev - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter: Standard deviation of attributes
AttrName - Variable in class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator: Property name
Author - Variable in class magpie.user.server.ModelPackage: Author of this model
Authors - Variable in class magpie.utility.interfaces.Citation: Author(s) associated with this citation
AveragingDuplicateResolver - Class in magpie.data.utilities.modifiers.duplicates: Resolve entries by averaging the duplicates.
AveragingDuplicateResolver() - Constructor for class magpie.data.utilities.modifiers.duplicates.AveragingDuplicateResolver

B

BaseAttributeEvaluator - Class in magpie.attributes.evaluators: Base class for objects designed to evaluate the predictive power of single attributes.
BaseAttributeEvaluator() - Constructor for class magpie.attributes.evaluators.BaseAttributeEvaluator
BaseAttributeExpander - Class in magpie.attributes.expanders: This class is a template for operations that expand the number of available attributes based on what is already in the dataset.
BaseAttributeExpander() - Constructor for class magpie.attributes.expanders.BaseAttributeExpander
BaseAttributeGenerator - Class in magpie.attributes.generators: Base class for objects that generate attributes.
BaseAttributeGenerator() - Constructor for class magpie.attributes.generators.BaseAttributeGenerator
BaseAttributeSelector - Class in magpie.attributes.selectors: Interface to select a subset of attributes for a dataset.
BaseAttributeSelector() - Constructor for class magpie.attributes.selectors.BaseAttributeSelector
BaseClassifier - Class in magpie.models.classification: Base class for all classification models.
BaseClassifier() - Constructor for class magpie.models.classification.BaseClassifier
BaseClusterer - Class in magpie.cluster: Abstract model for all clustering algorithms.
BaseClusterer() - Constructor for class magpie.cluster.BaseClusterer
BaseDatasetFilter - Class in magpie.data.utilities.filters: Abstract model for classes that filter undesired entries out of a dataset.
BaseDatasetFilter() - Constructor for class magpie.data.utilities.filters.BaseDatasetFilter
BaseDatasetModifier - Class in magpie.data.utilities.modifiers: Perform some kind of manipulation on a Dataset, and all of the entries.
BaseDatasetModifier() - Constructor for class magpie.data.utilities.modifiers.BaseDatasetModifier
BaseDatasetNormalizer - Class in magpie.data.utilities.normalizers: Base class for objects designed to scale attributes and or class variable to exist on the same range.
BaseDatasetNormalizer() - Constructor for class magpie.data.utilities.normalizers.BaseDatasetNormalizer
BaseDatasetOutput - Class in magpie.data.utilities.output: Base class for tools that output a dataset.
BaseDatasetOutput() - Constructor for class magpie.data.utilities.output.BaseDatasetOutput
BaseDatasetSplitter - Class in magpie.data.utilities.splitters: This class provides an interface to Dataset splitting operations.
BaseDatasetSplitter() - Constructor for class magpie.data.utilities.splitters.BaseDatasetSplitter
BaseDuplicateResolver - Class in magpie.data.utilities.modifiers.duplicates: Abstract class for modifiers that remove duplicate entries
BaseDuplicateResolver() - Constructor for class magpie.data.utilities.modifiers.duplicates.BaseDuplicateResolver
BaseElement - Variable in class magpie.data.utilities.generators.CompositionRangeEntryGenerator: ID of base element
BaseEntry - Class in magpie.data: This class is designed to store all information related to an entry in a Dataset
BaseEntry() - Constructor for class magpie.data.BaseEntry: Create a blank entry
BaseEntry(String) - Constructor for class magpie.data.BaseEntry: Generate an entry by parsing a text string
BaseEntryGenerator - Class in magpie.data.utilities.generators: Base for classes that generate new entries.
BaseEntryGenerator() - Constructor for class magpie.data.utilities.generators.BaseEntryGenerator
BaseEntryRanker - Class in magpie.optimization.rankers: This is a template for classes that rank entries based on some sort of objective function.
BaseEntryRanker() - Constructor for class magpie.optimization.rankers.BaseEntryRanker
BaselineLogLoss - Variable in class magpie.statistics.performance.ClassificationStatistics: Log-loss of zero-r classifier.
BaseModel - Class in magpie.models: Base class for any model, regression or classification.
BaseModel() - Constructor for class magpie.models.BaseModel
BaseRegression - Class in magpie.models.regression: Base class for all regression models.
BaseRegression() - Constructor for class magpie.models.regression.BaseRegression
BaseStatistics - Class in magpie.statistics.performance: This class stores basic statistics about model performance and contains methods to calculate each of these statistics.
BaseStatistics() - Constructor for class magpie.statistics.performance.BaseStatistics
BatchAttributeGenerator - Class in magpie.utility.tools: Compute attributes and save them to a file in batches.
BatchAttributeGenerator() - Constructor for class magpie.utility.tools.BatchAttributeGenerator: Create an batch writer using the default settings: comma-delimited file, batch size of 10000 entries
BatchAttributeGenerator(BaseDatasetOutput, int) - Constructor for class magpie.utility.tools.BatchAttributeGenerator: Create a batch evaluator with a specified output method and batch size
BatchModelEvaluator - Class in magpie.utility.tools: Generate attributes and simpleRun models in batches.
BatchModelEvaluator() - Constructor for class magpie.utility.tools.BatchModelEvaluator
BatchSize - Variable in class magpie.utility.tools.BatchAttributeGenerator: Number of entries to evaluate at a single time
BestInAlloySystemFilter - Class in magpie.data.utilities.filters: Select only the best N entries from any one phase diagram.
BestInAlloySystemFilter() - Constructor for class magpie.data.utilities.filters.BestInAlloySystemFilter
BestIndividualSelector - Class in magpie.attributes.selectors: Selects attributes based on their individual performance.
BestIndividualSelector() - Constructor for class magpie.attributes.selectors.BestIndividualSelector
BinEdges - Variable in class magpie.data.utilities.splitters.AttributeIntervalSplitter: Values to use as bin edges

C

calculateAttributes() - Method in class magpie.data.Dataset: Compute attributes that are specific to this class.
calculateAttributes() - Method in class magpie.data.materials.CompositionDataset
calculateAttributes() - Method in class magpie.data.materials.ElementDataset
calculateProbabilities() - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Calculate the probability of each compound and element being in a phase diagram.
calculateStructureProbabilities() - Method in class magpie.csp.diagramdata.OnTheFlyPhaseDiagramStatistics
calculateStructureProbabilities() - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Calculate the probability of each prototype appearing in a phase diagram.
CartesianSumGenerator<Type> - Class in magpie.utility: Generate Cartesian sum of several collections.
CartesianSumGenerator(List<Collection<Type>>) - Constructor for class magpie.utility.CartesianSumGenerator: Define collections to be summed
CartesianSumGenerator(Collection<Type>...) - Constructor for class magpie.utility.CartesianSumGenerator: Define collections to be summed
changeComposition(CompositionEntry) - Method in class magpie.data.materials.CrystalStructureEntry: Redecorate a structure with a new composition.
ChargeDependentAttributeGenerator - Class in magpie.attributes.generators.composition: Attributes derived from the oxidation states of elements in a material.
ChargeDependentAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.ChargeDependentAttributeGenerator
ChargeGuesser - Variable in class magpie.attributes.generators.composition.ChargeDependentAttributeGenerator: Tool used to compute electronegativity
checkElements(Collection<String>) - Method in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator: Given list of element abbreviations, make sure all are known elements
checkModelCount(int) - Method in class magpie.models.SplitModel: Checks if enough models are defined.
checkStatus() - Method in class magpie.models.regression.CompositeRegression
checkStatus() - Method in class magpie.models.regression.StagedRegression: Verify that this model is ready to be trained
ChemicalOrderingAttributeGenerator - Class in magpie.attributes.generators.crystal: Compute attributes based on chemical ordering of structure.
ChemicalOrderingAttributeGenerator() - Constructor for class magpie.attributes.generators.crystal.ChemicalOrderingAttributeGenerator: Create a default attribute generator.
Citable - Interface in magpie.utility.interfaces: Interface for objects that should be referenced if they are used.
Citation - Class in magpie.utility.interfaces: Class used by Citable to define a resource being cited.
Citation(Class, String, String[], String, String, String) - Constructor for class magpie.utility.interfaces.Citation: Create a new citation object.
ClassEliminationModifier - Class in magpie.data.utilities.modifiers: Remove a possible class from a dataset.
ClassEliminationModifier() - Constructor for class magpie.data.utilities.modifiers.ClassEliminationModifier
ClassFilter - Class in magpie.data.utilities.filters: Filter entries based on value of class variable.
ClassFilter() - Constructor for class magpie.data.utilities.filters.ClassFilter
ClassificationRegression - Class in magpie.models.regression: Use a classification algorithm to perform regression.
ClassificationRegression() - Constructor for class magpie.models.regression.ClassificationRegression: Create a instances of this model that uses ZeroR.
ClassificationStatistics - Class in magpie.statistics.performance: Computes performance statistics for classifiers.
ClassificationStatistics() - Constructor for class magpie.statistics.performance.ClassificationStatistics
ClassIntervalModifier - Class in magpie.data.utilities.modifiers: Transforms a Dataset with a continuous class variable into a dataset with multiple class based on the value of the class variable.
ClassIntervalModifier() - Constructor for class magpie.data.utilities.modifiers.ClassIntervalModifier
ClassIsDiscrete - Variable in class magpie.data.utilities.output.DelimitedClassOutput: Whether the class has multiple, discrete values
ClassMean - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter: Mean of class variable
ClassName - Variable in class magpie.data.utilities.modifiers.DiscreteToContinuousModifier: Name of class for which to compute probability.
ClassNames - Variable in class magpie.models.classification.BaseClassifier: Names of classes this model can distinguish between
ClassNames - Variable in class magpie.models.classification.SplitClassifier: Names of classes this model can distinguish between
ClassNames - Variable in class magpie.statistics.performance.ClassificationStatistics: Names of classes (used when printing)
ClassProbabilityFilter - Class in magpie.data.utilities.filters: Filter based on predicted probability that an entry is a certain class.
ClassProbabilityFilter() - Constructor for class magpie.data.utilities.filters.ClassProbabilityFilter
ClassProbabilityRanker - Class in magpie.optimization.rankers: Rank entries based on the probability that they are a certain class.
ClassProbabilityRanker() - Constructor for class magpie.optimization.rankers.ClassProbabilityRanker
ClassProbabilityRanker(String) - Constructor for class magpie.optimization.rankers.ClassProbabilityRanker: Create new instance of ranker.
ClassRangeFilter - Class in magpie.data.utilities.filters: Filter entries that have class variables within or outside a certain range.
ClassRangeFilter() - Constructor for class magpie.data.utilities.filters.ClassRangeFilter
ClassStdDev - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter: Standard deviation of class variable
clear() - Method in class magpie.csp.CSPPerformanceStats: Removes results from previous tests.
clearAlloyingElements() - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator: Clear the list of elements to be added
clearAttributeExpanders() - Method in class magpie.data.Dataset: Reset the list of attribute expanders
clearAttributeGenerators() - Method in class magpie.data.Dataset: Reset the list of attribute generators
clearAttributes() - Method in class magpie.data.BaseEntry: Clear all currently-set attributes.
clearAttributes() - Method in class magpie.data.Dataset: Clear attribute data.
clearCompositions() - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter: Clear the list of compositions in set
clearCompositions() - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier: Clear the list of compositions in set
clearCompositions() - Method in class magpie.optimization.rankers.CompositionDistanceRanker: Clear the list of compositions in set
clearData() - Method in class magpie.data.Dataset: Clear out all entries
clearElementalProperties() - Method in class magpie.attributes.generators.crystal.APRDFAttributeGenerator: Clear list of elemental properties.
clearElementGroups() - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter: Clear the current list of element groups
clearElementList() - Method in class magpie.attributes.generators.crystal.PRDFAttributeGenerator: Clear list of elements used when computing PRDF
clearElements() - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator: Clear the list of alloying elements
clearElements() - Method in class magpie.data.utilities.generators.FixedStoichiometryCompositionEntryGenerator: Clear the list of currently-defined elements
clearFilters() - Method in class magpie.data.utilities.filters.MultiFilter: Clear list of filters.
clearFunctionList() - Method in class magpie.attributes.expanders.FunctionExpander: Clear list of functions used to generate new attributes.
clearObjectiveFunctions() - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker: Clear out list of currently-defined objective functions
clearPNorms() - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator: Clear out the list of p norms to be computed
clearProperties() - Method in class magpie.attributes.generators.PropertyAsAttributeGenerator: Clear the list of properties being used as attributes.
clearPropertyData() - Method in class magpie.data.MultiPropertyDataset: Clear all property information from this dataset.
clearPropertyData() - Method in class magpie.data.MultiPropertyEntry: Remove all information about properties
clearRepresentations() - Method in class magpie.data.materials.CrystalStructureEntry: Clear out the representations used when computing attributes.
clearSelectedElementList() - Method in class magpie.data.utilities.output.CompositionOutput: Clear the list of user-specific elements
clearSelectorList() - Method in class magpie.attributes.selectors.StagedAttributeSelector: Clear the list of selectors
clearShells() - Method in class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator: Clear list of shells to use when computing attributes
clearSpecifiedAttributes() - Method in class magpie.attributes.selectors.UserSpecifiedAttributeSelector: Clear list of user-specified attributes
clearStoichiometries() - Method in class magpie.data.utilities.generators.FixedStoichiometryCompositionEntryGenerator: Clear the list of currently-defined stoichiometries
Clfr - Variable in class magpie.data.utilities.splitters.NonZeroClassificationSplitter: Model to use for splitting
clone() - Method in class magpie.attributes.selectors.BaseAttributeSelector
clone() - Method in class magpie.attributes.selectors.ExhaustiveAttributeSelector
clone() - Method in class magpie.attributes.selectors.StagedAttributeSelector
clone() - Method in class magpie.attributes.selectors.UserSpecifiedAttributeSelector
clone() - Method in class magpie.attributes.selectors.WekaAttributeSelector
clone() - Method in class magpie.cluster.BaseClusterer
clone() - Method in class magpie.cluster.WekaClusterer
clone() - Method in class magpie.data.BaseEntry: Generates a clone of an entry.
clone() - Method in class magpie.data.Dataset: Creates a new instance of this dataset, and clones of each entry.
clone() - Method in class magpie.data.materials.CompositionEntry
clone() - Method in class magpie.data.materials.CrystalStructureDataset
clone() - Method in class magpie.data.materials.CrystalStructureEntry
clone() - Method in class magpie.data.materials.PrototypeEntry
clone() - Method in class magpie.data.materials.util.PrototypeSiteInformation
clone() - Method in class magpie.data.MultiPropertyEntry
clone() - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
clone() - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
clone() - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
clone() - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
clone() - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
clone() - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
clone() - Method in class magpie.data.utilities.splitters.ClustererSplitter
clone() - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
clone() - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
clone() - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
clone() - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
clone() - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
clone() - Method in class magpie.models.BaseModel
clone() - Method in class magpie.models.classification.BaseClassifier
clone() - Method in class magpie.models.classification.ScikitLearnClassifier
clone() - Method in class magpie.models.classification.SplitClassifier
clone() - Method in class magpie.models.classification.WekaClassifier
clone() - Method in class magpie.models.regression.BaseRegression
clone() - Method in class magpie.models.regression.ClassificationRegression
clone() - Method in class magpie.models.regression.CompositeRegression
clone() - Method in class magpie.models.regression.crystal.StructureKRRBasedRegression
clone() - Method in class magpie.models.regression.LASSORegression
clone() - Method in class magpie.models.regression.LinearCorrectedRegression
clone() - Method in class magpie.models.regression.MixingRuleRegression
clone() - Method in class magpie.models.regression.MultiObjectiveRegression
clone() - Method in class magpie.models.regression.PolynomialRegression
clone() - Method in class magpie.models.regression.ScikitLearnRegression
clone() - Method in class magpie.models.regression.SingleGuessRegression
clone() - Method in class magpie.models.regression.SplitRegression
clone() - Method in class magpie.models.regression.StagedRegression
clone() - Method in class magpie.models.regression.WekaRegression
clone() - Method in class magpie.models.SplitModel
clone() - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
clone() - Method in class magpie.optimization.rankers.BaseEntryRanker
clone() - Method in class magpie.optimization.rankers.CompositionDistanceRanker
clone() - Method in class magpie.optimization.rankers.MultiObjectiveEntryRanker
clone() - Method in class magpie.optimization.rankers.PropertyFormulaRanker
clone() - Method in class magpie.statistics.performance.BaseStatistics
clone() - Method in class magpie.statistics.performance.ClassificationStatistics
clone() - Method in class magpie.statistics.performance.RegressionStatistics
close() - Method in class magpie.models.classification.ScikitLearnClassifier
close() - Method in class magpie.models.regression.ScikitLearnRegression
closeFile() - Method in class magpie.user.InputFileParser: Closes currently open file.
closeServer() - Method in class magpie.models.classification.ScikitLearnClassifier
closeServer() - Method in interface magpie.models.interfaces.ExternalModel: Set a command to the model server that we are done with it.
closeServer() - Method in class magpie.models.regression.ScikitLearnRegression
ClustererSplitter - Class in magpie.data.utilities.splitters: Split data based using unsupervised learning.
ClustererSplitter() - Constructor for class magpie.data.utilities.splitters.ClustererSplitter
ClustererStatistics - Class in magpie.statistics.performance: Characterize the results from a clusterer.
ClustererStatistics() - Constructor for class magpie.statistics.performance.ClustererStatistics
Coefficients - Variable in class magpie.models.regression.LASSORegression: Coefficients for linear model
coefficients - Variable in class magpie.models.regression.PolynomialRegression: Coefficients of each term in the polynomial
CombinatorialSubstitutionGenerator - Class in magpie.data.utilities.generators: Generate new crystalline compound by substituting elements onto all sites of a known prototype.
CombinatorialSubstitutionGenerator() - Constructor for class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator
CombinatorialSubstitutionGenerator.EnumerationType - Enum in magpie.data.utilities.generators: Types of enumeration
combine(Dataset) - Method in class magpie.data.Dataset: Combine the data structure with another.
combine(Dataset[]) - Method in class magpie.data.Dataset: Combine the data structure with an array of other Datasets.
combine(Collection<Dataset>) - Method in class magpie.data.Dataset: Combine the data structure with a collection of other data structures.
combine(Dataset) - Method in class magpie.data.MultiPropertyDataset: Combine the dataset with another.
combineCompositions(Map<Integer, Double>, Map<Integer, Double>, double) - Method in class magpie.data.materials.CompositionEntry: Add composition from one map to another
Commandable - Interface in magpie.utility.interfaces: Provides interface for classes that can handle commands.
CommandHandler - Class in magpie.user: This class turns text commands into actions.
CommandHandler() - Constructor for class magpie.user.CommandHandler
CommonCompositions - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics: List of common compositions and the names of prototypes found at that composition.
compare() - Method in class magpie.attributes.evaluators.AreaUnderROCEvaluator
compare() - Method in class magpie.attributes.evaluators.BaseAttributeEvaluator: Create a comparator that will sort entries from the best to worst
compare() - Method in class magpie.attributes.evaluators.PearsonsCorrelationEvaluator
compare() - Method in class magpie.attributes.evaluators.PolynomialFitEvaluator
compare() - Method in class magpie.attributes.evaluators.SpearmansCorrelationEvaluator
compare(Object, Object) - Method in class magpie.data.BaseEntry
compare(Object, Object) - Method in class magpie.data.materials.CompositionEntry
compare(Object, Object) - Method in class magpie.data.materials.CrystalStructureEntry
compare(Object, Object) - Method in class magpie.data.materials.PrototypeEntry
compareTo(Object) - Method in class magpie.data.BaseEntry
ComparisonOperatorFilter - Class in magpie.data.utilities.filters: Abstract class for filters that use comparison operators.
ComparisonOperatorFilter() - Constructor for class magpie.data.utilities.filters.ComparisonOperatorFilter
Component - Variable in class magpie.utility.interfaces.Citation: Component this citation is associated with
CompositeRegression - Class in magpie.models.regression: Ensemble of regression models.
CompositeRegression() - Constructor for class magpie.models.regression.CompositeRegression
CompositionBasedCSPEngine - Class in magpie.csp: Use machine learning model trained on the composition of the entries.
CompositionBasedCSPEngine() - Constructor for class magpie.csp.CompositionBasedCSPEngine
compositionCanFormIonic(CompositionEntry) - Method in class magpie.data.materials.CompositionDataset: Whether a composition can form a neutral compound assuming each element takes only a single oxidation state.
CompositionComparator - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics: Used to sort PhaseDiagramStatistics.CommonCompositions.
CompositionDataset - Class in magpie.data.materials: This class stores entries that describe a material based solely on its composition.
CompositionDataset() - Constructor for class magpie.data.materials.CompositionDataset: Create a dataset using the default set of attribute generators.
CompositionDataset(boolean) - Constructor for class magpie.data.materials.CompositionDataset: Create a blank dataset.
CompositionDistanceFilter - Class in magpie.data.utilities.filters: Filter compositions based on distance from a target composition.
CompositionDistanceFilter() - Constructor for class magpie.data.utilities.filters.CompositionDistanceFilter
CompositionDistanceRanker - Class in magpie.optimization.rankers: Rank entries based on distance from compositions in a user-provided dataset.
CompositionDistanceRanker() - Constructor for class magpie.optimization.rankers.CompositionDistanceRanker
CompositionEntry - Class in magpie.data.materials: Stores several properties about a compound and its composition.
CompositionEntry() - Constructor for class magpie.data.materials.CompositionEntry: Allows the creation of arbitrary constructors for superclasses.
CompositionEntry(String) - Constructor for class magpie.data.materials.CompositionEntry: Make a new instance by parsing the composition of an object, provided by a string.
CompositionEntry(int[], double[]) - Constructor for class magpie.data.materials.CompositionEntry: Given the element numbers (probably Z-1) and fractions, create an entry
CompositionOutput - Class in magpie.data.utilities.output: Output the fraction of each element in a material.
CompositionOutput() - Constructor for class magpie.data.utilities.output.CompositionOutput
CompositionOutput.ElementSelectionMethod - Enum in magpie.data.utilities.output: How to determine which elements to print
CompositionRangeEntryGenerator - Class in magpie.data.utilities.generators: Create compositions in a rectangular, user-specified grid.
CompositionRangeEntryGenerator() - Constructor for class magpie.data.utilities.generators.CompositionRangeEntryGenerator
Compositions - Variable in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier: Set of compositions to compute distance from
compositionsAreEqual(double[], double[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Determine whether two compositions are equal (within PhaseDiagramStatistics.MinDistance).
CompositionSetDistanceFilter - Class in magpie.data.utilities.filters: Filter based on whether the distance of a composition from any other composition in a dataset is past a threshold.
CompositionSetDistanceFilter() - Constructor for class magpie.data.utilities.filters.CompositionSetDistanceFilter
CompositionSetDistanceModifier - Class in magpie.data.utilities.modifiers: Compute the distance of composition from those in a user-supplied dataset, store as a property.
CompositionSetDistanceModifier() - Constructor for class magpie.data.utilities.modifiers.CompositionSetDistanceModifier
computeAPE(double[], int, int[]) - Static method in class magpie.attributes.generators.composition.APEAttributeGenerator: Compute the APE of a cluster, provided the identities of the central and 1st neighbor atoms.
computeAPE(int, double, double) - Static method in class magpie.attributes.generators.composition.APEAttributeGenerator: Compute the APE provided the number of neighbors and radii.
computeAttributeStatistics(int, double[]) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer: Compute statistics required to perform normalization/restoration.
computeAttributeStatistics(int, double[]) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
computeAttributeStatistics(int, double[]) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
computeClassStatistics(double[]) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer: Compute statistics regarding the class variable.
computeClassStatistics(double[]) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
computeClassStatistics(double[]) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
computeClusterCompositions(int[], List<List<int[]>>) - Static method in class magpie.attributes.generators.composition.APEAttributeGenerator: Compute the compositions of a list of atomic clusters.
computeCoulombMatrix(Cell) - Method in class magpie.models.regression.crystal.CoulombEwaldMatrixRegression: Computes the Coulomb sine matrix.
computeCoulombMatrix(Cell) - Method in class magpie.models.regression.crystal.CoulombSineMatrixRegression: Computes the Coulomb sine matrix.
computeDistance(CompositionEntry, CompositionEntry, int) - Static method in class magpie.data.utilities.filters.CompositionDistanceFilter: Compute the distance between two entries.
computeDistance(CompositionEntry) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter: Compute the distance between a composition and the set of other compositions stored in this object.
computeListLengthCurve(double, int) - Method in class magpie.csp.CSPPerformanceStats: Compute the minimum length of a list required to find the correct structure
computeLogLoss(int[], double[][]) - Static method in class magpie.statistics.performance.ClassificationStatistics: Compute the log-loss for the classifier.
computeMixingTerm(CompositionEntry) - Static method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer: Compute the mixing term for a solution model.
computeRepresentation(Cell) - Method in class magpie.models.regression.crystal.CoulombEwaldMatrixRegression
computeRepresentation(Cell) - Method in class magpie.models.regression.crystal.CoulombSineMatrixRegression
computeRepresentation(Cell) - Method in class magpie.models.regression.crystal.PRDFRegression: Compute the pair distribution function
computeRepresentation(Cell) - Method in class magpie.models.regression.crystal.StructureKRRBasedRegression: Given a structure, compute representation of the structure.
computeSimiliarity(Object, Object) - Method in class magpie.models.regression.crystal.CoulombEwaldMatrixRegression
computeSimiliarity(Object, Object) - Method in class magpie.models.regression.crystal.CoulombSineMatrixRegression
computeSimiliarity(Object, Object) - Method in class magpie.models.regression.crystal.PRDFRegression
computeSimiliarity(Object, Object) - Method in class magpie.models.regression.crystal.StructureKRRBasedRegression: Compute similarity between two crystal structures.
ComputeVoronoi - Variable in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator: Whether to compute the Voronoi tessellation before generation
computeVoronoiTessellation() - Method in class magpie.data.materials.CrystalStructureEntry: Compute the Voronoi tessellation of this structure.
ConfusionMatrix - Variable in class magpie.statistics.performance.ClassificationStatistics: Contingency table.
ContainsElementFilter - Class in magpie.data.utilities.filters: Filter entries that contain certain elements.
ContainsElementFilter() - Constructor for class magpie.data.utilities.filters.ContainsElementFilter
containsEntry(BaseEntry) - Method in class magpie.data.Dataset: Determine whether a dataset contains a certain entry
ContingencyTable - Variable in class magpie.statistics.performance.ClassificationStatistics: Description of how often instances are assigned to each class.
convertCommandToString(List<Object>) - Static method in class magpie.user.CommandHandler: Convert a command (List<Object>) to string.
convertCompositionsToInstances(Collection<CompositionEntry>) - Static method in class magpie.data.utilities.filters.CompositionSetDistanceFilter: Convert a collection of entries to a Weka Instances object.
convertCompositionToInstance(CompositionEntry) - Static method in class magpie.data.utilities.filters.CompositionSetDistanceFilter: Convert a composition to a Weka instance.
convertToCitation(TechnicalInformation, Class) - Static method in class magpie.utility.WekaUtility: Convert a Weka TechnicalInformation object to a Magpie Citation object.
convertToJSON(MultiPropertyDataset) - Method in class magpie.user.server.operations.SearchRunner: Convert the dataset into a JSON object
convertVolumeToLatticeParam(double) - Method in class magpie.data.utilities.modifiers.VolumeToLatticeParamModifier: Calculate the equivalent cubic lattice parameter corresponding to a volume per atom, given the number of atoms in the unit cell
CoordinationNumberAttributeGenerator - Class in magpie.attributes.generators.crystal: Compute attributes based on the coordination number.
CoordinationNumberAttributeGenerator() - Constructor for class magpie.attributes.generators.crystal.CoordinationNumberAttributeGenerator
CorrectionFactors - Variable in class magpie.models.regression.MixingRuleRegression: Coefficients used for correction factor.
CORSFilter - Class in magpie.user.server
CORSFilter() - Constructor for class magpie.user.server.CORSFilter
CoulombEwaldMatrixRegression - Class in magpie.models.regression.crystal: Perform regression based on the Ewald Matrix approach of Faber et al..
CoulombEwaldMatrixRegression() - Constructor for class magpie.models.regression.crystal.CoulombEwaldMatrixRegression
CoulombMatrixAttributeGenerator - Class in magpie.attributes.generators.crystal: Compute attributes using the Coulomb Sine Matrix representation.
CoulombMatrixAttributeGenerator() - Constructor for class magpie.attributes.generators.crystal.CoulombMatrixAttributeGenerator
CoulombSineMatrixRegression - Class in magpie.models.regression.crystal: Perform regression based on the Coulomb Sine Matrix approach of Faber et al..
CoulombSineMatrixRegression() - Constructor for class magpie.models.regression.crystal.CoulombSineMatrixRegression
createDatasetJSON(ModelPackage, List<String>, Dataset) - Static method in class magpie.user.server.ServerUtilityOperations: Turn a dataset into a JSON object.
createLookupKey(double[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Extend the length of a composition by padding the end with zeros.
createNames() - Method in class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator: Create names for the attributes
createTemplate() - Method in class magpie.data.Dataset: Create a template designed to be saved using serialization
createTemplate() - Method in class magpie.data.materials.CompositionDataset
createTemplate() - Method in class magpie.data.materials.ElementDataset
createTemplate() - Method in class magpie.data.MultiPropertyDataset
CrossExpander - Class in magpie.attributes.expanders: Creates new attributes as multiplicative cross terms of currently available ones.
CrossExpander() - Constructor for class magpie.attributes.expanders.CrossExpander
crossvalidate(int, int) - Method in class magpie.csp.CSPEngine: Validates predictive ability of this model.
crossValidate(int, Dataset) - Method in class magpie.models.BaseModel: Perform k-fold cross validation
crossValidate(int, Dataset, long) - Method in class magpie.models.BaseModel: Perform k-fold cross validation
crossValidate(double, int, Dataset, long) - Method in class magpie.models.BaseModel: Run a cross-validation test where the dataset is randomly partitioned into a training and test set.
CrystalStructureDataset - Class in magpie.data.materials: Holds a entries that represent crystal structures.
CrystalStructureDataset() - Constructor for class magpie.data.materials.CrystalStructureDataset: Create a instance with the default attribute generators
CrystalStructureDataset(boolean) - Constructor for class magpie.data.materials.CrystalStructureDataset: Create a new instance.
CrystalStructureEntry - Class in magpie.data.materials: Represents a crystal structure.
CrystalStructureEntry(Cell, String, double[]) - Constructor for class magpie.data.materials.CrystalStructureEntry: Create an entry given its crystal structure
CSPEngine - Class in magpie.csp: Predict what structure is likely to form at a specific composition from a list of possible candidates.
CSPEngine() - Constructor for class magpie.csp.CSPEngine
CSPPerformanceStats - Class in magpie.csp: Holds data about the performance of a CSP algorithm.
CSPPerformanceStats() - Constructor for class magpie.csp.CSPPerformanceStats
CumulantExpansionClassifier - Class in magpie.models.classification: Predict whether instance of a prototype structure will be a member of one of several mutually-exclusive classes.
CumulantExpansionClassifier() - Constructor for class magpie.models.classification.CumulantExpansionClassifier
CutoffDistance - Variable in class magpie.attributes.generators.crystal.APRDFAttributeGenerator: Cutoff distance for RDF
CutoffDistance - Variable in class magpie.attributes.generators.crystal.PRDFAttributeGenerator: Cutoff distance for PRDF
CVFraction - Variable in class magpie.attributes.selectors.LassoAttributeSelector: Fraction of entries to withhold of cv test set.
CVIterations - Variable in class magpie.attributes.selectors.LassoAttributeSelector: Number of times to repeat CV test.

D

DataDirectory - Variable in class magpie.data.materials.CompositionDataset: Location of lookup date files
Dataset - Class in magpie.data: Provides a basic storage container for data-mining tasks.
Dataset() - Constructor for class magpie.data.Dataset: Generate a blank dataset
Dataset - Variable in class magpie.user.server.ModelPackage: Dataset used to generate attributes
datasetMatches(Dataset) - Method in class magpie.user.server.ModelPackage: Check whether the dataset type is the same as a provided type.
Debug - Variable in class magpie.attributes.selectors.PythonBasedAttributeSelector: Debug mode.
Debug - Variable in class magpie.models.classification.ScikitLearnClassifier: Whether to print output from python stdout to screen
Debug - Variable in class magpie.models.regression.ScikitLearnRegression: Whether to print output from python stdout to screen
defineCoefficients() - Method in class magpie.models.regression.AbstractNonlinearRegression: Define the names and, if desired, initial guesses of fitting coefficients.
defineCoefficients() - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
defineCoefficients() - Method in class magpie.models.regression.nonlinear.SimpleLinearModelExample
defineKnownCompounds(String) - Method in class magpie.models.classification.CumulantExpansionClassifier: Define compositions of all known compounds.
definePropertyNames(String[]) - Method in class magpie.data.MultiPropertyDataset: Define all known properties for a dataset.
defineSitePossibilities(int, int, double, Collection<String>) - Method in class magpie.data.utilities.generators.PrototypeEntryGenerator: Define the possible compositions for each site.
defineVariables() - Method in class magpie.models.regression.AbstractNonlinearRegression: Define which attributes are used by the function.
defineVariables(String) - Method in class magpie.models.regression.AbstractParsedNonlinearRegression: Reads an expression and stores the names of all variables.
defineVariables() - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
defineVariables() - Method in class magpie.models.regression.nonlinear.SimpleLinearModelExample
defineVariables(String) - Method in class magpie.models.regression.NonlinearRegressionExpr: Reads an expression and stores the names of all variables.
deleteMeasuredClass() - Method in class magpie.data.BaseEntry: Delete measured class variable.
deleteMeasuredClass() - Method in class magpie.data.MultiPropertyEntry
deleteMeasuredClasses() - Method in class magpie.data.Dataset: Delete all measured classes from entries
deletePredictedClass() - Method in class magpie.data.BaseEntry: Delete predicted class variable.
deletePredictedClass() - Method in class magpie.data.MultiPropertyEntry
deletePredictedClasses() - Method in class magpie.data.Dataset: Delete all predicted classes from entries
DelimitedClassOutput - Class in magpie.data.utilities.output: Output only the measured and predicted class values to a delimited file.
DelimitedClassOutput() - Constructor for class magpie.data.utilities.output.DelimitedClassOutput
DelimitedClassOutput(String) - Constructor for class magpie.data.utilities.output.DelimitedClassOutput: Create a file writer with a certain delimiter
DelimitedOutput - Class in magpie.data.utilities.output: Write data file out to a delimited file (ex: comma separated values).
DelimitedOutput() - Constructor for class magpie.data.utilities.output.DelimitedOutput: Create a comma delimited file
DelimitedOutput(String) - Constructor for class magpie.data.utilities.output.DelimitedOutput: Create a file writer with a certain delimiter
Delimiter - Variable in class magpie.data.utilities.output.DelimitedOutput: Text used as delimeter.
Description - Variable in class magpie.user.server.ModelPackage: Short description of this model
determineOptimalAPE(int, CompositionEntry, double[]) - Static method in class magpie.attributes.generators.composition.APEAttributeGenerator: Compute the optimal APE for a cluster with a certain atom type in the center and composition in the cell.
DiagramStatistics - Variable in class magpie.csp.CSPEngine: Statistics about phase diagrams with certain number of constituents.
DiscreteToContinuousModifier - Class in magpie.data.utilities.modifiers: Convert multiple, discrete class values to single continuous class.
DiscreteToContinuousModifier() - Constructor for class magpie.data.utilities.modifiers.DiscreteToContinuousModifier
discretize(double[], int) - Static method in class magpie.statistics.performance.ClassificationStatistics: Takes a continuous class variable and converts it to discrete values that range between [0,nclass).
DistinctPermutationGenerator - Class in magpie.utility: Given a list of objects, generate the set of distinct permutations.
DistinctPermutationGenerator() - Constructor for class magpie.utility.DistinctPermutationGenerator
DMSPEngine - Class in magpie.csp: Data-Mining Structure Predictor (DMSP) from Fisher et al.
DMSPEngine() - Constructor for class magpie.csp.DMSPEngine
done() - Method in class magpie.models.BaseModel: Run if done with a model, clears any external resources.
doRobustRegression() - Method in interface magpie.models.regression.AbstractRegressionModel: Whether robust regression is desired.
doRobustRegression() - Method in class magpie.models.regression.BaseRegression
doRobustRegression() - Method in class magpie.models.regression.SplitRegression
downloadDataset() - Method in class magpie.user.server.operations.ModelOperator: Download the model file via serialization
downloadModel() - Method in class magpie.user.server.operations.ModelOperator: Download the model file via serialization

E

EchoCommands - Variable in class magpie.user.CommandHandler: Whether to echo commands to screen
EffectiveCoordinationNumberAttributeGenerator - Class in magpie.attributes.generators.crystal: Compute attributes based on the effective coordination number.
EffectiveCoordinationNumberAttributeGenerator() - Constructor for class magpie.attributes.generators.crystal.EffectiveCoordinationNumberAttributeGenerator
Element - Variable in class magpie.data.materials.CompositionEntry: Elements present in composition
ElementalProperties - Variable in class magpie.attributes.generators.crystal.APRDFAttributeGenerator: List of elemental properties to use for weighting
ElementalProperties - Variable in class magpie.attributes.generators.prototype.SingleSiteAttributeGenerator: List of properties used to compute attributes
ElementalProperties - Variable in class magpie.data.materials.CompositionDataset: List of properties used when generating attributes
ElementalProperties - Variable in class magpie.data.materials.ElementDataset: List of elemental properties used when computing attributes
ElementalProperties - Static variable in class magpie.data.materials.util.LookupData: Holds elemental property data.
ElementalProperties - Variable in class magpie.user.CommandHandler: Which elemental properties to use when calculating features
ElementalPropertyAttributeGenerator - Class in magpie.attributes.generators.composition: Generate attributes based on elemental property statistics.
ElementalPropertyAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.ElementalPropertyAttributeGenerator
ElementalPropertyAttributeGenerator - Class in magpie.attributes.generators.element: Compute attributes based on elemental properties.
ElementalPropertyAttributeGenerator() - Constructor for class magpie.attributes.generators.element.ElementalPropertyAttributeGenerator
ElementalPropertyDirectory - Variable in class magpie.user.CommandHandler: Directory that contain elemental property lookup files
ElementDataset - Class in magpie.data.materials: Store elemental properties.
ElementDataset() - Constructor for class magpie.data.materials.ElementDataset: Create a dataset using the default attribute generators: ElementalPropertyAttributeGenerator
ElementDataset(boolean) - Constructor for class magpie.data.materials.ElementDataset: Create a blank dataset.
ElementEntry - Class in magpie.data.materials: Holds identity and properties of an element.
ElementEntry(String) - Constructor for class magpie.data.materials.ElementEntry: Create a new entry
ElementEntry(int, boolean) - Constructor for class magpie.data.materials.ElementEntry: Create an entry given atomic number or element ID.
ElementFractionAttributeGenerator - Class in magpie.attributes.generators.composition: Stores the fraction of each element as attributes.
ElementFractionAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.ElementFractionAttributeGenerator
ElementList - Variable in class magpie.attributes.generators.crystal.PRDFAttributeGenerator: List of ElementList to use in PRDF
ElementList - Variable in class magpie.data.utilities.filters.ContainsElementFilter: Elements that compounds are not allowed to contain
ElementNames - Variable in class magpie.data.materials.CompositionDataset: List of element names
ElementNames - Variable in class magpie.data.materials.CompositionEntry: Names of each element
ElementNames - Static variable in class magpie.data.materials.util.LookupData: Name of elements, ordered by atomic number.
ElementPairProperties - Variable in class magpie.data.materials.CompositionDataset: List of properties of pairs of elements used when generating attributes
ElementPairProperties - Static variable in class magpie.data.materials.util.LookupData: Properties of a pair of elements.
ElementPairPropertyAttributeGenerator - Class in magpie.attributes.generators.composition: Attributes based on properties of constituent binary systems.
ElementPairPropertyAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.ElementPairPropertyAttributeGenerator
ElementProbability - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics: Probability that each element appears in a phase diagram
Elements - Variable in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator: Elements of composition to be added to
Elements - Variable in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator: List of elements to substitute
Elements - Variable in class magpie.data.utilities.generators.FixedStoichiometryCompositionEntryGenerator: Set of elements to use when generating entries
Elements - Variable in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator: List of elements to use (id is Z-1)
ElementsToIgnore - Variable in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator: List of elements ignore during substitution
ElementsToPrint - Variable in class magpie.data.utilities.output.CompositionOutput: User-defined set of elements to print
emptyClone() - Method in class magpie.data.Dataset: Creates a new instance with the same class and attribute names, but without any entries.
emptyClone() - Method in class magpie.data.materials.CompositionDataset
emptyClone() - Method in class magpie.data.materials.CrystalStructureDataset
emptyClone() - Method in class magpie.data.materials.ElementDataset
emptyClone() - Method in class magpie.data.materials.PrototypeDataset
emptyClone() - Method in class magpie.data.MultiPropertyDataset
Entries - Variable in class magpie.data.Dataset: Internal array that stores entries
entryContainsElement(CompositionEntry) - Method in class magpie.data.utilities.filters.ContainsElementFilter: Determine whether an entry contains one of the specified elements.
EntryLength - Variable in class magpie.data.utilities.output.SimpleOutput: Width of largest entry
EntryRankerFilter - Class in magpie.data.utilities.filters: Filter entries based on ranking.
EntryRankerFilter() - Constructor for class magpie.data.utilities.filters.EntryRankerFilter
EnumerationStyle - Variable in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator: Enumeration type for generating new compounds
Equal - Variable in class magpie.data.utilities.filters.ComparisonOperatorFilter: Should entries with Feature==Threshold be kept?
equals(Object) - Method in class magpie.data.BaseEntry
equals(Object) - Method in class magpie.data.materials.CompositionEntry
equals(Object) - Method in class magpie.data.materials.CrystalStructureEntry
equals(Object) - Method in class magpie.data.materials.PrototypeEntry
equals(Object) - Method in class magpie.data.materials.util.PrototypeSiteInformation
equals(Object) - Method in class magpie.utility.interfaces.Citation
EqualSumCombinations - Class in magpie.utility: Iterator over all combinations of nonnegative integers that have equal sum.
EqualSumCombinations(int, int) - Constructor for class magpie.utility.EqualSumCombinations: Create an iterator over all possible vectors with a certain number of entries that are all nonnegative integers that sum to the same amount.
ErrorSignalModifier - Class in magpie.data.utilities.modifiers: Subtract the predicted class from a dataset, leaving only the error signal as the measured class variable.
ErrorSignalModifier() - Constructor for class magpie.data.utilities.modifiers.ErrorSignalModifier
evaluate(Dataset) - Method in class magpie.statistics.performance.BaseStatistics: Generates statistics about the performance on a model.
evaluate(Dataset[]) - Method in class magpie.statistics.performance.ClustererStatistics: Characterize the performance of a cluster
evaluate() - Method in class magpie.utility.ParsedFunction: Evaluate function with current variable values
evaluate(Dataset, BaseEntryGenerator, BaseDatasetFilter) - Method in class magpie.utility.tools.BatchModelEvaluator: Generate entries and store them in a dataset.
evaluate(Dataset) - Method in class magpie.utility.tools.BatchModelEvaluator: Evaluate the model on a dataset in batch mode.
evaluate_protected(Dataset) - Method in class magpie.statistics.performance.BaseStatistics: Internal method for acutally computing results.
evaluate_protected(Dataset) - Method in class magpie.statistics.performance.ClassificationStatistics
evaluate_protected(Dataset) - Method in class magpie.statistics.performance.RegressionStatistics
evaluate_protected(Dataset) - Method in class magpie.statistics.performance.TargetRegressionStatistics
evaluateAttributes(Dataset) - Method in class magpie.attributes.evaluators.BaseAttributeEvaluator: Calculate the predictive power of each attributes in a dataset
evaluateAttributes_internal(Dataset) - Method in class magpie.attributes.evaluators.AreaUnderROCEvaluator
evaluateAttributes_internal(Dataset) - Method in class magpie.attributes.evaluators.BaseAttributeEvaluator: Operation that actually performs the work of evaluating attributes.
evaluateAttributes_internal(Dataset) - Method in class magpie.attributes.evaluators.PearsonsCorrelationEvaluator
evaluateAttributes_internal(Dataset) - Method in class magpie.attributes.evaluators.PolynomialFitEvaluator
evaluateAttributes_internal(Dataset) - Method in class magpie.attributes.evaluators.SpearmansCorrelationEvaluator
evaluateModel(BaseModel, CompositionDataset) - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator: Evaluate predictive accuracy of model by iteratively excluding elements from a certain phase diagram.
evaluateProbability(PrototypeEntry, double[][], double) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Given a prototype entry, generate its probability of having a certain condition.
Evaluator - Variable in class magpie.attributes.selectors.WekaAttributeSelector: Weka class that is used to rank subsets of attributes
evenSpacing - Variable in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator: Whether to use even spacing or small integers
ExcludedIndex - Variable in class magpie.data.utilities.filters.ContainsElementFilter: List of IDs of those elements
ExhaustiveAttributeSelector - Class in magpie.attributes.selectors: From all possible subsets, find the one that leads to the highest CV score.
ExhaustiveAttributeSelector() - Constructor for class magpie.attributes.selectors.ExhaustiveAttributeSelector
ExhaustiveAttributeSelector.EvaluationMethod - Enum in magpie.attributes.selectors: List of methods used to evaluate model performance
expand(Dataset) - Method in class magpie.attributes.expanders.BaseAttributeExpander: Generate new attributes based on the attributes already in Dataset
expand(Dataset) - Method in class magpie.attributes.expanders.CrossExpander
expand(Dataset) - Method in class magpie.attributes.expanders.FunctionExpander
expand(Dataset) - Method in class magpie.attributes.expanders.PowerExpander
expandAttributes(double[][], int) - Static method in class magpie.models.regression.PolynomialRegression: Expand attribute array in order to allow it to be used to fit a polynomial model.
Expanders - Variable in class magpie.data.Dataset: Tools to generate new attributes based on existing ones
expandTextCommand(List<String>) - Method in class magpie.user.CommandHandler: Given a text command, change any word marked with a "$" in the front to the corresponding variable.
externallyValidate(Dataset) - Method in class magpie.models.BaseModel: Use external testing data to validate a model (should not contain any data used to train the model)
ExternalModel - Interface in magpie.models.interfaces: Interface for models that run their model in a separate thread and communicate to it via a socket connection.
ExternalModelUtility - Class in magpie.models.utility: Utility operation for models that rely on an external (i.e., non-java) process and use a socket connection to exchage information.
ExternalModelUtility() - Constructor for class magpie.models.utility.ExternalModelUtility
extractVariables(String) - Method in class magpie.optimization.rankers.PropertyFormulaRanker: Parse a formula to find names of properties used as variables.

F

F1 - Variable in class magpie.statistics.performance.ClassificationStatistics: F1 Score
FDR - Variable in class magpie.statistics.performance.ClassificationStatistics: False Detection Rate
fileIsOpen - Variable in class magpie.user.InputFileParser: Whether an input file is open
fillPrototypeEntry(PrototypeEntry, int[]) - Method in class magpie.csp.CSPEngine: Adjust a PrototypeEntry so that each site is occupied by a specific element
filter(Dataset) - Method in class magpie.data.utilities.filters.BaseDatasetFilter: Filters entries out of dataset
Filter - Variable in class magpie.data.utilities.splitters.FilterSplitter: Filter used for splitting the data
filter(ContainerRequestContext, ContainerResponseContext) - Method in class magpie.user.server.CORSFilter
Filters - Variable in class magpie.data.utilities.filters.MultiFilter: List of filters currently in use
FilterSplitter - Class in magpie.data.utilities.splitters: Split entries based on whether they pass a BaseDatasetFilter.
FilterSplitter() - Constructor for class magpie.data.utilities.splitters.FilterSplitter
finalizeGeneration() - Method in class magpie.data.Dataset: Run after generating attributes.
findAllCompounds() - Method in class magpie.utility.tools.IonicCompoundFinder: Locate all ionic compounds within a certain distance of the target composition.
findClosestEntries(CrystalStructureEntry, int) - Method in class magpie.models.regression.crystal.StructureKRRBasedRegression: Find the name of the training entries that are closest in similarity to this entry.
findEfficientlyPackedClusters(double[], double) - Static method in class magpie.attributes.generators.composition.APEAttributeGenerator: Provided a list of atomic radii, find all clusters with better than a certain packing efficiency threshold.
findFile(String) - Static method in class magpie.utility.UtilityOperations: Given the path of a path relative to the Magpie jar, find the actual path.
findMaxCorrelation(double[][], double[], boolean[]) - Method in class magpie.models.regression.LASSORegression: Finds the feature with the maximum correlation out of all possible candidates
fitCorrectionFactors(CompositionDataset) - Method in class magpie.models.regression.MixingRuleRegression: Fit correction factors to the mixing rule model.
fitElementProperties(CompositionDataset) - Method in class magpie.models.regression.MixingRuleRegression: Fits properties for elements specified by user.
fitPolynomialModel(double[][], int, double[]) - Static method in class magpie.models.regression.PolynomialRegression: Fit a polynomial model based on a matrix of attribute values.
FittedElements - Variable in class magpie.models.regression.MixingRuleRegression: Elements to fit using least squares
FixedStoichiometryCompositionEntryGenerator - Class in magpie.data.utilities.generators: Generate compositions with a fixed stoichiometry.
FixedStoichiometryCompositionEntryGenerator() - Constructor for class magpie.data.utilities.generators.FixedStoichiometryCompositionEntryGenerator
FN - Variable in class magpie.statistics.performance.ClassificationStatistics: Number of False Negatives
FP - Variable in class magpie.statistics.performance.ClassificationStatistics: Number of False Positives
FPR - Variable in class magpie.statistics.performance.ClassificationStatistics: False Positive Rate
Fraction - Variable in class magpie.data.materials.CompositionEntry: Fraction of each element
FractionCorrect - Variable in class magpie.statistics.performance.ClassificationStatistics: Fraction of entries assigned to correct class
Fractions - Variable in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator: Fractions of each element of composition to be added to
function(double[], double[]) - Method in class magpie.models.regression.AbstractNonlinearRegression: Function defined by the user.
function(double[], double[]) - Method in class magpie.models.regression.nonlinear.SimpleLinearModelExample
function(double[], double[]) - Method in class magpie.models.regression.NonlinearRegressionExpr
FunctionExpander - Class in magpie.attributes.expanders: Generates new attributes that are arbitrary functions of other attributes.
FunctionExpander() - Constructor for class magpie.attributes.expanders.FunctionExpander

G

gcd(int, int) - Static method in class magpie.utility.MathUtils: Calculate the greatest common denominator of two integers.
GCLPAttributeGenerator - Class in magpie.attributes.generators.composition: Computes attributes based on the T=0K ground state.
GCLPAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.GCLPAttributeGenerator
GCLPCalculator - Class in magpie.data.materials.util: Grand-Canonical Linear Programming (GCLP) method to compute phase equilibria.
GCLPCalculator() - Constructor for class magpie.data.materials.util.GCLPCalculator: Initialize a GCLP calculator.
generateAll() - Method in class magpie.utility.EqualSumCombinations: Generate all possible vectors
generateAlloyCompositions() - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator: Generate evenly-spaced compositions.
generateAttributeNames(PrototypeSiteInformation) - Method in class magpie.attributes.generators.prototype.PairSiteAttributeGenerator
generateAttributeNames(PrototypeSiteInformation) - Method in class magpie.attributes.generators.prototype.SingleSiteAttributeGenerator: Generate names of attributes
generateAttributes(PrototypeSiteInformation, PrototypeEntry, PrototypeDataset, double[]) - Method in class magpie.attributes.generators.prototype.PairSiteAttributeGenerator
generateAttributes(PrototypeSiteInformation, PrototypeEntry, PrototypeDataset, double[]) - Method in class magpie.attributes.generators.prototype.SingleSiteAttributeGenerator: Compute attributes for a single entry
generateAttributes() - Method in class magpie.data.Dataset: Generate attributes for this dataset
generateAttributes(String) - Method in class magpie.user.server.operations.ModelOperator: Generate attributes with the dataset for a certain model
generateCombinations(String[], ParsedFunction) - Method in class magpie.attributes.expanders.FunctionExpander: Compute all acceptable combinations of attributes for a
generateCombinations(List<Set<Integer>>, List<Pair<Integer, Double>>) - Static method in class magpie.data.utilities.generators.PrototypeEntryGenerator: Generate all possible combinations of compositions generated using a list of settings.
generateCrystalCompositions() - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator: Generate compositions with small denominators.
generateEntries() - Method in class magpie.data.utilities.generators.BaseEntryGenerator: Generate a list of new entries according to the currently-defined settings.
generatePermutations(List<Object>) - Static method in class magpie.utility.DistinctPermutationGenerator: Given a list, generate all permutations that are not equal to each other
generatePermutations(double[]) - Static method in class magpie.utility.DistinctPermutationGenerator: Generate all distinct permutations of an array of doubles.
generatePermutations(int[]) - Static method in class magpie.utility.DistinctPermutationGenerator: Generate all distinct permutations of an array of doubles.
Generators - Variable in class magpie.data.Dataset: Tools to generate special-purpose attributes
GenericModel - Variable in class magpie.models.regression.CompositeRegression: Generic composite regression model (use wisely)
GenericModel - Variable in class magpie.models.regression.MultiObjectiveRegression: Generic model (in case one has not already been defined)
GenericModel - Variable in class magpie.models.SplitModel: Model used to if a model template for a certain split is not defined
getASEvaluator(String, String[]) - Static method in class magpie.attributes.selectors.WekaAttributeSelector: Generates a Weka ASEvaluator object, given name and options
getASSearch(String, String[]) - Static method in class magpie.attributes.selectors.WekaAttributeSelector: Generates a Weka ASSearch object, given names and options
getAtomProperties(VoronoiCellBasedAnalysis, Pair<int[][], double[][]>, double[]) - Method in class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator: Provided the Voronoi tessellation and properties of each atom type, compute the properties of a certain neighbor cell for each atom.
getAtomProperties(VoronoiCellBasedAnalysis, Pair<int[][], double[][]>, double[]) - Method in class magpie.attributes.generators.crystal.LocalPropertyVarianceAttributeGenerator
getAttribute(int) - Method in class magpie.data.BaseEntry: Retrieve a certain attribute for this entry
getAttributeArray() - Method in class magpie.data.Dataset: Output the attributes of each entry into an array
getAttributeExpanders() - Method in class magpie.data.Dataset: Get a copy of the list of currently-employed attribute expanders.
getAttributeGenerators() - Method in class magpie.data.Dataset: Get a copy of the list of currently-employed attribute generators.
getAttributeIndex(String) - Method in class magpie.data.Dataset: Get index of a certain attribute
getAttributeName(int) - Method in class magpie.data.Dataset: Get name of a specific attribute
getAttributeNames() - Method in class magpie.data.Dataset
getAttributeRanks(Dataset) - Method in class magpie.attributes.evaluators.BaseAttributeEvaluator: Generate rank of attributes sorted by their predictive power
getAttributes() - Method in class magpie.data.BaseEntry: Retrieve attributes for this entry
getAttributeSelector() - Method in class magpie.models.BaseModel: Return the BaseAttributeSelector used by this model
getAttributeSelector(String) - Method in class magpie.user.Workspace: Get an BaseAttributeSelector out of the Workspace
getAverageDeviation(double[]) - Method in class magpie.data.materials.CompositionEntry: Calculate the mean deviation of a property from the average.
getAverageDeviation(double[], double) - Method in class magpie.data.materials.CompositionEntry: Calculate the mean deviation of a property from the average.
getBatch() - Method in class magpie.utility.tools.BatchAttributeGenerator: Get a batch of entries.
getCitationDescriptions(String) - Method in class magpie.user.CommandHandler: Print out citation information associated with a single variable
getCitations() - Method in class magpie.attributes.expanders.FunctionExpander
getCitations() - Method in class magpie.attributes.generators.composition.ChargeDependentAttributeGenerator
getCitations() - Method in class magpie.attributes.generators.composition.IonicityAttributeGenerator
getCitations() - Method in class magpie.attributes.generators.composition.MeredigAttributeGenerator
getCitations() - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
getCitations() - Method in class magpie.attributes.generators.composition.ValenceShellAttributeGenerator
getCitations() - Method in class magpie.attributes.generators.composition.YangOmegaAttributeGenerator
getCitations() - Method in class magpie.attributes.generators.crystal.APRDFAttributeGenerator
getCitations() - Method in class magpie.attributes.generators.crystal.CoulombMatrixAttributeGenerator
getCitations() - Method in class magpie.attributes.generators.crystal.PRDFAttributeGenerator
getCitations() - Method in class magpie.attributes.selectors.LassoAttributeSelector
getCitations() - Method in class magpie.attributes.selectors.StagedAttributeSelector
getCitations() - Method in class magpie.data.Dataset
getCitations() - Method in class magpie.models.BaseModel
getCitations() - Method in class magpie.models.classification.WekaClassifier
getCitations() - Method in class magpie.models.regression.crystal.CoulombEwaldMatrixRegression
getCitations() - Method in class magpie.models.regression.crystal.CoulombSineMatrixRegression
getCitations() - Method in class magpie.models.regression.crystal.PRDFRegression
getCitations() - Method in class magpie.models.regression.WekaRegression
getCitations() - Method in class magpie.models.SplitModel
getCitations() - Method in interface magpie.utility.interfaces.Citable: Return a list of citations for this object and any underlying objects.
getClassName(int) - Method in class magpie.data.Dataset: Get the name of a certain class (for data with multiple possible classes)
getClassNames() - Method in class magpie.data.Dataset
getClassNames() - Method in class magpie.data.MultiPropertyDataset
getClassNames() - Method in interface magpie.models.classification.AbstractClassifier: Get names of classes this model distinguishes between.
getClassNames() - Method in class magpie.models.classification.BaseClassifier
getClassNames() - Method in class magpie.models.classification.SplitClassifier
getClassProbabilityArray() - Method in class magpie.data.Dataset: Get an array of class probabilities
getClassProbilities() - Method in class magpie.data.BaseEntry: Get the probability of an entry existing in each class.
getClassProbilities() - Method in class magpie.data.MultiPropertyEntry
getClosestBin(double[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Find the composition bin in PhaseDiagramStatistics.CommonCompositions) that has the same number of elements and is the closest
getClosestCompositions(CompositionEntry, Collection<CompositionEntry>, int, int) - Static method in class magpie.attributes.generators.composition.APEAttributeGenerator: Get closest compositions
getCluster(Dataset, int) - Method in class magpie.cluster.BaseClusterer: Retrieve a specific cluster from a dataset.
getClusterer(String) - Method in class magpie.user.Workspace: Get an BaseClusterer out of the Workspace
getClustererDetails(boolean) - Method in class magpie.cluster.BaseClusterer: Get any user-specified options of this clusterer.
getClustererDetails(boolean) - Method in class magpie.cluster.WekaClusterer
getClusterRange(double[], double) - Static method in class magpie.attributes.generators.composition.APEAttributeGenerator: Determine the maximum and minimum possible cluster sizes, provided a list of radii.
getCoefficientName(int) - Method in class magpie.models.regression.AbstractNonlinearRegression: Return name of coefficient, given index
getCoefficients() - Method in class magpie.models.regression.PolynomialRegression: Get coefficients of model.
getCommands() - Method in class magpie.user.InputFileParser: From the open input file, read in the next command.
getCommonCompositions(Map<CompositionEntry, String>, int[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Determine most common compositions from all structures.
getComponent(String) - Method in class magpie.csp.CSPEngine: Get a clone of a specific component of this CSP engine.
getComposition() - Method in class magpie.data.materials.CrystalStructureEntry: Get the composition of this entry.
getCompositionIndex(double[]) - Method in class magpie.csp.diagramdata.OnTheFlyPhaseDiagramStatistics: Look up a composition in PhaseDiagramStatistics.CommonCompositions.
getCompoundVector(int[]) - Method in class magpie.csp.diagramdata.OnTheFlyPhaseDiagramStatistics
getCompoundVector(int[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Given a list of elements on each site of a structure, determine which prototypes exist on each site of the corresponding phase diagram.
getCumulants(PrototypeDataset, boolean[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: For a certain training set, calculate the cumulant function between a condition being true and each variable being any allowed condition.
getDataDirectory() - Method in class magpie.data.materials.CompositionDataset: Get path to directory containing elemental property lookup-data
getDataset(String) - Method in class magpie.user.Workspace: Get a dataset out of the variable list
getDatasetByName(String) - Method in class magpie.user.server.operations.ModelQueryHandler: Given the name of a dataset object, return an instance of that class
getDatasetCopy() - Method in class magpie.user.server.ModelPackage: Get a copy of the dataset
getDelimiter() - Method in class magpie.data.utilities.output.DelimitedOutput: Get string used to separate words in output file
getDistribution() - Method in class magpie.data.Dataset: Get the distribution of entries between known classes
getDistributionCount() - Method in class magpie.data.Dataset: Get the distribution of entries between known classes
getDuplicates() - Method in class magpie.data.Dataset: Get a map of an example of a duplicate entry to all duplicates.
getElementalProperties() - Method in class magpie.data.materials.CompositionDataset: Get list of elemental properties currently being used to generate attributes.
getElementalProperties() - Method in class magpie.data.materials.ElementDataset: Get the list of elemental properties to be used to compute attributes.
getElementFraction(String) - Method in class magpie.data.materials.CompositionEntry: Return the fraction of a certain element found in an entry
getElementFraction(int) - Method in class magpie.data.materials.CompositionEntry: Return the fraction of a certain element found in an entry
getElementID() - Method in class magpie.data.materials.ElementEntry: Get the ID of this element
getElementIndices(String[]) - Static method in class magpie.data.utilities.filters.ContainsElementFilter: Given a list of elements, return their indices.
getElementIndices(List<String>, CompositionDataset) - Static method in class magpie.data.utilities.splitters.SingleElementGroupSplitter: Given a CompositionDataset, return the index corresponding to each element in a list of element names
getElementNames(int[]) - Static method in class magpie.utility.tools.PhaseDiagramExclusionValidator: Provided with a list of elements IDs, print out element names.
getElementPairProperties() - Method in class magpie.data.materials.CompositionDataset: Get list of properties of pairs of elements currently being used to generate attributes.
getElements() - Method in class magpie.data.materials.CompositionEntry
getElements() - Method in class magpie.data.utilities.generators.FixedStoichiometryCompositionEntryGenerator: Get set of elements used in generation
getElements(CompositionDataset) - Static method in class magpie.utility.tools.PhaseDiagramExclusionValidator: Provided a CompositionDataset, get list of all included elements.
getEnsembleMean(double[][]) - Method in class magpie.models.regression.CompositeRegression: Get mean prediction by the ensemble for each entry
getEnsembleMean(Dataset) - Method in class magpie.models.regression.CompositeRegression: Get mean prediction by the ensemble for each entry
getEnsemblePredictions(Dataset) - Method in class magpie.models.regression.CompositeRegression: Calculate the predicted class using each model
getEnsembleVariation(double[][]) - Method in class magpie.models.regression.CompositeRegression: Return the variance in predictions for each entry.
getEnsembleVariation(Dataset) - Method in class magpie.models.regression.CompositeRegression: Return the variance in predictions for each entry.
getEntries() - Method in class magpie.data.Dataset: Return copy of list of entries.
getEntries(JSONObject) - Method in class magpie.user.server.operations.SearchRunner: Generate a list of entries
getEntriesWriteAccess() - Method in class magpie.data.Dataset: Get the internal list of entries from this dataset.
getEntry(int) - Method in class magpie.data.Dataset: Retrieve a single entry from the dataset
getEntry(int) - Method in class magpie.data.materials.CompositionDataset
getEntry(int) - Method in class magpie.data.materials.CrystalStructureDataset
getEntry(int) - Method in class magpie.data.materials.ElementDataset
getEntry(int) - Method in class magpie.data.materials.PrototypeDataset
getEntry(int) - Method in class magpie.data.MultiPropertyDataset
getEntryArray() - Method in class magpie.data.Dataset: Output the attributes and class of each entry
getEntryData(String) - Method in class magpie.user.server.operations.ModelOperator: Given a JSON file send from a user, get the names of entries to be run
getEquivalentArragements() - Method in class magpie.data.materials.util.PrototypeSiteInformation: Get all equivalent orders of sites.
getEquivalentPrototypes() - Method in class magpie.data.materials.PrototypeEntry: Generate a list of prototypes equivalent to this entry.
getFilter() - Method in class magpie.models.BaseModel: Get filter used before training
getFittedCoefficient(int) - Method in class magpie.models.regression.AbstractNonlinearRegression: Get the value of fitted coefficient
getFractions() - Method in class magpie.data.materials.CompositionEntry
getGenericModel() - Method in interface magpie.models.interfaces.MultiModel: Get the model template
getGenericModel() - Method in class magpie.models.regression.CompositeRegression
getGenericModel() - Method in class magpie.models.regression.StagedRegression
getGenericModel() - Method in class magpie.models.SplitModel
getGroupLabel(int) - Method in class magpie.data.materials.util.PrototypeSiteInformation: Generate a label for a certain group of sites.
getGuess() - Method in class magpie.models.regression.SingleGuessRegression: Get the user's guess
getIdealRadiusRatio(int) - Static method in class magpie.attributes.generators.composition.APEAttributeGenerator: Get the ideal radius ratio for a cluster of a certain size.
getInput() - Method in class magpie.utility.ParsedFunction: Get the string that was provided as input
getLookupTable(String) - Method in class magpie.data.materials.ElementDataset: Get an elemental property lookup table
getLookupValue(double[]) - Method in class magpie.data.materials.ElementEntry: Given an elemental-property lookup array, get the property for this entry.
getMAE(double[]) - Static method in class magpie.models.regression.LASSORegression: Get Mean Absolute Error (MAE) given residuals
getMaxDifference(double[]) - Method in class magpie.data.materials.CompositionEntry: Calculate maximum difference between the properties of two elements that are present in this entry
getMaximum(double[]) - Method in class magpie.data.materials.CompositionEntry: Get the maximum of an elemental property
getMaxIter() - Method in class magpie.models.regression.AbstractNonlinearRegression: Get the maximum number of iterations allowed
getMaxNumEntries() - Method in class magpie.user.server.ModelPackage: Get the maximum number of entries this model is allowed to run.
getMean(double[]) - Method in class magpie.data.materials.CompositionEntry: Calculate the alloy mean of a property
getMeasuredClass() - Method in class magpie.data.BaseEntry: Get the measured class variable
getMeasuredClass() - Method in class magpie.data.MultiPropertyEntry
getMeasuredClassArray() - Method in class magpie.data.Dataset: Output an array of the measured classes for each entry.
getMeasuredProperties() - Method in class magpie.data.MultiPropertyEntry: Get copy all measured properties.
getMeasuredProperty(int) - Method in class magpie.data.MultiPropertyEntry: Get a single measured property.
getMeasuredPropertyArray(String) - Method in class magpie.data.MultiPropertyDataset: Get measured values for a certain property for all entries in the dataset.
getMeasuredPropertyArray(int) - Method in class magpie.data.MultiPropertyDataset: Get the measured value for a certain property for all entries in the dataset.
getMinimum(double[]) - Method in class magpie.data.materials.CompositionEntry: Get the minimum of an elemental property
getModel(int) - Method in interface magpie.models.interfaces.MultiModel: Get a specific submodel.
getModel(int) - Method in class magpie.models.regression.CompositeRegression
getModel(String) - Method in class magpie.models.regression.MultiObjectiveRegression: Get the model designed to predict a certain property.
getModel(int) - Method in class magpie.models.regression.StagedRegression
getModel(int) - Method in class magpie.models.SplitModel
getModel(String) - Method in class magpie.user.Workspace: Get a model out of the workspace
getModelDescription(ExternalModel) - Static method in class magpie.models.utility.ExternalModelUtility: Generate a description of the model
getModelFull() - Method in class magpie.models.classification.WekaClassifier
getModelFull() - Method in interface magpie.models.interfaces.WekaModel: Return model name and options
getModelFull() - Method in class magpie.models.regression.WekaRegression: Return model name and options
getModelInfo() - Method in class magpie.user.server.operations.ModelOperator: Get information about the model
getModelName() - Method in class magpie.models.classification.WekaClassifier
getModelName() - Method in interface magpie.models.interfaces.WekaModel: Return the model name
getModelName() - Method in class magpie.models.regression.WekaRegression: Return the model name
getModelOptions() - Method in class magpie.models.classification.WekaClassifier
getModelOptions() - Method in interface magpie.models.interfaces.WekaModel: Return the model options
getModelOptions() - Method in class magpie.models.regression.WekaRegression: Return the model options
getMost(double[]) - Method in class magpie.data.materials.CompositionEntry: Get the elemental property of the most-prevalent element.
getName() - Method in class magpie.data.materials.CrystalStructureEntry: Get name of this entry
getNClasses() - Method in interface magpie.models.classification.AbstractClassifier
getNClasses() - Method in class magpie.models.classification.BaseClassifier
getNClasses() - Method in class magpie.models.classification.SplitClassifier
getNewClass(Dataset, List<BaseEntry>) - Static method in class magpie.data.utilities.modifiers.duplicates.AveragingDuplicateResolver: Get the average of the measured class of an entry.
getNextComposition(Iterator<List<Double>>) - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator: Get the next alloy composition in the sequence.
getNFittingParameters() - Method in class magpie.models.regression.AbstractNonlinearRegression
getNFittingParameters() - Method in interface magpie.models.regression.AbstractRegressionModel: Number of fitting parameters in a model.
getNFittingParameters() - Method in class magpie.models.regression.ClassificationRegression
getNFittingParameters() - Method in class magpie.models.regression.CompositeRegression
getNFittingParameters() - Method in class magpie.models.regression.crystal.StructureKRRBasedRegression
getNFittingParameters() - Method in class magpie.models.regression.GuessMeanRegression
getNFittingParameters() - Method in class magpie.models.regression.LASSORegression
getNFittingParameters() - Method in class magpie.models.regression.LinearCorrectedRegression
getNFittingParameters() - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
getNFittingParameters() - Method in class magpie.models.regression.MixingRuleRegression
getNFittingParameters() - Method in class magpie.models.regression.MultiObjectiveRegression
getNFittingParameters() - Method in class magpie.models.regression.PolynomialRegression
getNFittingParameters() - Method in class magpie.models.regression.RandomGuessRegression
getNFittingParameters() - Method in class magpie.models.regression.ScikitLearnRegression
getNFittingParameters() - Method in class magpie.models.regression.SingleGuessRegression
getNFittingParameters() - Method in class magpie.models.regression.SplitRegression
getNFittingParameters() - Method in class magpie.models.regression.StagedRegression
getNFittingParameters() - Method in class magpie.models.regression.WekaRegression
getNumberEntriesEvaluated() - Method in class magpie.user.server.ModelPackage
getNumberRuns() - Method in class magpie.user.server.ModelPackage
getObject(String) - Method in class magpie.user.Workspace: Gets an object that has been created by the user
getObjectiveFunction(String) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker: Get objective function for a certain property.
getObjectivePercentile() - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
getObjectives() - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
getObjectives() - Method in class magpie.optimization.rankers.MultiObjectiveEntryRanker: Get properties currently used in objective functions.
getObjectives() - Method in class magpie.optimization.rankers.PropertyFormulaRanker
getOxidationStates() - Method in class magpie.data.materials.CompositionDataset: Get the list of known oxidation states
getP() - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker: Get tradeoff parameter.
getPairPropertyLookupTable(String) - Method in class magpie.data.materials.CompositionDataset: Get a lookup table for the properties of pairs of elements
getPort() - Method in class magpie.models.classification.ScikitLearnClassifier
getPort() - Method in interface magpie.models.interfaces.ExternalModel: Get the port number for this model's server
getPort() - Method in class magpie.models.regression.ScikitLearnRegression
getPossibleClasses() - Method in class magpie.user.server.ModelPackage: Get the names of classes for a classification model
getPossibleStates(CompositionEntry) - Method in class magpie.utility.tools.OxidationStateGuesser: Get list of possible charge states.
getPossibleStructures(String) - Method in class magpie.csp.CSPEngine: Get a list of possible structure types for a structure, given composition.
getPossibleStructures(CompositionEntry) - Method in class magpie.csp.CSPEngine: Get a list of possible structure types for a structure, given composition.
getPredictedClass() - Method in class magpie.data.BaseEntry: Get the predicted class variable
getPredictedClass() - Method in class magpie.data.MultiPropertyEntry
getPredictedClassArray() - Method in class magpie.data.Dataset: Get the predicted class for each entry
getPredictedProperty(int) - Method in class magpie.data.MultiPropertyEntry: Get the predicted properties for an instance.
getPredictedPropertyArray(String) - Method in class magpie.data.MultiPropertyDataset: Get predicted values for a certain property for all entries in the dataset.
getPredictedPropertyArray(int) - Method in class magpie.data.MultiPropertyDataset: Get the predicted value for a certain property for all entries in the dataset.
getProbabilities(BaseClassifier, List<String>, PrototypeSiteInformation, PrototypeEntry) - Method in class magpie.csp.CompositionBasedCSPEngine
getProbabilities(BaseClassifier, List<String>, PrototypeSiteInformation, PrototypeEntry) - Method in class magpie.csp.CSPEngine: Calculate probability that a compound will form as each of the known prototypes.
getProcess() - Method in class magpie.models.classification.ScikitLearnClassifier
getProcess() - Method in interface magpie.models.interfaces.ExternalModel: Get the process holding this external port
getProcess() - Method in class magpie.models.regression.ScikitLearnRegression
getPropertiesBeingModeled() - Method in class magpie.models.regression.MultiObjectiveRegression: Get a list of properties for which a model is defined.
getPropertiesToAdd() - Method in class magpie.data.utilities.modifiers.AddPropertyModifier: Retrieve list of properties that would be added to a dataset.
getPropertyClassCount(int) - Method in class magpie.data.MultiPropertyDataset: Get the number of classes for a certain property
getPropertyClasses(String) - Method in class magpie.data.MultiPropertyDataset: Get list of possible classes for a certain property
getPropertyClasses(int) - Method in class magpie.data.MultiPropertyDataset: Get list of possible classes for a certain property
getPropertyClassProbabilties(int) - Method in class magpie.data.MultiPropertyEntry: Get the predicted class probabilities for a certain property.
getPropertyIndex(String) - Method in class magpie.data.MultiPropertyDataset: Lookup the index of a property.
getPropertyLookupTable(String) - Method in class magpie.data.materials.CompositionDataset: Reads in a data file that contains properties for each element.
getPropertyName(int) - Method in class magpie.data.MultiPropertyDataset: Retrieve the name of a certain property.
getPropertyName() - Method in class magpie.models.regression.MixingRuleRegression: Retrieve the property used for alloy mean
getPropertyNames() - Method in class magpie.data.MultiPropertyDataset: Get the names of each property stored in this dataset.
getPropertySet(String) - Static method in class magpie.data.materials.util.PropertyLists: Generate a list of properties based on pre-defined sets.
getPrototypeNames(double[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Get list of all known prototype structures at a composition.
getR() - Method in class magpie.data.utilities.normalizers.SoftmaxNormalizer: Get the scaling constant
getRandomSplit(int) - Method in class magpie.data.Dataset: Split off a certain number of entries into a separate dataset.
getRandomSplit(int, long, boolean) - Method in class magpie.data.Dataset: Split off a certain number of entries into a separate dataset.
getRandomSplit(double) - Method in class magpie.data.Dataset: Split off a certain number of entries into a separate dataset.
getRandomSplit(double, long, boolean) - Method in class magpie.data.Dataset: Split off a certain number of entries into a separate dataset.
getRandomSubset(int) - Method in class magpie.data.Dataset: Generate a random subset of the original data, which is left intact
getRandomSubset(double) - Method in class magpie.data.Dataset: Generate a random subset of the original data, which is left intact
getReplacementIterator(CrystalStructureEntry) - Method in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator: Get an iterator over all possible combinations of elements on each site of this structure
getResidual(double[][], double[]) - Method in class magpie.models.regression.LASSORegression: Determines the residuals from a model
getRobustRegressionQ() - Method in interface magpie.models.regression.AbstractRegressionModel: Get desired False Discovery Rate
getRobustRegressionQ() - Method in class magpie.models.regression.BaseRegression
getRobustRegressionQ() - Method in class magpie.models.regression.SplitRegression
getROCCurve(int[], double[], int) - Method in class magpie.statistics.performance.BaseStatistics: Generate the receiver operating characteristic curve based on the measured and score variables for many instances.
getRSDR(double[], int) - Method in class magpie.statistics.utility.RobustRegressionUtility: Calculate the Robust Standard Deviation of Residuals.
getRSDR(double[], double, int) - Method in class magpie.statistics.utility.RobustRegressionUtility: Calculate RSDR if the mean is already known.
getRunTime() - Method in class magpie.user.server.ModelPackage
getScale() - Method in class magpie.data.utilities.normalizers.InverseNormalizer: Get scale factor used when inverting data
getScriptPath() - Method in class magpie.attributes.selectors.LassoAttributeSelector
getScriptPath() - Method in class magpie.attributes.selectors.PythonBasedAttributeSelector: Get the path to the Python script to be run.
getScriptPath() - Method in class magpie.attributes.selectors.RandomForestAttributeSelector
getSelectionNames() - Method in class magpie.attributes.selectors.BaseAttributeSelector: Get the selected attributes
getSelections() - Method in class magpie.attributes.selectors.BaseAttributeSelector: Get the selected attributes
getSelectors() - Method in class magpie.attributes.selectors.StagedAttributeSelector: Get the current list of selectors
getSingleAttributeArray(int) - Method in class magpie.data.Dataset: Output a single attribute for each entry
getSiteComposition(int) - Method in class magpie.data.materials.PrototypeEntry: Get composition of a certain site
getSiteGroup(int) - Method in class magpie.data.materials.util.PrototypeSiteInformation: Get indices of sites in a particular group.
getSiteGroupMean(int, double[]) - Method in class magpie.data.materials.PrototypeEntry: Calculate the mean of an elemental property for a certain site
getSiteInfo() - Method in class magpie.data.materials.PrototypeDataset: Get information about each site in this prototype structure
getSiteMean(int, double[]) - Method in class magpie.data.materials.PrototypeEntry: Calculate the mean of an elemental property for a certain site
getSortingOrder() - Method in class magpie.data.materials.CompositionDataset: Get the order in which elements are sorted when storing a composition.
getSortingOrder() - Method in class magpie.data.materials.CompositionEntry
getSplitNames() - Method in class magpie.data.utilities.splitters.AllMetalsSplitter
getSplitNames() - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
getSplitNames() - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter: Get the names of the splits this splitter creates
getSplitNames() - Method in class magpie.data.utilities.splitters.ClustererSplitter
getSplitNames() - Method in class magpie.data.utilities.splitters.FilterSplitter
getSplitNames() - Method in class magpie.data.utilities.splitters.MeasuredClassSplitter
getSplitNames() - Method in class magpie.data.utilities.splitters.MixedMetalsSplitter
getSplitNames() - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
getSplitNames() - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
getSplitNames() - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
getSplitNames() - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
getSplitNames() - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.AllMetalsSplitter
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter: Get details of splitter.
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.ClustererSplitter
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.FilterSplitter
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.MeasuredClassSplitter
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
getStatistics() - Method in class magpie.statistics.performance.BaseStatistics: Retrieve list of statistics stored in this class.
getStatistics() - Method in class magpie.statistics.performance.ClassificationStatistics
getStatistics(double[], double[]) - Method in class magpie.statistics.performance.RegressionStatistics: Calculate regression statistics
getStatistics() - Method in class magpie.statistics.performance.RegressionStatistics
getStatisticsNoNaNs() - Method in class magpie.statistics.performance.BaseStatistics: Get statistics, except for values that are NaNs or infinite
getStiochiometries() - Method in class magpie.data.utilities.generators.FixedStoichiometryCompositionEntryGenerator: Get the current list of stoichiometries
getStructure() - Method in class magpie.data.materials.CrystalStructureEntry: Get link to structure
getSubList() - Method in class magpie.utility.tools.BatchModelEvaluator: Get list of entries to be evaluated
getSubset(int[]) - Method in class magpie.data.Dataset: Get a specific list of entries from the dataset.
getTargetProperty() - Method in class magpie.data.MultiPropertyEntry: Look up which property is being used as the class variable.
getTargetPropertyIndex() - Method in class magpie.data.MultiPropertyDataset: Get the index of the currently active property.
getTargetPropertyName() - Method in class magpie.data.MultiPropertyDataset: Lookup what target property is being used.
getTrainingExamples() - Method in class magpie.data.Dataset: Get a dataset that only contains entries with a measured class variable.
getTrainingSet(CompositionEntry) - Method in class magpie.csp.CSPEngine: Get a training set of all examples of all possible crystal structures at a certain composition
getTrainTime() - Method in class magpie.models.BaseModel: Return when this model was trained
getUniqueEntries() - Method in class magpie.data.Dataset: Get a map of all unique entries, and their duplicates.
getUnits() - Method in class magpie.user.server.ModelPackage: Get the units for the model (regression), or the possible classes (classification)
getUseInverse() - Method in class magpie.models.regression.MixingRuleRegression
getValidationMethod() - Method in class magpie.models.BaseModel: Get a description of how this model was validated
getVariableName(int) - Method in class magpie.models.regression.AbstractNonlinearRegression
getVariableNames() - Method in class magpie.user.Workspace: Get the names of all variables stored in this class
getVariableNames() - Method in class magpie.utility.ParsedFunction: Get the list of variables.
getVariableVector(PrototypeEntry) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: For a certain prototype, get a vector that describes the characteristics of its phase diagram.
getVersion() - Method in class magpie.user.server.operations.ServerInformationGetter
getWekaObjectCitations(Object, Class) - Static method in class magpie.utility.WekaUtility: Generate citations from a Weka object
GreaterThan - Variable in class magpie.data.utilities.filters.ComparisonOperatorFilter: Should entries with Feature < Threshold be kept?
GridBaseEntryGenerator - Class in magpie.data.utilities.generators: Generate BaseEntry objects that represent a grid.
GridBaseEntryGenerator() - Constructor for class magpie.data.utilities.generators.GridBaseEntryGenerator
groupIsIncludedInAttributes(int) - Method in class magpie.data.materials.util.PrototypeSiteInformation: Determine whether a group sites of should be included in attributes.
Guess - Variable in class magpie.models.regression.SingleGuessRegression: Guess for all classes
GuessMeanRegression - Class in magpie.models.regression: Always guess the mean of the values provided during training.
GuessMeanRegression() - Constructor for class magpie.models.regression.GuessMeanRegression

H

handlePrinting(List<String>) - Method in class magpie.user.CommandHandler: Run commands that require printing something to screen.
handleSaving(List<String>) - Method in class magpie.user.CommandHandler: Save objects to disk as various formats.
handleSetCommand(List<Object>) - Method in class magpie.models.BaseModel: Handle setting components of a model via the command interface
handleSettings(List<String>) - Method in class magpie.user.CommandHandler: Handles commands that change global settings
handleSubmodelCommand(BaseModel, List<Object>) - Static method in class magpie.models.utility.MultiModelUtility: Runs commands that are specific to MultiModel-based classes.
handleSubmodelPrintCommand(MultiModel, List<String>) - Static method in class magpie.models.utility.MultiModelUtility: Handles printing commands specific to MultiModels.
hasClassProbabilities() - Method in class magpie.data.BaseEntry: Whether this entry has predicted probabilities
hasClassProbabilities() - Method in class magpie.data.MultiPropertyEntry
hashCode() - Method in class magpie.data.BaseEntry
hashCode() - Method in class magpie.data.materials.CompositionEntry
hashCode() - Method in class magpie.data.materials.CrystalStructureEntry
hashCode() - Method in class magpie.data.materials.PrototypeEntry
hashCode() - Method in class magpie.data.materials.util.PrototypeSiteInformation
hashCode() - Method in class magpie.utility.interfaces.Citation
hasMeasuredProperty(int) - Method in class magpie.data.MultiPropertyEntry: Whether a specific property of this entry has been measured
hasMeasurement() - Method in class magpie.data.BaseEntry
hasMeasurement() - Method in class magpie.data.MultiPropertyEntry
hasNext() - Method in class magpie.utility.NDGridIterator
hasPredictedProperty(int) - Method in class magpie.data.MultiPropertyEntry: Whether an specific property has any predicted value
hasPrediction() - Method in class magpie.data.BaseEntry
hasPrediction() - Method in class magpie.data.MultiPropertyEntry
hasProperty(String) - Method in class magpie.data.MultiPropertyDataset: Check whether dataset contains a certain property
hasPropertyClassProbabilities(int) - Method in class magpie.data.MultiPropertyEntry: Check whether a property has predicted class probabilities
hasVariable(String) - Method in class magpie.user.Workspace: Test whether the user has created a variable
HHICalculationModifier - Class in magpie.data.utilities.modifiers: Calculates the Herfindahl-Hirschman Index (HHI) for compounds, stores as property.
HHICalculationModifier() - Constructor for class magpie.data.utilities.modifiers.HHICalculationModifier
HTMLFormat - Variable in class magpie.data.materials.CompositionEntry: Whether to print composition in HTML Format

I

importCompoundDataset(String) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Load in file containing composition and prototypes of all known compounds.
importEntryProperties(String[]) - Method in class magpie.data.MultiPropertyDataset: Used by Dataset.importText(java.lang.String, java.lang.Object[]) to import property measurements for each entry.
importKnownCompounds(String) - Method in class magpie.csp.CSPEngine: Gather a list of known compounds an their prototypes.
importKnownCompounds(String, int, int[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Import all known compounds into phase diagram object
importKnownCompounds(Map<CompositionEntry, String>, int, int[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Import list of known compounds into phase diagram object
importPropertyNames(String) - Method in class magpie.data.MultiPropertyDataset: Given the line describing property names in the input file, read in property names and possible classes.
importText(String, Object[]) - Method in class magpie.data.Dataset: Imports data from a text file.
importText(String, Object[]) - Method in class magpie.data.materials.CompositionDataset: Read in an dataset from file.
importText(String, Object[]) - Method in class magpie.data.materials.CrystalStructureDataset: Import all structure files in a directory.
importText(String, Object[]) - Method in class magpie.data.materials.ElementDataset
importText(String, Object[]) - Method in class magpie.data.materials.PrototypeDataset
importWekaHome() - Static method in class magpie.utility.WekaUtility: Load in packages that were installed with the package manager.
IncludeMatching - Variable in class magpie.attributes.selectors.RegexAttributeSelector: Whether to include attributes that match
incrementCounter(int[]) - Method in class magpie.csp.diagramdata.OnTheFlyPhaseDiagramStatistics: Increment a counter that iterates through all combinations of elements in a phase diagram.
incrementCounter(int[]) - Method in class magpie.utility.CartesianSumGenerator: Increment position of counter.
incrementCounter(int[], int) - Static method in class magpie.utility.EqualSumCombinations: Increment a counter that iterates through all possible vectors.
incrementCounter() - Method in class magpie.utility.NDGridIterator: Increment position of counter.
IndependentVariableNormalizer - Class in magpie.data.utilities.normalizers: Base class for normalizers that treat attributes/class independently.
IndependentVariableNormalizer() - Constructor for class magpie.data.utilities.normalizers.IndependentVariableNormalizer
initializeServer(ExternalModel, boolean) - Static method in class magpie.models.utility.ExternalModelUtility: Assuming that a model server is already launched, get the port number and send the model object stream to the standard input of the server process.
inputFile - Variable in class magpie.user.InputFileParser: Reader holding the input file
InputFileParser - Class in magpie.user: Parses user input files.
InputFileParser() - Constructor for class magpie.user.InputFileParser: Create an instance that reads from standard in.
instantiateClass(String, List<Object>) - Static method in class magpie.user.CommandHandler: Create new instance of a class given type and options.
instantiateClusterer(String, String[]) - Static method in class magpie.cluster.WekaClusterer: Generate a new instance of a Weka-based clusterer.
instantiateWekaModel(String, String[]) - Static method in class magpie.utility.WekaUtility: Instantiate an AbstractClassifier object from Weka.
Intercept - Variable in class magpie.models.regression.LASSORegression: Intercept of the linear model
InverseNormalizer - Class in magpie.data.utilities.normalizers: Invert the attributes.
InverseNormalizer() - Constructor for class magpie.data.utilities.normalizers.InverseNormalizer
IonicCompoundFinder - Class in magpie.utility.tools: Given a nominal composition, find nearby compositions that can be charge neutral.
IonicCompoundFinder() - Constructor for class magpie.utility.tools.IonicCompoundFinder
IonicCompoundGenerator - Class in magpie.data.utilities.generators: Generate compositions of ionic compounds.
IonicCompoundGenerator() - Constructor for class magpie.data.utilities.generators.IonicCompoundGenerator
IonicCompoundProximityAttributeGenerator - Class in magpie.attributes.generators.composition: Generate attributes based on the distance of a composition from compositions that can form, charge-neutral ionic compounds.
IonicCompoundProximityAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.IonicCompoundProximityAttributeGenerator
IonicityAttributeGenerator - Class in magpie.attributes.generators.composition: Generate attributes based on the "ioncity" of a compound.
IonicityAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.IonicityAttributeGenerator
IonizationEnergies - Variable in class magpie.attributes.generators.composition.ChargeDependentAttributeGenerator: Ionization energies of each element
IonizationEnergies - Static variable in class magpie.data.materials.util.LookupData: Ionization energies of each element
IQROutlierFilter - Class in magpie.data.utilities.filters: Filters entries based on whether the class values are outliers using the interquartile range.
IQROutlierFilter() - Constructor for class magpie.data.utilities.filters.IQROutlierFilter
isClassifer() - Method in class magpie.user.server.ModelPackage: Get whether model is a classification model
isInteger(String) - Static method in class magpie.utility.UtilityOperations: Determine whether a string represents an integer.
isMaximizing() - Method in class magpie.optimization.rankers.BaseEntryRanker
isMetal - Variable in class magpie.data.utilities.filters.AllMetalsFilter: List indicating which elements are metals
isMetal - Variable in class magpie.data.utilities.splitters.AllMetalsSplitter: List indicating which elements are metals
isOutlier(Dataset) - Method in class magpie.statistics.utility.RobustRegressionUtility: Determines which entries in a dataset qualify as an outlier.
isOutlier(Dataset, int) - Method in class magpie.statistics.utility.RobustRegressionUtility: Determine which entries in a dataset qualify as an outlier, for nonlinear regression purposes.
isRunning(Process) - Static method in class magpie.models.utility.ExternalModelUtility: Check whether a process is running
isSet() - Method in class magpie.data.utilities.generators.PrototypeEntryGenerator: Check whether this generator is ready to go.
isTrained() - Method in class magpie.attributes.selectors.BaseAttributeSelector
isTrained() - Method in class magpie.cluster.BaseClusterer
isTrained() - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
isTrained() - Method in class magpie.models.BaseModel
isTrained() - Method in class magpie.statistics.performance.ClustererStatistics
isUsingMeasured() - Method in class magpie.optimization.rankers.BaseEntryRanker
isValidated() - Method in class magpie.models.BaseModel
iterator() - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
iterator() - Method in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator
iterator() - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
iterator() - Method in class magpie.data.utilities.generators.FixedStoichiometryCompositionEntryGenerator
iterator() - Method in class magpie.data.utilities.generators.GridBaseEntryGenerator
iterator() - Method in class magpie.data.utilities.generators.IonicCompoundGenerator
iterator() - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
iterator() - Method in class magpie.data.utilities.generators.PrototypeEntryGenerator
iterator() - Method in class magpie.utility.CartesianSumGenerator
iterator() - Method in class magpie.utility.EqualSumCombinations

J

Jitter - Variable in class magpie.models.regression.SingleGuessRegression: Amount of jitter added to the answer
JSONOutput - Class in magpie.data.utilities.output: Output data into JSON format.
JSONOutput() - Constructor for class magpie.data.utilities.output.JSONOutput

K

Kappa - Variable in class magpie.statistics.performance.ClassificationStatistics: Fraction correct modified such that 0 is random guessing and 1 is perfect classification
KFolds - Variable in class magpie.attributes.selectors.ExhaustiveAttributeSelector: If test method is K-Fold: Number of folds used in cross-validation test
KnownCompounds - Variable in class magpie.csp.CSPEngine: List of known compounds (used when making predictions)

L

label(Dataset) - Method in class magpie.cluster.BaseClusterer: Mark the most likely cluster for each entry
label(Dataset) - Method in class magpie.data.utilities.filters.AllMetalsFilter
label(Dataset) - Method in class magpie.data.utilities.filters.AttributeFilter
label(Dataset) - Method in class magpie.data.utilities.filters.BaseDatasetFilter: Given a dataset, determine which entries passes the filter.
label(Dataset) - Method in class magpie.data.utilities.filters.BestInAlloySystemFilter
label(Dataset) - Method in class magpie.data.utilities.filters.ClassFilter
label(Dataset) - Method in class magpie.data.utilities.filters.ClassProbabilityFilter
label(Dataset) - Method in class magpie.data.utilities.filters.ClassRangeFilter
label(Dataset) - Method in class magpie.data.utilities.filters.CompositionDistanceFilter
label(Dataset) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
label(Dataset) - Method in class magpie.data.utilities.filters.ContainsElementFilter
label(Dataset) - Method in class magpie.data.utilities.filters.EntryRankerFilter
label(Dataset) - Method in class magpie.data.utilities.filters.IQROutlierFilter
label(Dataset) - Method in class magpie.data.utilities.filters.MultiFilter
label(Dataset) - Method in class magpie.data.utilities.filters.PhaseDiagramExclusionFilter
label(Dataset) - Method in class magpie.data.utilities.filters.PredictionOutlierFilter
label(Dataset) - Method in class magpie.data.utilities.filters.PropertyFilter
label(Dataset) - Method in class magpie.data.utilities.filters.PropertyRangeFilter
label(Dataset) - Method in class magpie.data.utilities.filters.RegressionErrorFilter
label(Dataset) - Method in class magpie.data.utilities.filters.StabilityFilter
label(Dataset) - Method in class magpie.data.utilities.filters.ZScoreOutlierFilter
label(Dataset) - Method in class magpie.data.utilities.splitters.AllMetalsSplitter
label(Dataset) - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
label(Dataset) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter: Given a dataset, determine which subset each entry should belong to.
label(Dataset) - Method in class magpie.data.utilities.splitters.ClustererSplitter
label(Dataset) - Method in class magpie.data.utilities.splitters.FilterSplitter
label(Dataset) - Method in class magpie.data.utilities.splitters.MeasuredClassSplitter
label(Dataset) - Method in class magpie.data.utilities.splitters.MixedMetalsSplitter
label(Dataset) - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
label(Dataset) - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
label(Dataset) - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
label(Dataset) - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
label(Dataset) - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
label_protected(Dataset) - Method in class magpie.cluster.BaseClusterer: Actual implementation of BaseClusterer.label(magpie.data.Dataset).
label_protected(Dataset) - Method in class magpie.cluster.WekaClusterer
LassoAttributeSelector - Class in magpie.attributes.selectors: Uses a combination of LASSO and screening attribute sets with linear regression to select attributes.
LassoAttributeSelector() - Constructor for class magpie.attributes.selectors.LassoAttributeSelector
LASSORegression - Class in magpie.models.regression: This class enables regression using the LASSO algorithm, as described by this page.
LASSORegression() - Constructor for class magpie.models.regression.LASSORegression
LastCompositionBin - Variable in class magpie.csp.CSPEngine: Matched composition bin of last entry evaluated.
LastNComponents - Variable in class magpie.csp.CSPEngine: Number of elements in the last entry evaluated in this class.
LastResults - Variable in class magpie.utility.tools.PhaseDiagramExclusionValidator: Results from previous test.
LastStatistics - Variable in class magpie.utility.tools.PhaseDiagramExclusionValidator: Statistics from last test
LatticeSimilarityAttributeGenerator - Class in magpie.attributes.generators.crystal: Compute similarity of structure to several simple lattices.
LatticeSimilarityAttributeGenerator() - Constructor for class magpie.attributes.generators.crystal.LatticeSimilarityAttributeGenerator
LessThan - Variable in class magpie.data.utilities.filters.ComparisonOperatorFilter: Should entries with Feature > Threshold be kept?
LinearCorrectedRegression - Class in magpie.models.regression: Apply a linear correction to results from another model.
LinearCorrectedRegression() - Constructor for class magpie.models.regression.LinearCorrectedRegression
linearFit(double[], double[], boolean) - Static method in class magpie.models.regression.LASSORegression: Find the best linear fit
ListenPort - Static variable in class magpie.user.server.ServerLauncher: Port on which to listen
loadPairPropertyTable(String, String) - Static method in class magpie.data.materials.util.LookupData: Load in a binary property table
loadPropertyLookupTable(String, String) - Static method in class magpie.data.materials.util.LookupData: Load in an elemental property lookup table
loadState(String) - Static method in class magpie.data.Dataset: Read the state from file using serialization
loadState(String) - Static method in class magpie.models.BaseModel: Read the state from file using serialization
loadState(String) - Static method in class magpie.utility.UtilityOperations: Read the state from file using serialization
loadState(InputStream) - Static method in class magpie.utility.UtilityOperations: Read in a Magpie object from a stream
LocalPropertyDifferenceAttributeGenerator - Class in magpie.attributes.generators.crystal: Compute attributes based on the difference in elemental properties between neighboring atoms.
LocalPropertyDifferenceAttributeGenerator() - Constructor for class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator: Create Default attribute generator.
LocalPropertyDifferenceAttributeGenerator(int...) - Constructor for class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator: Create attribute generator that considers a certain list of shells.
LocalPropertyVarianceAttributeGenerator - Class in magpie.attributes.generators.crystal: Compute attributes based on the local variance in elemental properties around each atom.
LocalPropertyVarianceAttributeGenerator() - Constructor for class magpie.attributes.generators.crystal.LocalPropertyVarianceAttributeGenerator
LocalPropertyVarianceAttributeGenerator(int...) - Constructor for class magpie.attributes.generators.crystal.LocalPropertyVarianceAttributeGenerator
Location - Variable in class magpie.utility.interfaces.Citation: URL of resource being cited.
LogLoss - Variable in class magpie.statistics.performance.ClassificationStatistics: Log-loss
LookupData - Class in magpie.data.materials.util: Holds data that any CompositionDataset needs to lookup.
LookupData() - Constructor for class magpie.data.materials.util.LookupData
LookupData - Variable in class magpie.data.utilities.generators.IonicCompoundGenerator: Dataset used to compute ionic compounds
LookupDirectory - Variable in class magpie.data.materials.ElementDataset: Directory containing elemental property lookup tables
LookupTable - Variable in class magpie.models.regression.MixingRuleRegression: Lookup table for property of interest
LookupTableAttributeGenerator - Class in magpie.attributes.generators: Tool to add precomputed attributes from a lookup table.
LookupTableAttributeGenerator() - Constructor for class magpie.attributes.generators.LookupTableAttributeGenerator

M

MAE - Variable in class magpie.statistics.performance.RegressionStatistics: Mean absolute error
magpie - package magpie: Holds the main class for this program
Magpie - Class in magpie: Main program for text-based interface.
Magpie() - Constructor for class magpie.Magpie
magpie.attributes.evaluators - package magpie.attributes.evaluators: Methods to evaluate the predictive power of single attributes
magpie.attributes.expanders - package magpie.attributes.expanders: Classes that expand the number of available attributes
magpie.attributes.generators - package magpie.attributes.generators: Objects design to compute new attributes for a dataset.
magpie.attributes.generators.composition - package magpie.attributes.generators.composition: Attributes based on the composition of a material.
magpie.attributes.generators.crystal - package magpie.attributes.generators.crystal: Tools to generate attributes based on crystal structures
magpie.attributes.generators.element - package magpie.attributes.generators.element: Attribute generators for elements from the periodic table.
magpie.attributes.generators.prototype - package magpie.attributes.generators.prototype: Attributes for datasets where the material is entirely composed of materials with the same prototype crystal structure.
magpie.attributes.selectors - package magpie.attributes.selectors: Methods to select attribute subsets that might lead to more effective models
magpie.cluster - package magpie.cluster: Separate data into multiple subsets using unsupervised learning
magpie.csp - package magpie.csp: Models that predict what crystal structure will appear under different conditions.
magpie.csp.diagramdata - package magpie.csp.diagramdata
magpie.data - package magpie.data: Objects designed to store, manipulate, and output data
magpie.data.materials - package magpie.data.materials: Datasets specifically designed to handle data from OQMD
magpie.data.materials.util - package magpie.data.materials.util: Data structures used by several types of Dataset/Entry
magpie.data.utilities.filters - package magpie.data.utilities.filters: Classes that allow for filtering undesired entries out of a Dataset
magpie.data.utilities.generators - package magpie.data.utilities.generators: Holds classes designed to generate entries.
magpie.data.utilities.modifiers - package magpie.data.utilities.modifiers: Operations that make changes to a Dataset and the entries it contains
magpie.data.utilities.modifiers.duplicates - package magpie.data.utilities.modifiers.duplicates: Tools for removing duplicates in a dataset
magpie.data.utilities.normalizers - package magpie.data.utilities.normalizers: Adjust attributes and/or class to all exist on the same range.
magpie.data.utilities.output - package magpie.data.utilities.output: Utilities for writing datasets to disk or other outputs
magpie.data.utilities.splitters - package magpie.data.utilities.splitters: Operations to partition a Dataset into multiple subsets.
magpie.models - package magpie.models: Templates for different model types
magpie.models.classification - package magpie.models.classification: Models designed to classify data into multiple categories
magpie.models.interfaces - package magpie.models.interfaces: Holds interfaces that define certain classes of models
magpie.models.regression - package magpie.models.regression: Models that predict a single, continuous class variable
magpie.models.regression.crystal - package magpie.models.regression.crystal: Models based on the crystal structure of a material.
magpie.models.regression.nonlinear - package magpie.models.regression.nonlinear: Sample AbstractNonlinearRegression implementations
magpie.models.utility - package magpie.models.utility: Abstract classes that hold operations necessary to run different models
magpie.optimization.rankers - package magpie.optimization.rankers: Classes that rank entries based on arbitrary criteria
magpie.statistics.performance - package magpie.statistics.performance: Classes necessary to generate statistics about model
magpie.statistics.utility - package magpie.statistics.utility: Classes that handle calculation of useful statistics
magpie.user - package magpie.user: Classes that make the user interface possible
magpie.user.server - package magpie.user.server
magpie.user.server.operations - package magpie.user.server.operations
magpie.utility - package magpie.utility: Junk that does not fall under another category
magpie.utility.interfaces - package magpie.utility.interfaces: Interfaces that are useful for a variety of object types.
magpie.utility.tools - package magpie.utility.tools: Utilities that can be used from the command line.
main(String[]) - Static method in class magpie.Magpie: Launch Magpie.
main(String[]) - Static method in class magpie.user.server.ServerLauncher
makeClassifier(PhaseDiagramStatistics, PrototypeDataset) - Method in class magpie.csp.CompositionBasedCSPEngine
makeClassifier(PhaseDiagramStatistics, PrototypeDataset) - Method in class magpie.csp.CSPEngine: Given the dataset of training examples, make a classifier to predict the probability that a prototype will form at a certain composition.
makeClassifier(PhaseDiagramStatistics, PrototypeDataset) - Method in class magpie.csp.DMSPEngine
makeNeighborSearchTool() - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter: Generate a tool to enable fast searching for nearest compositions.
makeObjectiveFunction(Dataset) - Method in class magpie.models.regression.AbstractNonlinearRegression: Generate an anonymous MultivariateFunction object that calculates the error between the equation described by the user as a function of the fitting coefficients.
makeSiteInfo(double[]) - Method in class magpie.csp.CSPEngine: Generate PrototypeSiteInformation appropriate for a certain crystal prototype.
matchEntries(BaseEntry, int) - Method in class magpie.data.Dataset: Find entries in this dataset with attributes closest to a user-provided entry.
MathUtils - Class in magpie.utility: Math operations that are simple and useful for many operations
MathUtils() - Constructor for class magpie.utility.MathUtils
MaxAlloying - Variable in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator: Maximum amount to add.
MaxBaseElement - Variable in class magpie.data.utilities.generators.CompositionRangeEntryGenerator: Set maximum amount of base element
MaxCandidates - Variable in class magpie.statistics.performance.TargetRegressionStatistics: Maximum number of candidates for ranking analysis
MaxCount - Variable in class magpie.attributes.selectors.LassoAttributeSelector: Maximum number of attributes to select.
MaxFraction - Variable in class magpie.data.utilities.generators.CompositionRangeEntryGenerator: Maximum fraction of certain element.
MaxNTypes - Static variable in class magpie.attributes.generators.composition.APEAttributeGenerator: Maximum number of types over which to search for clusters.
MaxNumberTerms - Variable in class magpie.models.regression.LASSORegression: Maximum number of features allowed in model (-1 is unlimited)
MaxNumEntries - Variable in class magpie.user.server.ModelPackage: Maximum mumber of entries to run, overrules ServerLauncher.MaxNumEntries
MaxNumEntries - Static variable in class magpie.user.server.ServerLauncher: Maximum mumber of entries to run
MaxOrder - Variable in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator: Maximum number of constituents
MaxSubsetSize - Variable in class magpie.attributes.selectors.ExhaustiveAttributeSelector: Maximum attribute subset size
MaxWindowSize - Variable in class magpie.statistics.performance.TargetRegressionStatistics: Maximum tolerance during window size analysis
MCC - Variable in class magpie.statistics.performance.ClassificationStatistics: Matthews Correlation Coefficient
meanAbsoluteDeviation(double[], double) - Static method in class magpie.utility.MathUtils: Compute the mean absolute deviation from the mean.
meanAbsoluteDeviation(double[]) - Static method in class magpie.utility.MathUtils: Compute the mean absolute deviation from the mean.
Measure - Variable in class magpie.attributes.selectors.RemoveCorrelatedAttributeSelector: Correlation measure used for this class
measureCorrelation(double[], double[]) - Method in class magpie.attributes.selectors.RemoveCorrelatedAttributeSelector: Measure the strength correlation between two arrays
Measured - Variable in class magpie.statistics.performance.BaseStatistics: Measured value of class variable
MeasuredClassSplitter - Class in magpie.data.utilities.splitters: Splits based on measured class variable.
MeasuredClassSplitter() - Constructor for class magpie.data.utilities.splitters.MeasuredClassSplitter
MeasuredLargestClassFraction - Variable in class magpie.statistics.performance.ClassificationStatistics: Fraction of entries in the most-prevalent class
MeasuredMAD - Variable in class magpie.statistics.performance.RegressionStatistics: Mean absolute deviation of measured values
MeasuredMedian - Variable in class magpie.statistics.performance.RegressionStatistics: Median of mesaured values
MeasuredRange - Variable in class magpie.statistics.performance.RegressionStatistics: Range of measured values
MeasuredStdDev - Variable in class magpie.statistics.performance.RegressionStatistics: Standard deviation of measured values
MeredigAttributeGenerator - Class in magpie.attributes.generators.composition: Generates several attributes first demonstrated by Meredig & Agrawal et al..
MeredigAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.MeredigAttributeGenerator
MeredigAttributeSelector - Class in magpie.attributes.selectors: Select only attributes that were used by Meredig et al.
MeredigAttributeSelector() - Constructor for class magpie.attributes.selectors.MeredigAttributeSelector
MetallurgicalHeuristicRegression - Class in magpie.models.regression: Estimate formation energy for ternary+ alloys using a metallurgical heuristic.
MetallurgicalHeuristicRegression() - Constructor for class magpie.models.regression.MetallurgicalHeuristicRegression
millisecondsToString(long) - Static method in class magpie.utility.UtilityOperations: Print a time, stored in milliseconds, into a human-readable string.
MinBaseElement - Variable in class magpie.data.utilities.generators.CompositionRangeEntryGenerator: Set minimum amount of base element
MinDistance - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics: Minimum Manhattan distance between compositions to be considered equal
MinFraction - Variable in class magpie.data.utilities.generators.CompositionRangeEntryGenerator: Minimum fraction of certain element.
MinOrder - Variable in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator: Minimum number of constituents
MinSubsetSize - Variable in class magpie.attributes.selectors.ExhaustiveAttributeSelector: Minimum attribute subset size
MixedMetalsSplitter - Class in magpie.data.utilities.splitters: This class splits a CompositionDataset into three subsets: all metals (0), no metals (1), mixture (2)
MixedMetalsSplitter() - Constructor for class magpie.data.utilities.splitters.MixedMetalsSplitter
MixingRuleRegression - Class in magpie.models.regression: Predicts the class of a CompositionEntry based on the composition-weighted mean.
MixingRuleRegression() - Constructor for class magpie.models.regression.MixingRuleRegression
Model - Variable in class magpie.attributes.selectors.ExhaustiveAttributeSelector: Model used for cross-validation
Model - Variable in class magpie.models.classification.WekaClassifier: Link to Weka-based model
Model - Variable in class magpie.models.regression.CompositeRegression: Collections of models used by this class
Model - Variable in class magpie.models.regression.WekaRegression: Link to Weka-based model
Model - Variable in class magpie.models.SplitModel: List of of models used by this model
Model - Variable in class magpie.user.server.ModelPackage: Model to be evaluated
model_defined - Variable in class magpie.models.classification.WekaClassifier: Whether model type has been defined
model_defined - Variable in class magpie.models.regression.WekaRegression: Whether model type has been defined
Model_Options - Variable in class magpie.models.classification.WekaClassifier: Options supplied when instantiating Model
Model_Options - Variable in class magpie.models.regression.WekaRegression: Options supplied when instantiating Model
Model_Type - Variable in class magpie.models.classification.WekaClassifier: Name of model type currently in use
Model_Type - Variable in class magpie.models.regression.WekaRegression: Name of model type currently in use
ModelCitation - Variable in class magpie.user.server.ModelPackage: Citation for this model
modelIsDefined(String) - Method in class magpie.models.regression.MultiObjectiveRegression: Determine whether a model for a certain property is defined
modelIsTrained(String) - Method in class magpie.models.regression.MultiObjectiveRegression: Whether the model for a certain property is trained.
modelIsValidated(String) - Method in class magpie.models.regression.MultiObjectiveRegression: Whether the model for a certain property is validated
ModelOperator - Class in magpie.user.server.operations: Queries for getting the information about and running models.
ModelOperator() - Constructor for class magpie.user.server.operations.ModelOperator
ModelPackage - Class in magpie.user.server: Holds information about a model.
ModelPackage(Dataset, BaseModel) - Constructor for class magpie.user.server.ModelPackage: Initialize model package
ModelPredictionAttributeGenerator - Class in magpie.attributes.generators: Use the result from another model as an attribute.
ModelPredictionAttributeGenerator() - Constructor for class magpie.attributes.generators.ModelPredictionAttributeGenerator
ModelQueryHandler - Class in magpie.user.server.operations: Run operations to gather models that fit certain criteria.
ModelQueryHandler() - Constructor for class magpie.user.server.operations.ModelQueryHandler
Models - Variable in class magpie.models.regression.MultiObjectiveRegression: Map of property name to model used to predict it.
Models - Variable in class magpie.user.server.operations.SearchRunner: Set of models that have been run
Models - Static variable in class magpie.user.server.ServerLauncher: List of models available to this program
modelSupports(Dataset) - Method in class magpie.user.server.ModelPackage: Check whether dataset is a superclass of a certain class.
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.AddPropertyModifier
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.BaseDatasetModifier: Apply changes to the Dataset.
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.ClassEliminationModifier
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.ClassIntervalModifier
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.DiscreteToContinuousModifier
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.duplicates.BaseDuplicateResolver
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.ErrorSignalModifier
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.HHICalculationModifier
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.NaNToMeanModifier
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.NonZeroClassModifier
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.PartitionToClassModifier
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.SetClassNamesModifier
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.SetPropertyValueModifier
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.StabilityCalculationModifier
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.VolumeToLatticeParamModifier
MRE - Variable in class magpie.statistics.performance.RegressionStatistics: Mean relative error
MultiFilter - Class in magpie.data.utilities.filters: Filter that incorporates multiple other filters.
MultiFilter() - Constructor for class magpie.data.utilities.filters.MultiFilter
MultiModel - Interface in magpie.models.interfaces: Interface for models that contain submodels.
MultiModelUtility - Class in magpie.models.utility: Contains commands to handle MultiModel operations
MultiModelUtility() - Constructor for class magpie.models.utility.MultiModelUtility
MultiNormalizer - Class in magpie.data.utilities.normalizers: Use multiple strategies to normalize dataset.
MultiNormalizer() - Constructor for class magpie.data.utilities.normalizers.MultiNormalizer
MultiObjectiveEntryRanker - Class in magpie.optimization.rankers: Base class for multi-objective entry rankers.
MultiObjectiveEntryRanker() - Constructor for class magpie.optimization.rankers.MultiObjectiveEntryRanker
MultiObjectiveRegression - Class in magpie.models.regression: Employs multiple models, each designed to predict a different property that composes the class variable.
MultiObjectiveRegression() - Constructor for class magpie.models.regression.MultiObjectiveRegression
MultipleElementGroupsSplitter - Class in magpie.data.utilities.splitters: Splits entries into multiple groups depending on which elements they contain.
MultipleElementGroupsSplitter() - Constructor for class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
MultipleSites - Variable in class magpie.attributes.generators.prototype.SingleSiteAttributeGenerator: List of groups with a multiple site
MultiPropertyDataset - Class in magpie.data: Dataset that can store multiple properties for each entry.
MultiPropertyDataset() - Constructor for class magpie.data.MultiPropertyDataset
MultiPropertyEntry - Class in magpie.data: Entry that can have multiple properties.
MultiPropertyEntry() - Constructor for class magpie.data.MultiPropertyEntry
MultiPropertyEntry(double[]) - Constructor for class magpie.data.MultiPropertyEntry: Create a new entry, given attributes
MultiPropertyRegression - Class in magpie.models.regression: Extension of MultiObjectiveEntryRanker where one does not care about the class variable.
MultiPropertyRegression() - Constructor for class magpie.models.regression.MultiPropertyRegression

N

NaNToMeanModifier - Class in magpie.data.utilities.modifiers: Replace any attributes that are NaN or infinite with the mean value for that attribute.
NaNToMeanModifier() - Constructor for class magpie.data.utilities.modifiers.NaNToMeanModifier
NAttributes() - Method in class magpie.data.BaseEntry: Get number of attributes currently set
NAttributes() - Method in class magpie.data.Dataset
NBins() - Method in class magpie.data.utilities.modifiers.ClassIntervalModifier: Get number of intervals on which data is split.
NClasses() - Method in class magpie.data.Dataset
NClasses() - Method in class magpie.data.MultiPropertyDataset
NClasses - Variable in class magpie.data.utilities.output.DelimitedClassOutput: Number of class values
NClasses - Variable in class magpie.models.classification.BaseClassifier: Number of classes to distinguish between
NClasses - Variable in class magpie.models.classification.SplitClassifier: Number of classes model can distinguish between
NClusters() - Method in class magpie.cluster.BaseClusterer: How many different clusters data may be partitioned into
NClusters_protected() - Method in class magpie.cluster.BaseClusterer: Actual implementation of BaseClusterer.NClusters().
NClusters_protected() - Method in class magpie.cluster.WekaClusterer
NCoefficients() - Method in class magpie.models.regression.AbstractNonlinearRegression
NComponents - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics: Order of phase diagram
NComponents() - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Get the order of the phase diagram (number of elements).
NCompositions() - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
NCompounds - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics: Number compounds stored by this object
NCompounds() - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Get number of compounds stored by this object.
NDGridIterator - Class in magpie.utility: Iterate over a n-dimensional array.
NDGridIterator(int, int) - Constructor for class magpie.utility.NDGridIterator: Create a iterator over a
NDGridIterator(int[]) - Constructor for class magpie.utility.NDGridIterator: Initialize iterator
NDigits - Variable in class magpie.data.utilities.output.SimpleOutput: Number of digits in SimpleOutput.NToPrint.
NDownselect - Variable in class magpie.attributes.selectors.LassoAttributeSelector: Number of entries to downselect to based on correlations.
NEigenvalues - Variable in class magpie.attributes.generators.crystal.CoulombMatrixAttributeGenerator: Maximum number of atoms to consider.
NElements - Variable in class magpie.utility.tools.PhaseDiagramExclusionValidator: Number of elements to use.
NEntries() - Method in class magpie.data.Dataset
next() - Method in class magpie.utility.NDGridIterator
NGroups() - Method in class magpie.data.materials.util.PrototypeSiteInformation: Get the number of groups of equivalent sites.
NLASSO - Variable in class magpie.attributes.selectors.LassoAttributeSelector: Number of attributes to pick via LASSO.
NModels() - Method in interface magpie.models.interfaces.MultiModel
NModels() - Method in class magpie.models.regression.CompositeRegression: Get the number of models in ensemble
NModels() - Method in class magpie.models.regression.StagedRegression
NModels() - Method in class magpie.models.SplitModel: Returns the number of model slots currently available
NonlinearRegressionExpr - Class in magpie.models.regression: Performs non-linear regression on a function supplied as a string.
NonlinearRegressionExpr() - Constructor for class magpie.models.regression.NonlinearRegressionExpr
NOnSite(int) - Method in class magpie.data.materials.util.PrototypeSiteInformation: Get number of atoms on a certain site
NonZeroClassificationSplitter - Class in magpie.data.utilities.splitters: Split data based on whether an entry is likely to have a non-zero class variable.
NonZeroClassificationSplitter() - Constructor for class magpie.data.utilities.splitters.NonZeroClassificationSplitter: Create a new instances that uses ZeroR to classify.
NonZeroClassModifier - Class in magpie.data.utilities.modifiers: Takes a Dataset with a single class and a continuous class variable and change it into a dataset with two classes.
NonZeroClassModifier() - Constructor for class magpie.data.utilities.modifiers.NonZeroClassModifier
normalizationFunction(double, double, double) - Method in class magpie.data.utilities.normalizers.SoftmaxNormalizer
normalizationFunction(double, double, double) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer: Compute the normalized value of a variable
normalize(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer: Transform attributes from original to standardized range.
normalizeAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer: Perform the actual normalization on the attributes
normalizeAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
normalizeAttributes(double[]) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer: Normalize each attribute for an entry
normalizeAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
normalizeAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.MultiNormalizer
normalizeAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
normalizeAttributes(double[]) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
normalizeAttributes(double[]) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
normalizeClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer: Perform the actual normalization on the class variable.
normalizeClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
normalizeClassVariable(double) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer: Normalize a class variable
normalizeClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
normalizeClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.MultiNormalizer
normalizeClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
normalizeClassVariable(double) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
normalizeClassVariable(double) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
Notes - Variable in class magpie.user.server.ModelPackage: Long form description of model
Notes - Variable in class magpie.utility.interfaces.Citation: Anything else that a user should know about this resource.
NPoints - Variable in class magpie.attributes.generators.crystal.PRDFAttributeGenerator: Number of distance points to evaluate
NProperties() - Method in class magpie.data.MultiPropertyDataset
NProperties() - Method in class magpie.data.MultiPropertyEntry
NPV - Variable in class magpie.statistics.performance.ClassificationStatistics: Negative Predictive Value
NResults() - Method in class magpie.csp.CSPPerformanceStats: Number of crystal structure predictions that have been evaluated.
NSites() - Method in class magpie.data.materials.PrototypeDataset
NSites() - Method in class magpie.data.materials.PrototypeEntry
NSites() - Method in class magpie.data.materials.util.PrototypeSiteInformation: Get the number of sites.
NThreads - Static variable in class magpie.Magpie: Number of threads allowed
NToPrint - Variable in class magpie.data.utilities.output.SimpleOutput: Number of entries to print, if ranking.
NumAttributes - Variable in class magpie.attributes.selectors.RandomForestAttributeSelector: Number of attributes to select.
NumberCorrect - Variable in class magpie.statistics.performance.ClassificationStatistics: Number of entries assigned to the correct class
NumberEvaluated - Variable in class magpie.user.server.ModelPackage: Number of entries evaluated
NumberInCell - Variable in class magpie.data.materials.CompositionEntry: Number of atoms in cell (used to convert when printing)
NumberRuns - Variable in class magpie.user.server.ModelPackage: How many times this model has been run
NumberTested - Variable in class magpie.statistics.performance.BaseStatistics: Number of entries evaluated
numPhases() - Method in class magpie.data.materials.util.GCLPCalculator: Get the number of phases being considered for GCLP
NumPoints - Variable in class magpie.attributes.generators.crystal.APRDFAttributeGenerator: Number of points to evaluate
NumSteps - Variable in class magpie.attributes.selectors.RandomForestAttributeSelector: Number of selection steps
NumTrees - Variable in class magpie.attributes.selectors.RandomForestAttributeSelector: Number of trees to use in RandomForest
numVariables() - Method in class magpie.utility.ParsedFunction: Print the number of variables this function expects
NVariables() - Method in class magpie.models.regression.AbstractNonlinearRegression

O

ObjectiveFunction - Variable in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker: Map of property name to objective function
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.BaseEntryRanker: Some kind of objective function that returns a double when given an entry.
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.ClassProbabilityRanker
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.CompositionDistanceRanker
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.PropertyFormulaRanker
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.PropertyRanker
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.SimpleEntryRanker
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.TargetEntryRanker
ObjectiveFunctionSplitter - Class in magpie.data.utilities.splitters: Split based on value of objective function.
ObjectiveFunctionSplitter() - Constructor for class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
ObjectiveMaximum - Variable in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker: Maximum value of each objective function in training data
ObjectiveMinimum - Variable in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker: Minimum value of each objective function in training data
ObjFunction - Variable in class magpie.models.regression.MultiObjectiveRegression: Objective function used to calculate class variable.
OnTheFlyPhaseDiagramStatistics - Class in magpie.csp.diagramdata: Calculate phase diagrams as requested.
OnTheFlyPhaseDiagramStatistics() - Constructor for class magpie.csp.diagramdata.OnTheFlyPhaseDiagramStatistics
openFile(String) - Method in class magpie.user.InputFileParser: Open an input file
Options - Interface in magpie.utility.interfaces: This interface signals that the options of a class can be set by a properly-parsed string.
order - Variable in class magpie.attributes.evaluators.PolynomialFitEvaluator: Order of polynomial used to evaluate attributes
Order - Variable in class magpie.models.regression.PolynomialRegression: Desired Order of polynomial
orderComposition(int[], double[]) - Static method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Ensure that a composition is sorted such that elements are listed in ascending order by atomic fraction
output(Dataset, File) - Method in class magpie.utility.tools.BatchAttributeGenerator: Compute attributes and write entries to a file
output(Dataset, OutputStream) - Method in class magpie.utility.tools.BatchAttributeGenerator: Compute attributes and write entries to an output stream in batches
output(Dataset, Iterator<BaseEntry>, OutputStream) - Method in class magpie.utility.tools.BatchAttributeGenerator: Compute attributes and write entries to an output stream in batches
Outputter - Variable in class magpie.utility.tools.BatchAttributeGenerator: Tool used to output data
OxidationStateGuesser - Class in magpie.utility.tools: Given a composition, guess the most-likely oxidation states for each element.
OxidationStateGuesser() - Constructor for class magpie.utility.tools.OxidationStateGuesser
OxidationStates - Variable in class magpie.data.materials.CompositionDataset: Oxidation states of every element
OxidationStates - Static variable in class magpie.data.materials.util.LookupData: Holds oxidation states of individual elements

P

P - Variable in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker: Trade-off between best in single objective, and generally-good
PackingEfficiencyAttributeGenerator - Class in magpie.attributes.generators.crystal: Compute attributes based on packing efficiency.
PackingEfficiencyAttributeGenerator() - Constructor for class magpie.attributes.generators.crystal.PackingEfficiencyAttributeGenerator
PairPropertyData - Variable in class magpie.data.materials.CompositionDataset: Map of properties of pairs of elements
PairSiteAttributeGenerator - Class in magpie.attributes.generators.prototype: Generate attributes based on the differences in properties between pairs of sites.
PairSiteAttributeGenerator() - Constructor for class magpie.attributes.generators.prototype.PairSiteAttributeGenerator
parallelLabel(Dataset) - Method in class magpie.data.utilities.filters.BaseDatasetFilter: Label entries in parallel.
parallelMinimum() - Method in class magpie.data.utilities.filters.BaseDatasetFilter: Minimum number of entries to label in parallel.
parallelMinimum() - Method in class magpie.data.utilities.filters.BestInAlloySystemFilter
parallelMinimum() - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
parallelMinimum() - Method in class magpie.data.utilities.filters.StabilityFilter
ParsedFunction - Class in magpie.utility: Parses a function from text string.
ParsedFunction(String) - Constructor for class magpie.utility.ParsedFunction: Parse a function from a text string.
parseFormula(String) - Method in class magpie.models.regression.AbstractParsedNonlinearRegression: Parse formula to use as model.
parseInput(String[]) - Static method in class magpie.user.server.ServerLauncher: Handle input passed to the server.
partition(int[]) - Method in class magpie.data.Dataset: Given a list of labels, separate Dataset into multiple subsets
partition(int[], int) - Method in class magpie.data.Dataset: Given a list of labels, separate Dataset into multiple subsets (some may be empty)
partitionDataset(Dataset) - Method in class magpie.cluster.BaseClusterer: Separate the Dataset based on predicted classes.
Partitioner - Variable in class magpie.models.SplitModel: Class used to partition data into similar groups
partitionList(List<T>, int) - Static method in class magpie.utility.UtilityOperations: Split a list into smaller sublists that are as equally-sized as possible.
PartitionToClassModifier - Class in magpie.data.utilities.modifiers: Changes the class variable of an entry to be what partition a BaseDatasetSplitter assigns it to.
PartitionToClassModifier() - Constructor for class magpie.data.utilities.modifiers.PartitionToClassModifier
PearsonsCorrelationEvaluator - Class in magpie.attributes.evaluators: Evaluate attributes based on Pearson's Correlation Coefficient, which is the "R^2" correlation value that you are likely familiar with.
PearsonsCorrelationEvaluator() - Constructor for class magpie.attributes.evaluators.PearsonsCorrelationEvaluator
PerformanceStats - Variable in class magpie.csp.CSPEngine: Holds statistics about CSP algorithm performance.
performSearch(JSONObject) - Method in class magpie.user.server.operations.SearchRunner: Function that prepares the actual search
permutationIterator(int, int) - Static method in class magpie.utility.MathUtils: Iterator over all permutations of k choices of n integers.
PhaseDiagramCompositionEntryGenerator - Class in magpie.data.utilities.generators: Generate composition entries at many points in many phase diagrams.
PhaseDiagramCompositionEntryGenerator() - Constructor for class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
PhaseDiagramExclusionFilter - Class in magpie.data.utilities.filters: Filter entries from certain phase diagrams.
PhaseDiagramExclusionFilter() - Constructor for class magpie.data.utilities.filters.PhaseDiagramExclusionFilter
PhaseDiagramExclusionValidator - Class in magpie.utility.tools: Validate a model by using data each phase diagram as test set.
PhaseDiagramExclusionValidator() - Constructor for class magpie.utility.tools.PhaseDiagramExclusionValidator
PhaseDiagramStatistics - Class in magpie.csp.diagramdata: Holds what compounds exist in phase diagrams.
PhaseDiagramStatistics() - Constructor for class magpie.csp.diagramdata.PhaseDiagramStatistics: Create a blank instance of this class.
Phases - Variable in class magpie.data.materials.util.GCLPCalculator: Phases to consider for equilibria and their energy.
PNorms - Variable in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator: List of p norms to compute
PolynomialFitEvaluator - Class in magpie.attributes.evaluators: Evaluate an attribute based on the RMSE of polynomial model using that attribute.
PolynomialFitEvaluator() - Constructor for class magpie.attributes.evaluators.PolynomialFitEvaluator
PolynomialRegression - Class in magpie.models.regression: Performs linear regression using all attributes in a Dataset raised to integer exponents.
PolynomialRegression() - Constructor for class magpie.models.regression.PolynomialRegression
PowerExpander - Class in magpie.attributes.expanders: This class creates new attributes that are functions of single, already-existing attributes by simply raising them to a specified power
PowerExpander() - Constructor for class magpie.attributes.expanders.PowerExpander
PPV - Variable in class magpie.statistics.performance.ClassificationStatistics: Positive Predictive Value
PRDFAttributeGenerator - Class in magpie.attributes.generators.crystal: Compute attributes based on the Pair Radial Distribution Function (PRDF).
PRDFAttributeGenerator() - Constructor for class magpie.attributes.generators.crystal.PRDFAttributeGenerator
PRDFRegression - Class in magpie.models.regression.crystal: Uses the partial radial distribution function to perform regression.
PRDFRegression() - Constructor for class magpie.models.regression.crystal.PRDFRegression
Predicted - Variable in class magpie.statistics.performance.BaseStatistics: Predicted value of class variable
PredictedClassIntervalSplitter - Class in magpie.data.utilities.splitters: Splits data based on whether the class variable is predicted to be within certain intervals.
PredictedClassIntervalSplitter() - Constructor for class magpie.data.utilities.splitters.PredictedClassIntervalSplitter: Create a new instances that uses ZeroR to predict interval.
PredictionOutlierFilter - Class in magpie.data.utilities.filters: Filters entries based on whether they are outliers.
PredictionOutlierFilter() - Constructor for class magpie.data.utilities.filters.PredictionOutlierFilter
predictStructure(String) - Method in class magpie.csp.CSPEngine: Predict what structure is most likely at a certain composition
predictStructure(CompositionEntry) - Method in class magpie.csp.CSPEngine: Predict what structure is most likely at a certain composition
prepareAttributeArrays(int) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer: Prepare arrays that will hold attribute statistics.
prepareAttributeArrays(int) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
prepareAttributeArrays(int) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
prepareEvaluator(String) - Method in class magpie.models.regression.AbstractParsedNonlinearRegression: Define the internal Evaluator and parse the user-defined function
prepareEvaluator(String) - Method in class magpie.models.regression.NonlinearRegressionExpr: Define the internal Evaluator and parse the user-defined function
prepareException(String) - Static method in class magpie.user.server.ServerUtilityOperations: Prepare an Exception in a form that will get the CORS headers
Printable - Interface in magpie.utility.interfaces: Dictates commands that must be fulfilled for an object to be "printable".
printAttributeDescription(boolean) - Method in class magpie.data.Dataset: Print out description of attributes.
printAttributeNames(Dataset, PrintWriter) - Method in class magpie.data.utilities.output.CompositionOutput
printAttributeNames(Dataset, PrintWriter) - Method in class magpie.data.utilities.output.PropertiesOutput: Print out attribute names
printAttributes() - Method in class magpie.statistics.performance.ClustererStatistics: Print the name and separation power of all attributes used during clustering
printAttributes(int) - Method in class magpie.statistics.performance.ClustererStatistics: Print the name and separation power of a certain number of attributes
printBaselineStats() - Method in class magpie.statistics.performance.BaseStatistics: Print statistics about the measured class values.
printBaselineStats() - Method in class magpie.statistics.performance.ClassificationStatistics
printBaselineStats() - Method in class magpie.statistics.performance.RegressionStatistics
printCandidateAnalysis() - Method in class magpie.statistics.performance.TargetRegressionStatistics: Print results of the candidate ranking analysis.
printCitations(List<String>) - Method in class magpie.user.CommandHandler: Run command to print out citations.
printClusters() - Method in class magpie.statistics.performance.ClustererStatistics: Print out attributes name, separation power, and mean for each cluster for all attributes used in clustering
printClusters(int) - Method in class magpie.statistics.performance.ClustererStatistics: Print out attributes name, separation power, and mean for each cluster for a certain number of attributes
printCommand(List<String>) - Method in class magpie.attributes.selectors.BaseAttributeSelector
printCommand(List<String>) - Method in class magpie.cluster.BaseClusterer
printCommand(List<String>) - Method in class magpie.csp.CSPEngine
printCommand(List<String>) - Method in class magpie.csp.CSPPerformanceStats
printCommand(List<String>) - Method in class magpie.data.Dataset
printCommand(List<String>) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
printCommand(List<String>) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
printCommand(List<String>) - Method in class magpie.models.BaseModel
printCommand(List<String>) - Method in class magpie.models.classification.CumulantExpansionClassifier
printCommand(List<String>) - Method in class magpie.models.regression.MixingRuleRegression
printCommand(List<String>) - Method in class magpie.models.regression.StagedRegression
printCommand(List<String>) - Method in class magpie.models.SplitModel
printCommand(List<String>) - Method in class magpie.statistics.performance.BaseStatistics
printCommand(List<String>) - Method in class magpie.statistics.performance.ClassificationStatistics
printCommand(List<String>) - Method in class magpie.statistics.performance.ClustererStatistics
printCommand(List<String>) - Method in class magpie.statistics.performance.TargetRegressionStatistics
printCommand(List<String>) - Method in interface magpie.utility.interfaces.Printable: Handles more complicated printing commands.
printCommand(List<String>) - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
printContingencyTable() - Method in class magpie.statistics.performance.ClassificationStatistics: Print out the contingency table
printCumulants(double[][], int) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Print out values of each cumulant and their names.
printDescription(boolean) - Method in class magpie.attributes.generators.BaseAttributeGenerator: Print out description of attributes.
printDescription(boolean) - Method in class magpie.attributes.generators.composition.APEAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.composition.ChargeDependentAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.composition.ElementalPropertyAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.composition.ElementFractionAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.composition.ElementPairPropertyAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.composition.GCLPAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.composition.IonicCompoundProximityAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.composition.IonicityAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.composition.MeredigAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.composition.ValenceShellAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.composition.YangOmegaAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.crystal.APRDFAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.crystal.ChemicalOrderingAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.crystal.CoordinationNumberAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.crystal.CoulombMatrixAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.crystal.EffectiveCoordinationNumberAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.crystal.LatticeSimilarityAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.crystal.PackingEfficiencyAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.crystal.PRDFAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.crystal.StructuralHeterogeneityAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.element.ElementalPropertyAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.LookupTableAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.ModelPredictionAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.PropertyAsAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.prototype.PairSiteAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.generators.prototype.SingleSiteAttributeGenerator
printDescription(boolean) - Method in class magpie.attributes.selectors.BaseAttributeSelector
printDescription(boolean) - Method in class magpie.attributes.selectors.ExhaustiveAttributeSelector
printDescription(boolean) - Method in class magpie.attributes.selectors.LassoAttributeSelector
printDescription(boolean) - Method in class magpie.attributes.selectors.RandomForestAttributeSelector
printDescription(boolean) - Method in class magpie.attributes.selectors.RegexAttributeSelector
printDescription(boolean) - Method in class magpie.attributes.selectors.RemoveCorrelatedAttributeSelector
printDescription(boolean) - Method in class magpie.attributes.selectors.RemoveDuplicateAttributeSelector
printDescription(boolean) - Method in class magpie.attributes.selectors.RemoveNaNAttributeSelector
printDescription(boolean) - Method in class magpie.attributes.selectors.StagedAttributeSelector
printDescription(boolean) - Method in class magpie.attributes.selectors.UserSpecifiedAttributeSelector
printDescription(boolean) - Method in class magpie.attributes.selectors.UserSpecifiedExcludingAttributeSelector
printDescription(boolean) - Method in class magpie.attributes.selectors.WekaAttributeSelector
printDescription(boolean) - Method in class magpie.cluster.BaseClusterer
printDescription(boolean) - Method in class magpie.csp.CSPEngine
printDescription(boolean) - Method in class magpie.csp.CSPPerformanceStats
printDescription(boolean) - Method in class magpie.data.Dataset: Print out name of dataset and what attributes are generated.
printDescription(boolean) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
printDescription(boolean) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
printDescription(boolean) - Method in class magpie.models.BaseModel
printDescription(boolean) - Method in class magpie.statistics.performance.BaseStatistics
printDescription(boolean) - Method in class magpie.statistics.performance.ClustererStatistics
printDescription(boolean) - Method in interface magpie.utility.interfaces.Printable: Print full name of object, and a simple description of the options.
printDescription(boolean) - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
printDistribution() - Method in class magpie.data.Dataset: Print out the distribution of entries in the known classes
printDistribution() - Method in class magpie.statistics.performance.ClustererStatistics: Print the distribution between each cluster
printElementalProperties(boolean) - Method in class magpie.attributes.generators.prototype.SingleSiteAttributeGenerator: Print list of elemental properties used in computing attributes
printEnd(OutputStream) - Method in class magpie.data.utilities.output.ARFFOutput
printEnd(OutputStream) - Method in class magpie.data.utilities.output.BaseDatasetOutput: Print the end to a data file
printEnd(OutputStream) - Method in class magpie.data.utilities.output.DelimitedClassOutput
printEnd(OutputStream) - Method in class magpie.data.utilities.output.DelimitedOutput
printEnd(OutputStream) - Method in class magpie.data.utilities.output.JSONOutput
printEnd(OutputStream) - Method in class magpie.data.utilities.output.PropertiesOutput
printEnd(OutputStream) - Method in class magpie.data.utilities.output.SimpleOutput
printEntries(int[]) - Method in class magpie.data.Dataset: Print out data regarding a list of entries.
printEntries(Collection<BaseEntry>, OutputStream) - Method in class magpie.data.utilities.output.ARFFOutput
printEntries(Collection<BaseEntry>, OutputStream) - Method in class magpie.data.utilities.output.BaseDatasetOutput: Write out entries to file.
printEntries(Collection<BaseEntry>, OutputStream) - Method in class magpie.data.utilities.output.DelimitedClassOutput
printEntries(Collection<BaseEntry>, OutputStream) - Method in class magpie.data.utilities.output.DelimitedOutput
printEntries(Collection<BaseEntry>, OutputStream) - Method in class magpie.data.utilities.output.JSONOutput
printEntries(Collection<BaseEntry>, OutputStream) - Method in class magpie.data.utilities.output.PropertiesOutput
printEntries(Collection<BaseEntry>, OutputStream) - Method in class magpie.data.utilities.output.SimpleOutput
printEntryAttributes(MultiPropertyEntry, PrintWriter) - Method in class magpie.data.utilities.output.CompositionOutput
printEntryAttributes(MultiPropertyEntry, PrintWriter) - Method in class magpie.data.utilities.output.PropertiesOutput: Print out attributes of an entry
printEntryDescription(boolean) - Method in class magpie.data.Dataset: Print out what the entries to this dataset are.
printEntryDescription(boolean) - Method in class magpie.data.materials.CompositionDataset
printEntryDescription(boolean) - Method in class magpie.data.materials.ElementDataset
printEntryProperties(MultiPropertyEntry, PrintWriter) - Method in class magpie.data.utilities.output.PropertiesOutput: Print out measured and predicted properties of an entry
printHeader(Dataset, OutputStream) - Method in class magpie.data.utilities.output.ARFFOutput
printHeader(Dataset, OutputStream) - Method in class magpie.data.utilities.output.BaseDatasetOutput: Write header to output.
printHeader(Dataset, OutputStream) - Method in class magpie.data.utilities.output.CompositionOutput
printHeader(Dataset, OutputStream) - Method in class magpie.data.utilities.output.DelimitedClassOutput
printHeader(Dataset, OutputStream) - Method in class magpie.data.utilities.output.DelimitedOutput
printHeader(Dataset, OutputStream) - Method in class magpie.data.utilities.output.JSONOutput
printHeader(Dataset, OutputStream) - Method in class magpie.data.utilities.output.PropertiesOutput
printHeader(Dataset, OutputStream) - Method in class magpie.data.utilities.output.SimpleOutput
printInformation() - Method in class magpie.utility.interfaces.Citation: Print out a description of this citation.
printLastResults() - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator: Print last results as formatted text.
printModel() - Method in class magpie.models.BaseModel: If a model is trained, return it formatted as a string.
printModel_protected() - Method in class magpie.models.BaseModel: Internal method that handles printing the model as a string.
printModel_protected() - Method in class magpie.models.classification.CumulantExpansionClassifier
printModel_protected() - Method in class magpie.models.classification.ScikitLearnClassifier
printModel_protected() - Method in class magpie.models.classification.WekaClassifier
printModel_protected() - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
printModel_protected() - Method in class magpie.models.regression.ClassificationRegression
printModel_protected() - Method in class magpie.models.regression.CompositeRegression
printModel_protected() - Method in class magpie.models.regression.crystal.StructureKRRBasedRegression
printModel_protected() - Method in class magpie.models.regression.LASSORegression
printModel_protected() - Method in class magpie.models.regression.LinearCorrectedRegression
printModel_protected() - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
printModel_protected() - Method in class magpie.models.regression.MixingRuleRegression
printModel_protected() - Method in class magpie.models.regression.MultiObjectiveRegression
printModel_protected() - Method in class magpie.models.regression.nonlinear.SimpleLinearModelExample
printModel_protected() - Method in class magpie.models.regression.PolynomialRegression
printModel_protected() - Method in class magpie.models.regression.RandomGuessRegression
printModel_protected() - Method in class magpie.models.regression.ScikitLearnRegression
printModel_protected() - Method in class magpie.models.regression.SingleGuessRegression
printModel_protected() - Method in class magpie.models.regression.StagedRegression
printModel_protected() - Method in class magpie.models.regression.WekaRegression
printModel_protected() - Method in class magpie.models.SplitModel
printModelDescriptionDetails(boolean) - Method in class magpie.models.BaseModel: Print details of the model.
printModelDescriptionDetails(boolean) - Method in class magpie.models.classification.CumulantExpansionClassifier
printModelDescriptionDetails(boolean) - Method in class magpie.models.classification.ScikitLearnClassifier
printModelDescriptionDetails(boolean) - Method in class magpie.models.classification.WekaClassifier
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.ClassificationRegression
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.CompositeRegression
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.LASSORegression
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.LinearCorrectedRegression
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.MixingRuleRegression
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.MultiObjectiveRegression
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.nonlinear.SimpleLinearModelExample
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.PolynomialRegression
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.RandomGuessRegression
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.ScikitLearnRegression
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.SingleGuessRegression
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.StagedRegression
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.WekaRegression
printModelDescriptionDetails(boolean) - Method in class magpie.models.SplitModel
printNumber(double[], double) - Static method in class magpie.data.materials.CompositionEntry: Print out the number of atoms in a formula unit for each element given its fraction
printRankings(Dataset, int) - Method in class magpie.attributes.evaluators.BaseAttributeEvaluator: Print the predictive powers of the top attributes
printROCCurve() - Method in class magpie.statistics.performance.BaseStatistics: Print the ROC Curve as a plottable string.
printRunTime(long) - Static method in class magpie.utility.UtilityOperations: Print elapsed time to screen
printSelections() - Method in class magpie.attributes.selectors.BaseAttributeSelector: This operation prints out the names of attributes that were selected
printStates(int[], int[]) - Method in class magpie.utility.tools.OxidationStateGuesser: Print out the elements and charges in a nice way.
printUsage() - Method in class magpie.attributes.evaluators.AreaUnderROCEvaluator
printUsage() - Method in class magpie.attributes.evaluators.PearsonsCorrelationEvaluator
printUsage() - Method in class magpie.attributes.evaluators.PolynomialFitEvaluator
printUsage() - Method in class magpie.attributes.evaluators.SpearmansCorrelationEvaluator
printUsage() - Method in class magpie.attributes.expanders.CrossExpander
printUsage() - Method in class magpie.attributes.expanders.FunctionExpander
printUsage() - Method in class magpie.attributes.expanders.PowerExpander
printUsage() - Method in class magpie.attributes.generators.composition.APEAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.composition.ChargeDependentAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.composition.ElementalPropertyAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.composition.ElementFractionAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.composition.ElementPairPropertyAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.composition.GCLPAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.composition.IonicCompoundProximityAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.composition.IonicityAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.composition.MeredigAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.composition.ValenceShellAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.composition.YangOmegaAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.crystal.APRDFAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.crystal.ChemicalOrderingAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.crystal.CoordinationNumberAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.crystal.CoulombMatrixAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.crystal.EffectiveCoordinationNumberAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.crystal.LatticeSimilarityAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.crystal.PackingEfficiencyAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.crystal.PRDFAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.crystal.StructuralHeterogeneityAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.element.ElementalPropertyAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.LookupTableAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.ModelPredictionAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.PropertyAsAttributeGenerator
printUsage() - Method in class magpie.attributes.generators.prototype.SingleSiteAttributeGenerator
printUsage() - Method in class magpie.attributes.selectors.BestIndividualSelector
printUsage() - Method in class magpie.attributes.selectors.ExhaustiveAttributeSelector
printUsage() - Method in class magpie.attributes.selectors.LassoAttributeSelector
printUsage() - Method in class magpie.attributes.selectors.MeredigAttributeSelector
printUsage() - Method in class magpie.attributes.selectors.RandomForestAttributeSelector
printUsage() - Method in class magpie.attributes.selectors.RegexAttributeSelector
printUsage() - Method in class magpie.attributes.selectors.RemoveCorrelatedAttributeSelector
printUsage() - Method in class magpie.attributes.selectors.RemoveDuplicateAttributeSelector
printUsage() - Method in class magpie.attributes.selectors.RemoveNaNAttributeSelector
printUsage() - Method in class magpie.attributes.selectors.StagedAttributeSelector
printUsage() - Method in class magpie.attributes.selectors.UserSpecifiedAttributeSelector
printUsage() - Method in class magpie.attributes.selectors.WekaAttributeSelector
printUsage() - Method in class magpie.cluster.WekaClusterer
printUsage() - Method in class magpie.csp.CompositionBasedCSPEngine
printUsage() - Method in class magpie.csp.DMSPEngine
printUsage() - Method in class magpie.data.Dataset
printUsage() - Method in class magpie.data.materials.PrototypeDataset
printUsage() - Method in class magpie.data.utilities.filters.AllMetalsFilter
printUsage() - Method in class magpie.data.utilities.filters.AttributeFilter
printUsage() - Method in class magpie.data.utilities.filters.BestInAlloySystemFilter
printUsage() - Method in class magpie.data.utilities.filters.ClassFilter
printUsage() - Method in class magpie.data.utilities.filters.ClassProbabilityFilter
printUsage() - Method in class magpie.data.utilities.filters.ClassRangeFilter
printUsage() - Method in class magpie.data.utilities.filters.CompositionDistanceFilter
printUsage() - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
printUsage() - Method in class magpie.data.utilities.filters.ContainsElementFilter
printUsage() - Method in class magpie.data.utilities.filters.EntryRankerFilter
printUsage() - Method in class magpie.data.utilities.filters.IQROutlierFilter
printUsage() - Method in class magpie.data.utilities.filters.MultiFilter
printUsage() - Method in class magpie.data.utilities.filters.PredictionOutlierFilter
printUsage() - Method in class magpie.data.utilities.filters.PropertyFilter
printUsage() - Method in class magpie.data.utilities.filters.PropertyRangeFilter
printUsage() - Method in class magpie.data.utilities.filters.RegressionErrorFilter
printUsage() - Method in class magpie.data.utilities.filters.StabilityFilter
printUsage() - Method in class magpie.data.utilities.filters.ZScoreOutlierFilter
printUsage() - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
printUsage() - Method in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator
printUsage() - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
printUsage() - Method in class magpie.data.utilities.generators.FixedStoichiometryCompositionEntryGenerator
printUsage() - Method in class magpie.data.utilities.generators.GridBaseEntryGenerator
printUsage() - Method in class magpie.data.utilities.generators.IonicCompoundGenerator
printUsage() - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
printUsage() - Method in class magpie.data.utilities.generators.PrototypeEntryGenerator
printUsage() - Method in class magpie.data.utilities.modifiers.AddPropertyModifier
printUsage() - Method in class magpie.data.utilities.modifiers.ClassEliminationModifier
printUsage() - Method in class magpie.data.utilities.modifiers.ClassIntervalModifier
printUsage() - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier
printUsage() - Method in class magpie.data.utilities.modifiers.DiscreteToContinuousModifier
printUsage() - Method in class magpie.data.utilities.modifiers.duplicates.AveragingDuplicateResolver
printUsage() - Method in class magpie.data.utilities.modifiers.duplicates.RankingDuplicateResolver
printUsage() - Method in class magpie.data.utilities.modifiers.ErrorSignalModifier
printUsage() - Method in class magpie.data.utilities.modifiers.HHICalculationModifier
printUsage() - Method in class magpie.data.utilities.modifiers.NaNToMeanModifier
printUsage() - Method in class magpie.data.utilities.modifiers.NonZeroClassModifier
printUsage() - Method in class magpie.data.utilities.modifiers.PartitionToClassModifier
printUsage() - Method in class magpie.data.utilities.modifiers.SetClassNamesModifier
printUsage() - Method in class magpie.data.utilities.modifiers.SetPropertyValueModifier
printUsage() - Method in class magpie.data.utilities.modifiers.StabilityCalculationModifier
printUsage() - Method in class magpie.data.utilities.modifiers.VolumeToLatticeParamModifier
printUsage() - Method in class magpie.data.utilities.normalizers.InverseNormalizer
printUsage() - Method in class magpie.data.utilities.normalizers.MultiNormalizer
printUsage() - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
printUsage() - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
printUsage() - Method in class magpie.data.utilities.normalizers.SoftmaxNormalizer
printUsage() - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
printUsage() - Method in class magpie.data.utilities.output.ARFFOutput
printUsage() - Method in class magpie.data.utilities.output.CompositionOutput
printUsage() - Method in class magpie.data.utilities.output.DelimitedOutput
printUsage() - Method in class magpie.data.utilities.output.JSONOutput
printUsage() - Method in class magpie.data.utilities.output.PropertiesOutput
printUsage() - Method in class magpie.data.utilities.output.SimpleOutput
printUsage() - Method in class magpie.data.utilities.splitters.AllMetalsSplitter
printUsage() - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
printUsage() - Method in class magpie.data.utilities.splitters.ClustererSplitter
printUsage() - Method in class magpie.data.utilities.splitters.FilterSplitter
printUsage() - Method in class magpie.data.utilities.splitters.MeasuredClassSplitter
printUsage() - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
printUsage() - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
printUsage() - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
printUsage() - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
printUsage() - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
printUsage() - Method in class magpie.models.classification.CumulantExpansionClassifier
printUsage() - Method in class magpie.models.classification.ScikitLearnClassifier
printUsage() - Method in class magpie.models.classification.WekaClassifier
printUsage() - Method in class magpie.models.regression.AbstractNonlinearRegression
printUsage() - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
printUsage() - Method in class magpie.models.regression.ClassificationRegression
printUsage() - Method in class magpie.models.regression.CompositeRegression
printUsage() - Method in class magpie.models.regression.crystal.CoulombEwaldMatrixRegression
printUsage() - Method in class magpie.models.regression.crystal.CoulombSineMatrixRegression
printUsage() - Method in class magpie.models.regression.crystal.PRDFRegression
printUsage() - Method in class magpie.models.regression.GuessMeanRegression
printUsage() - Method in class magpie.models.regression.LASSORegression
printUsage() - Method in class magpie.models.regression.LinearCorrectedRegression
printUsage() - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
printUsage() - Method in class magpie.models.regression.MixingRuleRegression
printUsage() - Method in class magpie.models.regression.MultiObjectiveRegression
printUsage() - Method in class magpie.models.regression.MultiPropertyRegression
printUsage() - Method in class magpie.models.regression.PolynomialRegression
printUsage() - Method in class magpie.models.regression.RandomGuessRegression
printUsage() - Method in class magpie.models.regression.ScikitLearnRegression
printUsage() - Method in class magpie.models.regression.SingleGuessRegression
printUsage() - Method in class magpie.models.regression.StagedRegression
printUsage() - Method in class magpie.models.regression.WekaRegression
printUsage() - Method in class magpie.models.SplitModel
printUsage() - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
printUsage() - Method in class magpie.optimization.rankers.ClassProbabilityRanker
printUsage() - Method in class magpie.optimization.rankers.CompositionDistanceRanker
printUsage() - Method in class magpie.optimization.rankers.PropertyFormulaRanker
printUsage() - Method in class magpie.optimization.rankers.PropertyRanker
printUsage() - Method in class magpie.optimization.rankers.SimpleEntryRanker
printUsage() - Method in class magpie.optimization.rankers.TargetEntryRanker
printUsage() - Method in class magpie.statistics.performance.BaseStatistics
printUsage() - Method in class magpie.statistics.performance.TargetRegressionStatistics
printUsage() - Method in interface magpie.utility.interfaces.Options: Print out required format for options.
printUsage() - Method in class magpie.utility.tools.BatchAttributeGenerator
printUsage() - Method in class magpie.utility.tools.BatchModelEvaluator
printUsage() - Method in class magpie.utility.tools.OxidationStateGuesser
printUsage() - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
printWindowAnalysis() - Method in class magpie.statistics.performance.TargetRegressionStatistics: Print results of the tolerance size analysis.
printWorkspace() - Method in class magpie.user.Workspace: Prints a table containing all variables currently in Workspace.
ProbabilityThreshold - Variable in class magpie.data.utilities.splitters.NonZeroClassificationSplitter: Probability of being of class #0 below which entry gets placed in entry #1
processCompounds(Map<CompositionEntry, String>) - Method in class magpie.csp.diagramdata.OnTheFlyPhaseDiagramStatistics
processCompounds(Map<CompositionEntry, String>) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Given a list of compounds, mark which phase diagrams they appear in.
processEntries(List<BaseEntry>, Map<String, Object>) - Method in class magpie.utility.tools.BatchModelEvaluator: Operation to be performed on a batch of entries
Properties - Variable in class magpie.attributes.generators.PropertyAsAttributeGenerator: List of properties to use as attributes.
PropertiesOutput - Class in magpie.data.utilities.output: Write attributes and properties out to a CSV file.
PropertiesOutput() - Constructor for class magpie.data.utilities.output.PropertiesOutput
Property - Variable in class magpie.user.server.ModelPackage: Name of property being modeled.
PropertyAsAttributeGenerator - Class in magpie.attributes.generators: Use measured property of entry as an attribute.
PropertyAsAttributeGenerator() - Constructor for class magpie.attributes.generators.PropertyAsAttributeGenerator
PropertyData - Variable in class magpie.data.materials.CompositionDataset: Map of elemental property names to values
PropertyData - Variable in class magpie.data.materials.ElementDataset: Lookup table of elemental properties
PropertyFilter - Class in magpie.data.utilities.filters: Filter entries based on a measured or predicted property.
PropertyFilter() - Constructor for class magpie.data.utilities.filters.PropertyFilter
PropertyFormulaRanker - Class in magpie.optimization.rankers: Use a formula of several properties.
PropertyFormulaRanker() - Constructor for class magpie.optimization.rankers.PropertyFormulaRanker
PropertyIndex - Variable in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker: Index of each property of interest
PropertyIndex - Variable in class magpie.optimization.rankers.PropertyRanker: Index of property used for ranking
PropertyLists - Class in magpie.data.materials.util: Supplies lists of properties used when generating attributes.
PropertyLists() - Constructor for class magpie.data.materials.util.PropertyLists
PropertyName - Variable in class magpie.data.utilities.modifiers.SetPropertyValueModifier: Name of property to be set
PropertyName - Variable in class magpie.models.regression.MixingRuleRegression: Property used for weighting
PropertyName - Variable in class magpie.optimization.rankers.PropertyRanker: Name of property used for ranking
PropertyRangeFilter - Class in magpie.data.utilities.filters: Filter entries that have property variables within or outside a certain range.
PropertyRangeFilter() - Constructor for class magpie.data.utilities.filters.PropertyRangeFilter
PropertyRanker - Class in magpie.optimization.rankers: Shortcut for an BaseEntryRanker to operate on a certain property, rather than the default class.
PropertyRanker() - Constructor for class magpie.optimization.rankers.PropertyRanker
PropertyValue - Variable in class magpie.data.utilities.modifiers.SetPropertyValueModifier: Value to set for property.
PrototypeDataset - Class in magpie.data.materials: Store data about compounds based on a single crystal structure prototype.
PrototypeDataset() - Constructor for class magpie.data.materials.PrototypeDataset: Create a prototype dataset with default attribute
PrototypeDataset(boolean) - Constructor for class magpie.data.materials.PrototypeDataset: Create a prototype dataset.
PrototypeEntry - Class in magpie.data.materials: Entry in a PrototypeDataset.
PrototypeEntry(PrototypeSiteInformation, String) - Constructor for class magpie.data.materials.PrototypeEntry: Create a new PrototypeEntry.
PrototypeEntry(PrototypeSiteInformation) - Constructor for class magpie.data.materials.PrototypeEntry: Create a Prototype entry without specifying composition.
PrototypeEntryGenerator - Class in magpie.data.utilities.generators: Generate PrototypeEntry with certain elements (or combination of elements on each site).
PrototypeEntryGenerator() - Constructor for class magpie.data.utilities.generators.PrototypeEntryGenerator
Prototypes - Variable in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator: List of prototype structures
PrototypeSiteInformation - Class in magpie.data.materials.util: Stores information about all sites in a prototype crystal structure.
PrototypeSiteInformation() - Constructor for class magpie.data.materials.util.PrototypeSiteInformation
PythonBasedAttributeSelector - Class in magpie.attributes.selectors: Abstract class for performing attribute selection with a Python code.
PythonBasedAttributeSelector() - Constructor for class magpie.attributes.selectors.PythonBasedAttributeSelector

Q

Q - Variable in class magpie.statistics.utility.RobustRegressionUtility: Threshold for considering an entry an outlier.

R

R - Variable in class magpie.statistics.performance.RegressionStatistics: Pearson's correlation coefficient
RandomForestAttributeSelector - Class in magpie.attributes.selectors: Select attributes using the feature-importance scores from RandomForest.
RandomForestAttributeSelector() - Constructor for class magpie.attributes.selectors.RandomForestAttributeSelector
RandomGuessRegression - Class in magpie.models.regression: Randomly assign class values.
RandomGuessRegression() - Constructor for class magpie.models.regression.RandomGuessRegression
RandomTestCount - Variable in class magpie.attributes.selectors.ExhaustiveAttributeSelector: If method is random split, number of times to repeat test
RandomTestFraction - Variable in class magpie.attributes.selectors.ExhaustiveAttributeSelector: If method is random split, fraction of entries withheld for test set
rankEntries(Dataset, double[]) - Method in class magpie.optimization.rankers.BaseEntryRanker: Return the rank of entries that were sorted based on the objective function defined in this class (also depends on the settings for Maximize and Measured.
rankEntries(Dataset) - Method in class magpie.optimization.rankers.BaseEntryRanker: Calculate the rank of entries based on this objective function
rankEntries(Dataset, boolean) - Method in class magpie.optimization.rankers.BaseEntryRanker: Calculate the rank of entries based on this objective function
Ranker - Variable in class magpie.data.utilities.output.SimpleOutput: Tool used to rank entries before printing them.
RankingDuplicateResolver - Class in magpie.data.utilities.modifiers.duplicates: Use a ranking algorithm to determine which duplicate to pick.
RankingDuplicateResolver() - Constructor for class magpie.data.utilities.modifiers.duplicates.RankingDuplicateResolver
readAttributeTable(String) - Method in class magpie.attributes.generators.LookupTableAttributeGenerator: Read in lookup table containing attribute names and values for selected entries.
readFile(String) - Method in class magpie.user.CommandHandler: Reads commands from a text file
readFromFile(String) - Static method in class magpie.data.materials.util.PrototypeSiteInformation: Read site information from a specially-formatted file.
readInformationFile(String) - Static method in class magpie.user.server.ServerLauncher: Given model information file, configure the handler
readIonizationEnergies(String) - Static method in class magpie.data.materials.util.LookupData: Read in ionization energies
readLine() - Method in class magpie.user.InputFileParser: Gets a complete, nonempty line out of the input stream.
readModel(InputStream) - Method in class magpie.models.classification.ScikitLearnClassifier: Read model from an input stream
readModel(InputStream) - Method in interface magpie.models.interfaces.ExternalModel: Read file describing model into memory
readModel(InputStream) - Method in class magpie.models.regression.ScikitLearnRegression: Read model from an input stream
readOxidationStates(String) - Static method in class magpie.data.materials.util.LookupData: Reads in a data file that contains known oxidation states for each element.
readPairTable(double[][], String, String) - Static method in class magpie.data.materials.util.LookupData: Helper function for reading from a binary property lookup table
readPairTable(double[][], int, int) - Static method in class magpie.data.materials.util.LookupData: Helper function for reading from a binary property lookup table
readStructureInformation(String) - Method in class magpie.data.materials.PrototypeDataset: Read information about a prototype crystal structure from file.
rectifyEntry(boolean) - Method in class magpie.data.materials.CompositionEntry: Makes sure this entry is in a proper format.
reduceMemoryFootprint() - Method in class magpie.data.BaseEntry: Delete any cached information stored within this entry.
reduceMemoryFootprint() - Method in class magpie.data.materials.CrystalStructureEntry
Regex - Variable in class magpie.attributes.selectors.RegexAttributeSelector: Regular expression to be matched
RegexAttributeSelector - Class in magpie.attributes.selectors: Selects attributes based on whether their name matches a regular expression.
RegexAttributeSelector() - Constructor for class magpie.attributes.selectors.RegexAttributeSelector
RegressionErrorFilter - Class in magpie.data.utilities.filters: Filter entries based on absolute error.
RegressionErrorFilter() - Constructor for class magpie.data.utilities.filters.RegressionErrorFilter
RegressionStatistics - Class in magpie.statistics.performance: Calculates performance statistics for regression models.
RegressionStatistics() - Constructor for class magpie.statistics.performance.RegressionStatistics
RegularSolutionNormalizer - Class in magpie.data.utilities.normalizers: Normalize data using regular solution model.
RegularSolutionNormalizer() - Constructor for class magpie.data.utilities.normalizers.RegularSolutionNormalizer
remove() - Method in class magpie.utility.NDGridIterator
RemoveCorrelatedAttributeSelector - Class in magpie.attributes.selectors: Finds pairs of attributes that are correlated with each other, and removes one of the two.
RemoveCorrelatedAttributeSelector() - Constructor for class magpie.attributes.selectors.RemoveCorrelatedAttributeSelector
RemoveCorrelatedAttributeSelector.CorrelationMeasure - Enum in magpie.attributes.selectors: List of correlation measures
RemoveDuplicateAttributeSelector - Class in magpie.attributes.selectors: Select only attributes that have unique values.
RemoveDuplicateAttributeSelector() - Constructor for class magpie.attributes.selectors.RemoveDuplicateAttributeSelector
removeDuplicates() - Method in class magpie.data.Dataset: Remove all duplicate entries without any selection strategy
removeElementalProperty(String) - Method in class magpie.data.materials.CompositionDataset: Remove an elemental property from the list used when generating attributes
removeElementalProperty(String) - Method in class magpie.data.materials.ElementDataset: Remove an elemental property from the list of those used when computing attributes.
removeElementPairProperty(String) - Method in class magpie.data.materials.CompositionDataset: Remove an elemental property from the list used when generating attributes
removeKnownCompoundsContainingElements(List<String>) - Method in class magpie.csp.CSPEngine: Given a list of elements, remove all entries that contain those elements from the list of known compounds.
RemoveNaNAttributeSelector - Class in magpie.attributes.selectors: Select attributes that have no NaN values.
RemoveNaNAttributeSelector() - Constructor for class magpie.attributes.selectors.RemoveNaNAttributeSelector
removeVariable(String) - Method in class magpie.user.Workspace: Removes a variable from the workspace
replaceDelimiter(String) - Method in class magpie.data.utilities.output.DelimitedOutput: Replace a delimiter in a string with something else.
replaceElements(Map<String, String>) - Method in class magpie.data.materials.CrystalStructureEntry: Create a new entry by replacing elements on this entry
RescalingNormalizer - Class in magpie.data.utilities.normalizers: Scale variables using the maximum and minimum values of the training set.
RescalingNormalizer() - Constructor for class magpie.data.utilities.normalizers.RescalingNormalizer
resetModel() - Method in class magpie.models.BaseModel: Mark this model as untrained and unvalidated
resolveBaseEntry(Dataset, List<BaseEntry>) - Static method in class magpie.data.utilities.modifiers.duplicates.AveragingDuplicateResolver: Average base entries.
resolveDuplicates(BaseDuplicateResolver) - Method in class magpie.data.Dataset: Resolve duplicates according to some strategy
resolveDuplicates(Dataset, List<BaseEntry>) - Method in class magpie.data.utilities.modifiers.duplicates.AveragingDuplicateResolver
resolveDuplicates(Dataset, List<BaseEntry>) - Method in class magpie.data.utilities.modifiers.duplicates.BaseDuplicateResolver: Given a list of duplicate entries, pick a representative entry or generate a new one
resolveDuplicates(Dataset, List<BaseEntry>) - Method in class magpie.data.utilities.modifiers.duplicates.RankingDuplicateResolver
resolveMultipropertyEntry(Dataset, List<BaseEntry>) - Static method in class magpie.data.utilities.modifiers.duplicates.AveragingDuplicateResolver: Average each property of a MultiPropertyEntry
restorationFunction(double, double, double) - Method in class magpie.data.utilities.normalizers.SoftmaxNormalizer
restorationFunction(double, double, double) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer: Compute the restored value a variable
restore(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer: Restore attributes from scaled to original range.
restoreAttributes(Instances) - Method in class magpie.data.Dataset: Restore attribute data to each entry.
restoreAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer: Perform the actual restoration on the attributes
restoreAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
restoreAttributes(double[]) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer: Restore each attribute for an entry
restoreAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
restoreAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.MultiNormalizer
restoreAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
restoreAttributes(double[]) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
restoreAttributes(double[]) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
restoreClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer: Perform the actual restoration on the class variables (measured and predicted!)
restoreClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
restoreClassVariable(double) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer: Restore a class variable
restoreClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
restoreClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.MultiNormalizer
restoreClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
restoreClassVariable(double) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
restoreClassVariable(double) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
Rho - Variable in class magpie.statistics.performance.RegressionStatistics: Spearman's correlation coefficient
RMSE - Variable in class magpie.statistics.performance.RegressionStatistics: Root mean squared error
RobustRegressionUtility - Class in magpie.statistics.utility: Calculates statistics useful to robust regression.
RobustRegressionUtility() - Constructor for class magpie.statistics.utility.RobustRegressionUtility
robustTraining(Dataset) - Method in interface magpie.models.regression.AbstractRegressionModel: Robustly train a model.
robustTraining(Dataset) - Method in class magpie.models.regression.BaseRegression
robustTraining(Dataset) - Method in class magpie.models.regression.SplitRegression
ROC - Variable in class magpie.statistics.performance.BaseStatistics: Receiver operating characteristic curve
ROC_AUC - Variable in class magpie.statistics.performance.BaseStatistics: Area under receiver operating characteristic curve normalized such that 1.0 is a perfect classifier and 0.0 is a perfectly-random classifier.
roundComposition(double[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics: Round a compound such that it's composition exactly equals that of a common composition, and return the index of that composition
run(Dataset) - Method in class magpie.attributes.selectors.BaseAttributeSelector: Adjust the attribute list of a dataset, based on a trained selection algorithm
run(Dataset) - Method in class magpie.models.BaseModel: Run a model on provided data.
run(Dataset) - Method in class magpie.models.classification.BaseClassifier
run_protected(Dataset) - Method in class magpie.models.BaseModel: Run a model without checking if stuff is trained (use carefully)
run_protected(Dataset) - Method in class magpie.models.classification.CumulantExpansionClassifier
run_protected(Dataset) - Method in class magpie.models.classification.ScikitLearnClassifier
run_protected(Dataset) - Method in class magpie.models.classification.SplitClassifier
run_protected(Dataset) - Method in class magpie.models.classification.WekaClassifier
run_protected(Dataset) - Method in class magpie.models.regression.AbstractNonlinearRegression
run_protected(Dataset) - Method in class magpie.models.regression.ClassificationRegression
run_protected(Dataset) - Method in class magpie.models.regression.CompositeRegression
run_protected(Dataset) - Method in class magpie.models.regression.crystal.StructureKRRBasedRegression
run_protected(Dataset) - Method in class magpie.models.regression.LASSORegression
run_protected(Dataset) - Method in class magpie.models.regression.LinearCorrectedRegression
run_protected(Dataset) - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
run_protected(Dataset) - Method in class magpie.models.regression.MixingRuleRegression
run_protected(Dataset) - Method in class magpie.models.regression.MultiObjectiveRegression
run_protected(Dataset) - Method in class magpie.models.regression.PolynomialRegression
run_protected(Dataset) - Method in class magpie.models.regression.RandomGuessRegression
run_protected(Dataset) - Method in class magpie.models.regression.ScikitLearnRegression
run_protected(Dataset) - Method in class magpie.models.regression.SingleGuessRegression
run_protected(Dataset) - Method in class magpie.models.regression.StagedRegression
run_protected(Dataset) - Method in class magpie.models.regression.WekaRegression
run_protected(Dataset) - Method in class magpie.models.SplitModel
runAndFilter(BaseModel, Dataset, BaseDatasetFilter) - Method in class magpie.utility.tools.BatchModelEvaluator: Create entries, evaluate them, filter out acceptable candidates
runAttributeCommand(List<Object>) - Method in class magpie.data.Dataset: Run commands related to attributes of each entry.
runAttributeCommand(List<Object>) - Method in class magpie.data.materials.CompositionDataset
runAttributeCommand(List<Object>) - Method in class magpie.data.materials.ElementDataset
runAttributeExpanders() - Method in class magpie.data.Dataset: Expand the list of attributes using the currently-set list of attribute expanders.
runAttributeExpansionCommand(List<Object>) - Method in class magpie.data.Dataset: Run commands relating to expanding the attribute pool.
runAttributeGeneratorCommand(List<Object>) - Method in class magpie.data.Dataset: Run commands relating to generating new attributes.
runAttributeGenerators() - Method in class magpie.data.Dataset: Expand the list of attributes using the currently-set list of attribute generators.
runAttributeGenerators() - Method in class magpie.data.materials.CrystalStructureDataset
runCandidateAnalysis(double[], double[]) - Method in class magpie.statistics.performance.TargetRegressionStatistics: Perform a candidate selection analysis (described in documentation for this class as a whole).
runCommand(List<Object>) - Method in class magpie.attributes.generators.BaseAttributeGenerator
runCommand(List<Object>) - Method in class magpie.attributes.selectors.BaseAttributeSelector
runCommand(List<Object>) - Method in class magpie.cluster.BaseClusterer
runCommand(List<Object>) - Method in class magpie.csp.CompositionBasedCSPEngine
runCommand(List<Object>) - Method in class magpie.csp.CSPEngine
runCommand(List<Object>) - Method in class magpie.data.Dataset
runCommand(List<Object>) - Method in class magpie.data.materials.CompositionDataset
runCommand(List<Object>) - Method in class magpie.data.MultiPropertyDataset
runCommand(List<Object>) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
runCommand(List<Object>) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
runCommand(List<Object>) - Method in class magpie.models.BaseModel
runCommand(List<Object>) - Method in class magpie.models.regression.AbstractNonlinearRegression
runCommand(List<Object>) - Method in class magpie.models.regression.BaseRegression
runCommand(List<Object>) - Method in class magpie.models.regression.CompositeRegression
runCommand(List<Object>) - Method in class magpie.models.regression.crystal.StructureKRRBasedRegression
runCommand(List<Object>) - Method in class magpie.models.regression.MultiObjectiveRegression
runCommand(List<Object>) - Method in class magpie.models.regression.SplitRegression
runCommand(List<Object>) - Method in class magpie.models.regression.StagedRegression
runCommand(List<Object>) - Method in class magpie.models.SplitModel
runCommand(List<Object>) - Method in class magpie.statistics.performance.BaseStatistics
runCommand(List<String>) - Method in class magpie.user.CommandHandler: Given a command, run some actions
runCommand(List<Object>) - Method in interface magpie.utility.interfaces.Commandable: Process some command described by a list of Objects.
runCommand(List<Object>) - Method in class magpie.utility.tools.BatchAttributeGenerator
runCommand(List<Object>) - Method in class magpie.utility.tools.BatchModelEvaluator
runCommand(List<Object>) - Method in class magpie.utility.tools.IonicCompoundFinder
runCommand(List<Object>) - Method in class magpie.utility.tools.OxidationStateGuesser
runCommand(List<Object>) - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
runCommandOnVariable(String, List<Object>) - Method in class magpie.user.CommandHandler: Pass commands to variables.
runEvaluationCommand(List<Object>) - Static method in class magpie.user.CommandHandler: Run an evaluation command.
runExclusionTest(int[], BaseModel, CompositionDataset) - Static method in class magpie.utility.tools.PhaseDiagramExclusionValidator: Evaluate model by using excluding certain combinations of elements from a dataset, and using the excluded data as a test set.
runFilter(MultiPropertyDataset, JSONObject) - Method in class magpie.user.server.operations.SearchRunner: Run a new model, add entries to dataset
runGCLP(CompositionEntry) - Method in class magpie.data.materials.util.GCLPCalculator: Compute the ground state phase equilibria for a certain composition.
runModel(double[][]) - Method in class magpie.models.regression.LASSORegression: Runs the model contained within object
runModel(ExternalModel, Dataset) - Static method in class magpie.models.utility.ExternalModelUtility: Connect to server and run model
runModel(Dataset) - Method in class magpie.user.server.ModelPackage: Run the model stored in this package.
runModel(String) - Method in class magpie.user.server.operations.ModelOperator: Run a certain model
runModel(MultiPropertyDataset, JSONObject) - Method in class magpie.user.server.operations.SearchRunner: Run a new model, add entries to dataset
runNonlinearCommand(List<Object>) - Method in class magpie.models.regression.AbstractNonlinearRegression: Handle commands for nonliear models
runObjectiveFunction(Dataset) - Method in class magpie.optimization.rankers.BaseEntryRanker: Evaluate every entry in a dataset using the objective function
runPairPropertyCommand(List<Object>) - Method in class magpie.data.materials.CompositionDataset: Run commands that set the element pair properties to be used when generating attributes.
runPolynomialModel(double[][], int, double[]) - Static method in class magpie.models.regression.PolynomialRegression: Run a polynomial model based on a matrix of attribute values.
runPropertyCommand(List<Object>) - Method in class magpie.data.materials.CompositionDataset: Run commands that control which elemental properties are used when generating attributes
runPropertyCommand(List<Object>) - Method in class magpie.data.materials.ElementDataset: Run commands that control which elemental properties are used when generating attributes
runRanker(MultiPropertyDataset, JSONObject) - Method in class magpie.user.server.operations.SearchRunner: Run the entry ranker to get the top entries
runSearch(String) - Method in class magpie.user.server.operations.SearchRunner
runSubmodelCommand(List<Object>) - Method in class magpie.models.regression.MultiObjectiveRegression: Run commands associated with operating on submodels
RunTime - Variable in class magpie.user.server.ModelPackage: How long this model has been run for, in milliseconds
runTimerCommand(List<String>) - Method in class magpie.user.CommandHandler: Run a certain time command.
runWindowAnalysis(double[], double[]) - Method in class magpie.statistics.performance.TargetRegressionStatistics: Perform a window-size analysis.

S

Savable - Interface in magpie.utility.interfaces: Dictates commands that must be fulfilled for an object to be "savable".
saveCommand(String, String) - Method in class magpie.data.Dataset
saveCommand(String, String) - Method in class magpie.data.materials.CompositionDataset
saveCommand(String, String) - Method in class magpie.data.materials.CrystalStructureDataset
saveCommand(String, String) - Method in class magpie.data.MultiPropertyDataset
saveCommand(String, String) - Method in class magpie.models.BaseModel
saveCommand(String, String) - Method in class magpie.models.classification.CumulantExpansionClassifier
saveCommand(String, String) - Method in class magpie.statistics.performance.BaseStatistics
saveCommand(String, String) - Method in interface magpie.utility.interfaces.Savable: Handles complicated saving commands.
saveCommand(String, String) - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
savePerformanceData(String) - Method in class magpie.statistics.performance.BaseStatistics: Write out measured and predicted class variables used to compute statistics.
saveState(String) - Method in class magpie.data.Dataset: Save the state of this object using serialization
saveState(String) - Method in class magpie.models.BaseModel: Save the state of this object using serialization
saveState(Object, String) - Static method in class magpie.utility.UtilityOperations: Use serialization to save object state to file
saveState(Object, OutputStream) - Static method in class magpie.utility.UtilityOperations: Use serialization to save object state to an output stream
saveTemplate(String) - Method in class magpie.data.Dataset: Save a template of this dataset to disk using
ScikitLearnClassifier - Class in magpie.models.classification: Uses Scikit-learn to train a classification model.
ScikitLearnClassifier() - Constructor for class magpie.models.classification.ScikitLearnClassifier
ScikitLearnRegression - Class in magpie.models.regression: Uses Scikit-learn to train a regression model.
ScikitLearnRegression() - Constructor for class magpie.models.regression.ScikitLearnRegression
ScikitServer - Variable in class magpie.models.classification.ScikitLearnClassifier: Scikit server process
ScikitServer - Variable in class magpie.models.regression.ScikitLearnRegression: Scikit server process
ScreenAttributes - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter: Whether to screen based on attributes
ScreenClass - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter: Whether to screen based on class variable
Searcher - Variable in class magpie.attributes.selectors.WekaAttributeSelector: Weka class used to populate a list of attributes
SearchRunner - Class in magpie.user.server.operations: Perform searches that involve several different ML models.
SearchRunner() - Constructor for class magpie.user.server.operations.SearchRunner
selectAttributes(List<String>) - Method in class magpie.attributes.selectors.MeredigAttributeSelector
selectAttributes(List<String>) - Method in class magpie.attributes.selectors.UserSpecifiedAttributeSelector: Define a list of attributes that will be used when training a model
selectAttributes(List<String>) - Method in class magpie.attributes.selectors.UserSpecifiedExcludingAttributeSelector: Define list of attributes that will be excluded before training a model.
SelectedAttributes - Variable in class magpie.attributes.selectors.UserSpecifiedAttributeSelector: Names of attributes to be used
SelectionMethod - Variable in class magpie.data.utilities.output.CompositionOutput: Method used to determine which elements to select
Selectors - Variable in class magpie.attributes.selectors.StagedAttributeSelector: List of attribute selectors to use for selection.
SelectSizeAutomatically - Variable in class magpie.attributes.selectors.LassoAttributeSelector: Whether to pick dataset size via cross-validation.
Sensitivity - Variable in class magpie.statistics.performance.ClassificationStatistics: Sensitivity (aka True Positive Rate
serveModels(String, String) - Method in class magpie.user.server.operations.ModelQueryHandler: Get all models that match the users query
Server - Static variable in class magpie.user.server.ServerLauncher: Server currently being used
ServerInformationGetter - Class in magpie.user.server.operations: REST responses that give the status of the server
ServerInformationGetter() - Constructor for class magpie.user.server.operations.ServerInformationGetter
serverIsRunning() - Method in class magpie.models.classification.ScikitLearnClassifier
serverIsRunning() - Method in interface magpie.models.interfaces.ExternalModel: Check whether the server is running
serverIsRunning() - Method in class magpie.models.regression.ScikitLearnRegression
ServerLauncher - Class in magpie.user.server: Main class for launching a Magpie server.
ServerLauncher() - Constructor for class magpie.user.server.ServerLauncher
serverStatistics() - Method in class magpie.user.server.operations.ServerInformationGetter
ServerUtilityOperations - Class in magpie.user.server: Utility operations useful for the REST server.
ServerUtilityOperations() - Constructor for class magpie.user.server.ServerUtilityOperations
setAlloyStep(double) - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator: Set the step size
setAttribute(int, double) - Method in class magpie.data.BaseEntry: Set a certain attribute for this entry
setAttributeComputer(Dataset) - Method in class magpie.utility.tools.BatchModelEvaluator: Set dataset used to generate attributes
setAttributeName(String) - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter: Define which attribute to use for splitting
setAttributeNames(List<String>) - Method in class magpie.data.Dataset: Set the names of each attributes.
setAttributes(double[]) - Method in class magpie.data.BaseEntry: Sets attributes for this entry
setAttributeSelector(BaseAttributeSelector) - Method in class magpie.cluster.BaseClusterer: Define an attribute selector to be used before clustering
setAttributeSelector(BaseAttributeSelector) - Method in class magpie.models.BaseModel: Define an attribute selector that will force this model to only use a subset of the attributes supplied with a Dataset
setBaseElement(int, double, double) - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator: Set the base element.
setBaseElement(String, double, double) - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator: Set the base element.
setBatchSize(int) - Method in class magpie.utility.tools.BatchAttributeGenerator: Define maximum number of entries to compute at a single time
setBatchSize(int) - Method in class magpie.utility.tools.BatchModelEvaluator: Define how many entries to evaluate at once.
setBinaryConvexHulls(CompositionDataset) - Method in class magpie.models.regression.MetallurgicalHeuristicRegression: Define binary convex hull data.
setBinEdges(double[]) - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter: Define the edges of bins on which to split data.
setClassifier(BaseModel) - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter: Define the classifier used to predict on which interval a class variable most likely lies.
setClassifier(BaseModel) - Method in class magpie.models.regression.ClassificationRegression: Classifier behind this regression algorithm
setClassifierTempate(BaseClassifier) - Method in class magpie.csp.CompositionBasedCSPEngine: Define a template for the classifier used by this class
setClassName(String) - Method in class magpie.data.utilities.filters.ClassProbabilityFilter: Set the name of the class considered for filtering.
setClassName(String) - Method in class magpie.data.utilities.modifiers.DiscreteToContinuousModifier: Set name of class for which to compute probability.
setClassNames(String[]) - Method in class magpie.data.Dataset: Set name of class variable (or possible classes)
setClassNames(String[]) - Method in class magpie.data.MultiPropertyDataset
setClassNames(String[]) - Method in class magpie.data.utilities.modifiers.SetClassNamesModifier: Define the new class names
SetClassNamesModifier - Class in magpie.data.utilities.modifiers: Sets the class names of a Dataset.
SetClassNamesModifier() - Constructor for class magpie.data.utilities.modifiers.SetClassNamesModifier
setClassProbabilities(double[]) - Method in class magpie.data.BaseEntry: Set the predicted probability of a entry existing in each class
setClassProbabilities(double[][]) - Method in class magpie.data.Dataset: Set class probabilities for each entry
setClassProbabilities(double[]) - Method in class magpie.data.MultiPropertyEntry
setClassToEliminate(String) - Method in class magpie.data.utilities.modifiers.ClassEliminationModifier: Define the name of the class to eliminate.
setClusterer(BaseClusterer) - Method in class magpie.data.utilities.splitters.ClustererSplitter: Set the clusterer used for splitting.
setCombinationIterator(Dataset) - Method in class magpie.attributes.selectors.ExhaustiveAttributeSelector: Create an iterator over all attribute subsets being considered.
setComparisonOperator(String) - Method in class magpie.data.utilities.filters.ComparisonOperatorFilter: Define comparison operator.
setComponent(String, Object) - Method in class magpie.models.BaseModel: Set a specific component of a model
setComposition(int[], double[], boolean) - Method in class magpie.data.materials.CompositionEntry: Set the composition of this entry.
setComposition(CompositionEntry) - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator: Set starting composition for alloys
setCompositions(CompositionDataset) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter: Set the list of compositions to be considered
setCompositions(CompositionDataset) - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier: Set the list of compositions to be considered
setCompositions(CompositionDataset) - Method in class magpie.optimization.rankers.CompositionDistanceRanker: Set the list of compositions to be considered
setCompounds(CompositionDataset) - Method in class magpie.data.utilities.filters.StabilityFilter: Define the data used to compute stability.
setCompounds(CompositionDataset) - Method in class magpie.data.utilities.modifiers.StabilityCalculationModifier: Define the data used to compute stability.
setCompressionLevel(int) - Method in class magpie.models.classification.ScikitLearnClassifier: Define how well model is compressed after training.
setCompressionLevel(int) - Method in interface magpie.models.interfaces.ExternalModel: Define how well model file is compressed
setCompressionLevel(int) - Method in class magpie.models.regression.ScikitLearnRegression: Define how well model is compressed after training.
setComputeVoronoi(boolean) - Method in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator: Set whether to compute the Voronoi tessellation before generating entries.
setCountPhases(boolean) - Method in class magpie.attributes.generators.composition.GCLPAttributeGenerator: Set whether to count number of phases at equilibrium.
setCutoff(double) - Method in class magpie.models.regression.crystal.PRDFRegression: Set the cutoff distance used when computing the PRDF
setCutoffDistance(double) - Method in class magpie.attributes.generators.crystal.APRDFAttributeGenerator: Define cutoff distance for AP-RDF.
setCutoffDistance(double) - Method in class magpie.attributes.generators.crystal.PRDFAttributeGenerator: Define the maximum distance to consider when computing the PRDF
setCVFraction(double) - Method in class magpie.attributes.selectors.LassoAttributeSelector: Set the fraction of entries to without during cross-validation.
setCVIterations(int) - Method in class magpie.attributes.selectors.LassoAttributeSelector: Set the number of iterations to perform during cross-validation.
setDataDirectory(String) - Method in class magpie.data.materials.CompositionDataset: Define whether to look for elemental property lookup tables.
setDataset(Dataset) - Method in class magpie.utility.tools.BatchModelEvaluator: Set dataset to be evaluated.
setDelimiter(String) - Method in class magpie.data.utilities.output.DelimitedOutput: Set the delimiter used to separate words
setDimension(int) - Method in class magpie.data.utilities.generators.GridBaseEntryGenerator: Define dimension of grid.
setDistanceThreshold(double) - Method in class magpie.data.utilities.filters.CompositionDistanceFilter: Define the threshold composition distance.
setDistanceThreshold(double) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter: Set the distance threshold
setEdges(double[]) - Method in class magpie.data.utilities.modifiers.ClassIntervalModifier: Set the Edges that define the class intervals on which data is discretized.
setEdges(double[]) - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter: Define edges describing different values of the class variable on which entries are partitioned.
setElectronegativity(double[]) - Method in class magpie.utility.tools.OxidationStateGuesser: Set the lookup table for electronegativity values.
setElectronegativity(String) - Method in class magpie.utility.tools.OxidationStateGuesser: Set the lookup table for electronegativity values.
setElementalProperties(List<String>) - Method in class magpie.data.materials.ElementDataset: Define the list of elemental properties to be used to compute attributes.
setElementList(String[]) - Method in class magpie.data.utilities.filters.ContainsElementFilter: Define list of elements to use for filter.
setElementListByIndex(int[]) - Method in class magpie.data.utilities.filters.ContainsElementFilter: Define a list of elements to use for the filter
setElements(CompositionDataset) - Method in class magpie.attributes.generators.crystal.PRDFAttributeGenerator: Set the elements when computing PRDF
setElements(List<String>) - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter: Define list of elements to define the split.
setElementsByIndex(Set<Integer>) - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator: Define the lit of elements included in the phase diagrams.
setElementsByName(Set<String>) - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator: Define the lit of elements included in the phase diagrams.
setElementsToIgnore(Collection<String>) - Method in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator: Set list of elements that, if present, will not be replaced
setElementsToSubstitute(Collection<String>) - Method in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator: Set list of elements to use for substitutions.
setEnergyName(String) - Method in class magpie.data.utilities.modifiers.StabilityCalculationModifier: Define the name of the property containing energy data
setEntryIterator(Iterator<BaseEntry>) - Method in class magpie.utility.tools.BatchAttributeGenerator: Set the iterator over entries being processed
setEntryIterator(Iterator<BaseEntry>) - Method in class magpie.utility.tools.BatchModelEvaluator: Set iterator over entries to be acted on
setEnumerationStyle(CombinatorialSubstitutionGenerator.EnumerationType) - Method in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator: Set method used to enumerate different sets of elements
setEvaluator(String, String[]) - Method in class magpie.attributes.selectors.WekaAttributeSelector: Set the method used to evaluate subsets of entries.
setEvenSpacing(boolean) - Method in class magpie.data.utilities.generators.IonicCompoundGenerator: Not applicable for this class.
setEvenSpacing(boolean) - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator: Set whether to use evenly-spaced compositions (or low-denominator).
setExclude(boolean) - Method in class magpie.data.utilities.filters.BaseDatasetFilter: Define whether entries that pass should be removed, or whether an entry must pass the filter to be kept.
setFilter(BaseDatasetFilter) - Method in class magpie.data.utilities.splitters.FilterSplitter: Set the filter used to partition data
setFilter(BaseDatasetFilter) - Method in class magpie.models.BaseModel: Set filter used to clean data before training
setFittedElements(List<String>) - Method in class magpie.models.regression.MixingRuleRegression: Set which elements to fit.
setFormula(String) - Method in class magpie.optimization.rankers.PropertyFormulaRanker: Define the formula used by this class.
setGenericModel(BaseModel) - Method in class magpie.models.classification.SplitClassifier
setGenericModel(BaseModel) - Method in interface magpie.models.interfaces.MultiModel: Set the model template
setGenericModel(BaseModel) - Method in class magpie.models.regression.CompositeRegression
setGenericModel(BaseModel) - Method in class magpie.models.regression.MultiObjectiveRegression: Define the model to be used for a property if one is not specifically defined.
setGenericModel(BaseModel) - Method in class magpie.models.regression.SplitRegression
setGenericModel(BaseModel) - Method in class magpie.models.regression.StagedRegression
setGenericModel(BaseModel) - Method in class magpie.models.SplitModel: Set the model template
setGridSpacing(double) - Method in class magpie.data.utilities.generators.GridBaseEntryGenerator: Define grid step size.
setGroupIncludedInAttribute(int, boolean) - Method in class magpie.data.materials.util.PrototypeSiteInformation: Define whether a group of sites should be included when generating attributes.
setGuess(double) - Method in class magpie.models.regression.SingleGuessRegression: Sets the user's guess
setIncludeMatching(boolean) - Method in class magpie.attributes.selectors.RegexAttributeSelector: Set whether to include (or exclude) attributes whose name matches the pattern.
setInitialGuess(String, double) - Method in class magpie.models.regression.AbstractNonlinearRegression: Set the initial guess for a coefficient
SetIterator - Variable in class magpie.attributes.selectors.ExhaustiveAttributeSelector: Iterator over subsets of attributes to be tested
setK(int) - Method in class magpie.data.utilities.filters.PredictionOutlierFilter: Define number of fitting parameters in model.
setKnownCompounds(Map<CompositionEntry, String>) - Method in class magpie.csp.CSPEngine: Define the composition and prototype of already-known compounds.
setLambda(double) - Method in class magpie.models.regression.crystal.StructureKRRBasedRegression: Set the ridge regularization parameter.
setLookupData(CompositionDataset) - Method in class magpie.data.utilities.generators.IonicCompoundGenerator: Define the dataset used to lookup oxidation states.
setLookupPath(String) - Method in class magpie.utility.tools.IonicCompoundFinder: Set where to look for oxidation state data
setMaxAlloying(double) - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator: Set the maximum amount of element to add.
setMaxCandidates(int) - Method in class magpie.statistics.performance.TargetRegressionStatistics: Set the maximum number of candidates for an analysis of how the number of candidates affects prediction accuracy.
setMaxFormulaUnit(int) - Method in class magpie.attributes.generators.composition.IonicCompoundProximityAttributeGenerator: Set the maximum formula unit size when searching for ionic compounds.
setMaxFormulaUnitSize(int) - Method in class magpie.utility.tools.IonicCompoundFinder: Set maximum number of atoms in formula unit.
setMaximizeFunction(boolean) - Method in class magpie.optimization.rankers.BaseEntryRanker: Set whether this entry ranker will maximize objective function
setMaximizeFunction(boolean) - Method in class magpie.optimization.rankers.PropertyRanker
setMaximumDimension(int) - Method in class magpie.attributes.selectors.LassoAttributeSelector: Set the maximum number of attributes to select
setMaximumDistance(double) - Method in class magpie.utility.tools.IonicCompoundFinder: Set the maximum allowed distance from the target value.
setMaxIterations(int) - Method in class magpie.models.regression.AbstractNonlinearRegression: Define the maximum number of iterations allowed.
setMaxNumberTerms(int) - Method in class magpie.models.regression.LASSORegression
setMaxSubsetSize(int) - Method in class magpie.attributes.selectors.ExhaustiveAttributeSelector: Set maximum size of subset to be tested
setMaxValue(double) - Method in class magpie.data.utilities.generators.GridBaseEntryGenerator: Define maximum value in all directions
setMaxWindowSize(double) - Method in class magpie.statistics.performance.TargetRegressionStatistics: Set the maximum window size for an analysis of how tolerance window size affects prediction accuracy.
setMeasure(RemoveCorrelatedAttributeSelector.CorrelationMeasure) - Method in class magpie.attributes.selectors.RemoveCorrelatedAttributeSelector: Define the method used to measure correlation
setMeasuredClass(double) - Method in class magpie.data.BaseEntry: Set the measured class variable
setMeasuredClass(double) - Method in class magpie.data.MultiPropertyEntry
setMeasuredClasses(double[]) - Method in class magpie.data.Dataset: Set measured class for each entry, given an array of measurements
setMeasuredProperties(double[]) - Method in class magpie.data.MultiPropertyEntry: Define the values of all measured properties of this entry.
setMeasuredProperty(int, double) - Method in class magpie.data.MultiPropertyEntry: Set the measured value of a specific property of this entry.
setMinSubsetSize(int) - Method in class magpie.attributes.selectors.ExhaustiveAttributeSelector: Set minimum size of subset to be tested
setMinValue(double) - Method in class magpie.data.utilities.generators.GridBaseEntryGenerator: Define minimum value in all directions.
setModel(String, BaseModel, Dataset) - Method in class magpie.attributes.generators.ModelPredictionAttributeGenerator: Set the model used to create attribute(s).
setModel(BaseModel) - Method in class magpie.attributes.selectors.ExhaustiveAttributeSelector: Set model used to test subset performance
setModel(BaseModel) - Method in class magpie.data.utilities.modifiers.ErrorSignalModifier: Set the model used to make predictions.
setModel(BaseModel) - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter: Define the model used to split data.
setModel(int, BaseModel) - Method in class magpie.models.classification.SplitClassifier
setModel(String, String[]) - Method in class magpie.models.classification.WekaClassifier
setModel(int, BaseModel) - Method in interface magpie.models.interfaces.MultiModel: Set a specific submodel.
setModel(String, String[]) - Method in interface magpie.models.interfaces.WekaModel: Set the underlying Weka-based model
setModel(int, BaseModel) - Method in class magpie.models.regression.CompositeRegression
setModel(String, BaseModel) - Method in class magpie.models.regression.MultiObjectiveRegression: Define a model for a certain property.
setModel(int, BaseModel) - Method in class magpie.models.regression.SplitRegression
setModel(int, BaseModel) - Method in class magpie.models.regression.StagedRegression
setModel(String, String[]) - Method in class magpie.models.regression.WekaRegression: Set the underlying Weka-based model
setModel(int, BaseModel) - Method in class magpie.models.SplitModel
setModel(BaseModel) - Method in class magpie.utility.tools.BatchModelEvaluator: Define which model this class is used to evaluate
setMu(String, double) - Method in class magpie.data.materials.util.GCLPCalculator: Define the chemical potential of an element
setNBins(int[]) - Method in class magpie.models.classification.CumulantExpansionClassifier: Define number of desired bins of common compositions.
setNBins(int) - Method in class magpie.models.regression.crystal.PRDFRegression: Set the number of bins used when computing the PRDF.
setNComponents(int) - Method in class magpie.models.classification.CumulantExpansionClassifier: Set the number of components in the material being considered.
setNDownselect(int) - Method in class magpie.attributes.selectors.LassoAttributeSelector: Set number of attributes to downselect to by removing strongly-correlated entries.
setNEigenvalues(int) - Method in class magpie.attributes.generators.crystal.CoulombMatrixAttributeGenerator: Set the number of eigenvalues used in representation
setNElements(int) - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator: Set the number of elements in phase diagrams being iterated through
setNewClassName(String) - Method in class magpie.data.utilities.modifiers.ClassEliminationModifier: Define the name of the new class for entries measured to exist in the undesired class.
setNFolds(int) - Method in class magpie.attributes.selectors.ExhaustiveAttributeSelector: Set the number of folds used in K-fold cross-validation.
setNLASSO(int) - Method in class magpie.attributes.selectors.LassoAttributeSelector: Set the number of parameters to determine via LASSO
setNNearestToEval(Collection<Integer>) - Method in class magpie.attributes.generators.composition.APEAttributeGenerator: Set the number of nearest clusters to evaluate when computing attributes.
setNominalComposition(CompositionEntry) - Method in class magpie.utility.tools.IonicCompoundFinder: Set the target composition of the ionic compound.
setNPerDiagram(int) - Method in class magpie.data.utilities.filters.BestInAlloySystemFilter: Set number of entries to collect per diagram
setNPoints(int) - Method in class magpie.attributes.generators.crystal.PRDFAttributeGenerator: Define the number of points on each PRDF to store
setNProperties(int) - Method in class magpie.data.MultiPropertyEntry: Define the number of properties this entry can support.
setNSteps(int) - Method in class magpie.statistics.performance.TargetRegressionStatistics: Set the number of steps to use when calculating model performance for ranking or filtering.
setNToPrint(int) - Method in class magpie.data.utilities.output.SimpleOutput: Define number of top entries to print.
setNumAttributes(int) - Method in class magpie.attributes.selectors.RandomForestAttributeSelector: Set the target number of attributes to be selected
setNumberOfModels(int) - Method in interface magpie.models.interfaces.MultiModel: Defines the number of models to be trained.
setNumberOfModels(int) - Method in class magpie.models.regression.CompositeRegression
setNumberOfModels(int) - Method in class magpie.models.regression.StagedRegression
setNumberOfModels(int) - Method in class magpie.models.SplitModel
setNumberToFilter(int) - Method in class magpie.data.utilities.filters.EntryRankerFilter: Define how many entries will pass this filter
setNumPoints(int) - Method in class magpie.attributes.generators.crystal.APRDFAttributeGenerator: Set number of distances to evaluated for AP-RDF
setNumSteps(int) - Method in class magpie.attributes.selectors.RandomForestAttributeSelector: Number of iterations during attribute selection
setNumTrees(int) - Method in class magpie.attributes.selectors.RandomForestAttributeSelector: Number of trees for the RandomForest model
setObjectiveFunction(BaseEntryRanker) - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter: Define objective function by which to split entries
setObjectiveFunction(BaseEntryRanker) - Method in class magpie.models.regression.ClassificationRegression: Define the objective function used to order entries
setObjectiveFunction(MultiObjectiveEntryRanker) - Method in class magpie.models.regression.MultiObjectiveRegression: Define the objective function used to calculate perform of each entry.
setObjectivePercentile(double) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker: Define percentile to use for approximating the minimum value of each objective function.
setOptions(List<Object>) - Method in class magpie.attributes.evaluators.AreaUnderROCEvaluator
setOptions(List<Object>) - Method in class magpie.attributes.evaluators.PearsonsCorrelationEvaluator
setOptions(List<Object>) - Method in class magpie.attributes.evaluators.PolynomialFitEvaluator
setOptions(List<Object>) - Method in class magpie.attributes.evaluators.SpearmansCorrelationEvaluator
setOptions(List<Object>) - Method in class magpie.attributes.expanders.CrossExpander
setOptions(List<Object>) - Method in class magpie.attributes.expanders.FunctionExpander
setOptions(List<Object>) - Method in class magpie.attributes.expanders.PowerExpander
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.APEAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.ChargeDependentAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.ElementalPropertyAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.ElementFractionAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.ElementPairPropertyAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.GCLPAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.IonicCompoundProximityAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.IonicityAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.MeredigAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.ValenceShellAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.YangOmegaAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.crystal.APRDFAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.crystal.ChemicalOrderingAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.crystal.CoordinationNumberAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.crystal.CoulombMatrixAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.crystal.EffectiveCoordinationNumberAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.crystal.LatticeSimilarityAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.crystal.PackingEfficiencyAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.crystal.PRDFAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.crystal.StructuralHeterogeneityAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.element.ElementalPropertyAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.LookupTableAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.ModelPredictionAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.PropertyAsAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.generators.prototype.SingleSiteAttributeGenerator
setOptions(List<Object>) - Method in class magpie.attributes.selectors.BestIndividualSelector
setOptions(List<Object>) - Method in class magpie.attributes.selectors.ExhaustiveAttributeSelector
setOptions(List<Object>) - Method in class magpie.attributes.selectors.LassoAttributeSelector
setOptions(List<Object>) - Method in class magpie.attributes.selectors.MeredigAttributeSelector
setOptions(List<Object>) - Method in class magpie.attributes.selectors.RandomForestAttributeSelector
setOptions(List<Object>) - Method in class magpie.attributes.selectors.RegexAttributeSelector
setOptions(List<Object>) - Method in class magpie.attributes.selectors.RemoveCorrelatedAttributeSelector
setOptions(List<Object>) - Method in class magpie.attributes.selectors.RemoveDuplicateAttributeSelector
setOptions(List<Object>) - Method in class magpie.attributes.selectors.RemoveNaNAttributeSelector
setOptions(List<Object>) - Method in class magpie.attributes.selectors.StagedAttributeSelector
setOptions(List<Object>) - Method in class magpie.attributes.selectors.UserSpecifiedAttributeSelector: Sets the object to select only attributes listed in input
setOptions(List<Object>) - Method in class magpie.attributes.selectors.WekaAttributeSelector
setOptions(List<Object>) - Method in class magpie.cluster.WekaClusterer
setOptions(List<Object>) - Method in class magpie.csp.CompositionBasedCSPEngine
setOptions(List<Object>) - Method in class magpie.csp.DMSPEngine
setOptions(List<Object>) - Method in class magpie.data.Dataset
setOptions(List<Object>) - Method in class magpie.data.materials.PrototypeDataset
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.AllMetalsFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.AttributeFilter
setOptions(String, String, String) - Method in class magpie.data.utilities.filters.AttributeFilter: Configure the filter by defining which entries should be kept
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.BestInAlloySystemFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.ClassFilter
setOptions(String, String, String) - Method in class magpie.data.utilities.filters.ClassFilter: Configure the filter by defining which entries should be kept
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.ClassProbabilityFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.ClassRangeFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.CompositionDistanceFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.ContainsElementFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.EntryRankerFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.IQROutlierFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.MultiFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.PredictionOutlierFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.PropertyFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.PropertyRangeFilter
setOptions(List) - Method in class magpie.data.utilities.filters.RegressionErrorFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.StabilityFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.ZScoreOutlierFilter
setOptions(List<Object>) - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
setOptions(List<Object>) - Method in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator
setOptions(List<Object>) - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
setOptions(List<Object>) - Method in class magpie.data.utilities.generators.FixedStoichiometryCompositionEntryGenerator
setOptions(List<Object>) - Method in class magpie.data.utilities.generators.GridBaseEntryGenerator
setOptions(List<Object>) - Method in class magpie.data.utilities.generators.IonicCompoundGenerator
setOptions(List<Object>) - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
setOptions(List<Object>) - Method in class magpie.data.utilities.generators.PrototypeEntryGenerator
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.AddPropertyModifier
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.ClassEliminationModifier
setOptions(List) - Method in class magpie.data.utilities.modifiers.ClassIntervalModifier
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.DiscreteToContinuousModifier
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.duplicates.AveragingDuplicateResolver
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.duplicates.RankingDuplicateResolver
setOptions(List) - Method in class magpie.data.utilities.modifiers.ErrorSignalModifier
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.HHICalculationModifier
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.NaNToMeanModifier
setOptions(List) - Method in class magpie.data.utilities.modifiers.NonZeroClassModifier
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.PartitionToClassModifier
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.SetClassNamesModifier
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.SetPropertyValueModifier
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.StabilityCalculationModifier
setOptions(List) - Method in class magpie.data.utilities.modifiers.VolumeToLatticeParamModifier
setOptions(List<Object>) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
setOptions(List<Object>) - Method in class magpie.data.utilities.normalizers.MultiNormalizer
setOptions(List<Object>) - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
setOptions(List<Object>) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
setOptions(List<Object>) - Method in class magpie.data.utilities.normalizers.SoftmaxNormalizer
setOptions(List<Object>) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
setOptions(List<Object>) - Method in class magpie.data.utilities.output.ARFFOutput
setOptions(List<Object>) - Method in class magpie.data.utilities.output.CompositionOutput
setOptions(List<Object>) - Method in class magpie.data.utilities.output.DelimitedOutput
setOptions(List<Object>) - Method in class magpie.data.utilities.output.JSONOutput
setOptions(List<Object>) - Method in class magpie.data.utilities.output.PropertiesOutput
setOptions(List<Object>) - Method in class magpie.data.utilities.output.SimpleOutput
setOptions(List) - Method in class magpie.data.utilities.splitters.AllMetalsSplitter
setOptions(List) - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
setOptions(List) - Method in class magpie.data.utilities.splitters.ClustererSplitter
setOptions(List<Object>) - Method in class magpie.data.utilities.splitters.FilterSplitter
setOptions(List) - Method in class magpie.data.utilities.splitters.MeasuredClassSplitter
setOptions(List) - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
setOptions(List) - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
setOptions(List<Object>) - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
setOptions(List<Object>) - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
setOptions(List) - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
setOptions(List<Object>) - Method in class magpie.models.classification.CumulantExpansionClassifier
setOptions(List<Object>) - Method in class magpie.models.classification.ScikitLearnClassifier
setOptions(List) - Method in class magpie.models.classification.SplitClassifier
setOptions(List) - Method in class magpie.models.classification.WekaClassifier
setOptions(List) - Method in class magpie.models.regression.AbstractNonlinearRegression
setOptions(List) - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
setOptions(List<Object>) - Method in class magpie.models.regression.ClassificationRegression
setOptions(List) - Method in class magpie.models.regression.CompositeRegression
setOptions(List<Object>) - Method in class magpie.models.regression.crystal.CoulombEwaldMatrixRegression
setOptions(List<Object>) - Method in class magpie.models.regression.crystal.CoulombSineMatrixRegression
setOptions(List<Object>) - Method in class magpie.models.regression.crystal.PRDFRegression
setOptions(List) - Method in class magpie.models.regression.GuessMeanRegression
setOptions(List) - Method in class magpie.models.regression.LASSORegression
setOptions(List<Object>) - Method in class magpie.models.regression.LinearCorrectedRegression
setOptions(List<Object>) - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
setOptions(List) - Method in class magpie.models.regression.MixingRuleRegression
setOptions(List<Object>) - Method in class magpie.models.regression.MultiObjectiveRegression
setOptions(List<Object>) - Method in class magpie.models.regression.MultiPropertyRegression
setOptions(List) - Method in class magpie.models.regression.PolynomialRegression
setOptions(List) - Method in class magpie.models.regression.RandomGuessRegression
setOptions(List<Object>) - Method in class magpie.models.regression.ScikitLearnRegression
setOptions(List) - Method in class magpie.models.regression.SingleGuessRegression
setOptions(List) - Method in class magpie.models.regression.StagedRegression
setOptions(List) - Method in class magpie.models.regression.WekaRegression
setOptions(List) - Method in class magpie.models.SplitModel
setOptions(List<Object>) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
setOptions(List<Object>) - Method in class magpie.optimization.rankers.ClassProbabilityRanker
setOptions(List<Object>) - Method in class magpie.optimization.rankers.CompositionDistanceRanker
setOptions(List<Object>) - Method in class magpie.optimization.rankers.PropertyFormulaRanker
setOptions(List<Object>) - Method in class magpie.optimization.rankers.PropertyRanker
setOptions(List) - Method in class magpie.optimization.rankers.SimpleEntryRanker
setOptions(List) - Method in class magpie.optimization.rankers.TargetEntryRanker
setOptions(List<Object>) - Method in class magpie.statistics.performance.BaseStatistics
setOptions(List<Object>) - Method in class magpie.statistics.performance.TargetRegressionStatistics
setOptions(List<Object>) - Method in interface magpie.utility.interfaces.Options: Set any options for this object.
setOptions(List<Object>) - Method in class magpie.utility.tools.BatchAttributeGenerator
setOptions(List<Object>) - Method in class magpie.utility.tools.BatchModelEvaluator
setOptions(List<Object>) - Method in class magpie.utility.tools.OxidationStateGuesser
setOptions(List<Object>) - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
setOrder(int, int) - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator: Define the order of generated phase diagrams
setOrder(int) - Method in class magpie.models.regression.PolynomialRegression: Define Order of polynomial.
setOutputter(BaseDatasetOutput) - Method in class magpie.utility.tools.BatchAttributeGenerator: Define tool used to output data
setOxidationStates(int[][]) - Method in class magpie.utility.tools.OxidationStateGuesser: Set the oxidation states
setOxidationStates(double[][]) - Method in class magpie.utility.tools.OxidationStateGuesser: Set the oxidation states
setOxidationStates(String) - Method in class magpie.utility.tools.OxidationStateGuesser: Set the oxidation states
setP(double) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker: Set tradeoff parameter between optimal in single category and decent in all
setPackingThreshold(double) - Method in class magpie.attributes.generators.composition.APEAttributeGenerator: Define the threshold at which to define a cluster as efficiently packed.
setPartitioner(BaseDatasetSplitter) - Method in class magpie.models.SplitModel: Set the partitioner.
setPerCell(int) - Method in class magpie.data.utilities.modifiers.VolumeToLatticeParamModifier: Set number of atoms in unit cell.
setPhaseDiagramStats(PhaseDiagramStatistics) - Method in class magpie.models.classification.CumulantExpansionClassifier: Define the phase diagram statistics object used to make predictions.
setPhases(CompositionDataset) - Method in class magpie.attributes.generators.composition.GCLPAttributeGenerator: Define phases used when computing ground states
setPredictedClass(double) - Method in class magpie.data.BaseEntry: Set the predicted class variable
setPredictedClass(double) - Method in class magpie.data.MultiPropertyEntry
setPredictedClasses(double[]) - Method in class magpie.data.Dataset: Set predicted class for each entry, given an array of predictions
setPredictedProperty(int, double) - Method in class magpie.data.MultiPropertyEntry: Directly set the predicted value of a property.
setPredictedProperty(int, double[]) - Method in class magpie.data.MultiPropertyEntry: Directly set the probabilities of an entry existing in one of several classes.
setPrintAccuracy(int) - Method in class magpie.models.regression.PolynomialRegression: Set the number of digits printed when outputting model
setProbabilityThreshold(double) - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter: Define the probability of being in class 0 on which to partition data.
setPropertiesToAdd(List<String>) - Method in class magpie.data.utilities.modifiers.AddPropertyModifier: Define list of properties to add to a dataset.
setPropertyClasses(int, String[]) - Method in class magpie.data.MultiPropertyDataset: Define possible classes for a certain property (like "Metal" or "Nonmetal")
setPropertyName(String) - Method in class magpie.models.regression.MixingRuleRegression: Define which property to use for alloy mean
setPropertyName(String) - Method in class magpie.optimization.rankers.PropertyRanker: Set the name of property used for ranking
setPropertyValue(String, String) - Method in class magpie.data.utilities.modifiers.SetPropertyValueModifier: Set the name and value of property to be set
setPropertyValue(String, double) - Method in class magpie.data.utilities.modifiers.SetPropertyValueModifier: Set the name and value of property to be set
SetPropertyValueModifier - Class in magpie.data.utilities.modifiers: Set the value of a certain property of each entry.
SetPropertyValueModifier() - Constructor for class magpie.data.utilities.modifiers.SetPropertyValueModifier
setPrototypes(List<CrystalStructureEntry>) - Method in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator: Define the list of prototype structures to use to create entries.
setPrototypes(CrystalStructureDataset) - Method in class magpie.data.utilities.generators.CombinatorialSubstitutionGenerator: Define the list of prototype structures used to create entries.
setQ(double) - Method in class magpie.data.utilities.filters.PredictionOutlierFilter: Set target False Discovery rate.
setQ(double) - Method in class magpie.statistics.utility.RobustRegressionUtility: Define the target False Discovery Rate for outlier selection
setR(double) - Method in class magpie.data.utilities.normalizers.SoftmaxNormalizer: Set the scaling constant
setRadiusProperty(String) - Method in class magpie.attributes.generators.composition.APEAttributeGenerator: Set the name of the elemental property used to define radii.
setRandomSplit(double, int) - Method in class magpie.attributes.selectors.ExhaustiveAttributeSelector: Set the size of test set split and number of times to repeat CV.
setRanker(BaseEntryRanker) - Method in class magpie.data.utilities.filters.BestInAlloySystemFilter: Set how to rank entries
setRanker(BaseEntryRanker) - Method in class magpie.data.utilities.filters.EntryRankerFilter: Define the ranker used to filter entries.
setRanker(BaseEntryRanker) - Method in class magpie.data.utilities.modifiers.duplicates.RankingDuplicateResolver: Set the ranker used to select between entries
setRanker(BaseEntryRanker) - Method in class magpie.data.utilities.output.SimpleOutput: Define tool used to rank entries before printing.
setRegex(String) - Method in class magpie.attributes.selectors.RegexAttributeSelector: Define the regular expression.
setRobustRegressionQ(double) - Method in interface magpie.models.regression.AbstractRegressionModel: Set the desired False Discovery Rate for outlier detection.
setRobustRegressionQ(double) - Method in class magpie.models.regression.BaseRegression
setRobustRegressionQ(double) - Method in class magpie.models.regression.SplitRegression
setScale(double) - Method in class magpie.data.utilities.normalizers.InverseNormalizer: Define scale of attributes / class.
setScreenAttributes(boolean) - Method in class magpie.data.utilities.filters.ZScoreOutlierFilter: Set whether to screen based on whether any attribute value is an outlier.
setScreenClass(boolean) - Method in class magpie.data.utilities.filters.ZScoreOutlierFilter: Set whether to screen based on whether measured class value is an outlier
setSearcher(String, String[]) - Method in class magpie.attributes.selectors.WekaAttributeSelector: Set the method used to search for optimal subsets.
setSelectionMethod(CompositionOutput.ElementSelectionMethod) - Method in class magpie.data.utilities.output.CompositionOutput: Set the method used to determine which elements to print.
setSelectors(List<BaseAttributeSelector>) - Method in class magpie.attributes.selectors.StagedAttributeSelector: Set the list of selectors used by this tool
setSelectSizeAutomatically(boolean) - Method in class magpie.attributes.selectors.LassoAttributeSelector: Set whether to determine number of attributes through cross-validation.
setShells(Collection<Integer>) - Method in class magpie.attributes.generators.crystal.ChemicalOrderingAttributeGenerator: Define which nearest-neighbor shells to consider when generating attributes.
setSigma(double) - Method in class magpie.models.regression.crystal.CoulombEwaldMatrixRegression: Set the normalization parameter in the kernel function.
setSigma(double) - Method in class magpie.models.regression.crystal.CoulombSineMatrixRegression: Set the normalization parameter in the kernel function.
setSigma(double) - Method in class magpie.models.regression.crystal.PRDFRegression: Set the normalization parameter in the kernel function.
setSiteComposition(int, CompositionEntry) - Method in class magpie.data.materials.PrototypeEntry: Set the composition of a certain site
setSiteInfo(PrototypeSiteInformation) - Method in class magpie.data.materials.PrototypeDataset: Define information about the prototypes contained by this dataset.
setSiteInfo(PrototypeSiteInformation) - Method in class magpie.data.utilities.generators.PrototypeEntryGenerator: Define the information about the sites in the prototype.
setSize(int) - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator: Define the number of points per binary diagram (in using even spacing) or the maximum denominator (for low-denominator)
setSmoothParameter(double) - Method in class magpie.attributes.generators.crystal.APRDFAttributeGenerator: Set smoothing parameter for RDF.
setSplitAbove(boolean) - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter: Set whether class #0 should be entries above a threshold
setSplitter(BaseDatasetSplitter) - Method in class magpie.data.utilities.modifiers.PartitionToClassModifier: Set the splitter used to generate new class variables.
setStabilityName(String) - Method in class magpie.data.utilities.modifiers.StabilityCalculationModifier: Set the name of the property in which to store stability data
setSubmodel(BaseModel) - Method in class magpie.models.regression.LinearCorrectedRegression: Define the model that this class corrects.
setSubRanker(BaseEntryRanker) - Method in class magpie.optimization.rankers.PropertyRanker: Set the ranker employed by this class.
setTarget(double) - Method in class magpie.statistics.performance.TargetRegressionStatistics: Define target value of class variable.
setTargetAttribute(String) - Method in class magpie.data.utilities.filters.AttributeFilter: Set the attribute being compared
setTargetClass(String) - Method in class magpie.attributes.evaluators.AreaUnderROCEvaluator: Define the class for which the ability to classify is being assessed.
setTargetClass(String) - Method in class magpie.optimization.rankers.ClassProbabilityRanker: Set the name of the class of interest
setTargetComposition(CompositionEntry) - Method in class magpie.data.utilities.filters.CompositionDistanceFilter: Define the target composition
setTargetProperty(String, boolean) - Method in class magpie.data.MultiPropertyDataset: Define which property to use as the class variable.
setTargetProperty(int, boolean) - Method in class magpie.data.MultiPropertyDataset: Define which property to set as the measured class of each entry.
setTargetProperty(int) - Method in class magpie.data.MultiPropertyEntry: Define which property to use as the class variable.
setTestFraction(double) - Method in class magpie.statistics.utility.RobustRegressionUtility: Define the fraction of entries that will be tested as potential outliers.
setTestMethod(ExhaustiveAttributeSelector.EvaluationMethod) - Method in class magpie.attributes.selectors.ExhaustiveAttributeSelector: Set method used to evaluate model performance
setThreshold(double) - Method in class magpie.attributes.selectors.RemoveCorrelatedAttributeSelector: Define the threshold at which attributes are declared "correlated"
setThreshold(double) - Method in class magpie.data.utilities.filters.ClassProbabilityFilter: Set the probability threshold used for filtering.
setThreshold(double) - Method in class magpie.data.utilities.filters.ComparisonOperatorFilter: Set the comparison threshold.
setThreshold(double) - Method in class magpie.data.utilities.filters.IQROutlierFilter: Define number of IQRs away from the median that an entries is an outliers.
setThreshold(double) - Method in class magpie.data.utilities.filters.StabilityFilter: Set threshold at which compounds are declared "unstable".
setThreshold(double) - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter: Set threshold on which to partition entries
setThreshold(double) - Method in class magpie.models.regression.ClassificationRegression: Define threshold of objective function on which to split entries.
setTolerance(double) - Method in class magpie.attributes.selectors.RemoveDuplicateAttributeSelector: Define the maximum difference at which two numbers are considered equal.
setTolerance(double) - Method in class magpie.data.utilities.filters.ZScoreOutlierFilter: Set the tolerance defining what is an outlier.
setTolerance(double) - Method in class magpie.statistics.performance.TargetRegressionStatistics: Define the error threshold that is considered a successful prediction.
setToNormalizeAttributes(boolean) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer: Set whether to normalize attributes
setToNormalizeClass(boolean) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer: Set whether to normalize class variable
setUnits(String) - Method in class magpie.user.server.ModelPackage
setUseClass(boolean) - Method in class magpie.attributes.selectors.RemoveCorrelatedAttributeSelector: Define whether to select the attribute most correlated with the class variable when selecting which pair of correlated attributes to keep.
setUseCorrection(boolean) - Method in class magpie.models.regression.MetallurgicalHeuristicRegression: Set whether to employ correction factors
setUseCorrection(boolean) - Method in class magpie.models.regression.MixingRuleRegression: Whether to fit a linear model to correct differences between the alloy mean and class variable
setUseEuclidean() - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter: Use Euclidean distance as the distance metric
setUseInverse(boolean) - Method in class magpie.models.regression.MixingRuleRegression: Define whether to take the average of the property, or the average of the inverse of the property.
setUseManhattan(boolean) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter: Set whether to use Manhattan (vs Euclidean) distance
setUseManhattan() - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter: Use Manhattan distance as the distance metric
setUseManhattan(boolean) - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier: Set whether to use Manhattan (vs Euclidean) distance
setUseManhattan(boolean) - Method in class magpie.optimization.rankers.CompositionDistanceRanker: Set whether to use
setUseMeasured(boolean) - Method in class magpie.data.utilities.filters.ClassFilter: Set whether to use the measured class variable.
setUseMeasured(boolean) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
setUseMeasured(boolean) - Method in class magpie.optimization.rankers.BaseEntryRanker: Set whether to used measured (or predicted) class values
setUseMeasured(boolean) - Method in class magpie.optimization.rankers.PropertyRanker
setUsePredicted(boolean) - Method in class magpie.data.utilities.filters.StabilityFilter: Set whether to use the measured or predicted class variable.
setVariable(String, double) - Method in class magpie.utility.ParsedFunction: Define the value of a certain variable in this expression
setVariable(int, double) - Method in class magpie.utility.ParsedFunction: Define the value of a certain variable in this expression
setWeighted(boolean) - Method in class magpie.attributes.generators.crystal.ChemicalOrderingAttributeGenerator: Set whether to consider face sizes when computing ordering parameters.
SimpleEntryRanker - Class in magpie.optimization.rankers: BaseEntryRanker that ranks entries based on class variable.
SimpleEntryRanker() - Constructor for class magpie.optimization.rankers.SimpleEntryRanker
SimpleLinearModelExample - Class in magpie.models.regression.nonlinear: Example for the AbstractNonlinearRegression Class.
SimpleLinearModelExample() - Constructor for class magpie.models.regression.nonlinear.SimpleLinearModelExample
SimpleOutput - Class in magpie.data.utilities.output: Print the name and measured class values of each attribute.
SimpleOutput() - Constructor for class magpie.data.utilities.output.SimpleOutput
SingleElementGroupSplitter - Class in magpie.data.utilities.splitters: Split dataset into two groups based on whether it contains certain elements.
SingleElementGroupSplitter() - Constructor for class magpie.data.utilities.splitters.SingleElementGroupSplitter
SingleGuessRegression - Class in magpie.models.regression: Guess a single, user-specified value for the class variable of all entries.
SingleGuessRegression() - Constructor for class magpie.models.regression.SingleGuessRegression
SingleSiteAttributeGenerator - Class in magpie.attributes.generators.prototype: Create attributes based on the properties of elements on each group of equivalent sites in a crystal.
SingleSiteAttributeGenerator() - Constructor for class magpie.attributes.generators.prototype.SingleSiteAttributeGenerator
SingleSites - Variable in class magpie.attributes.generators.prototype.SingleSiteAttributeGenerator: List of groups with a single site
SiteComp - Variable in class magpie.data.materials.PrototypeEntry: Composition of each site
SiteElements - Variable in class magpie.data.utilities.generators.PrototypeEntryGenerator: Lists of possible elements on each site
SiteInfo - Variable in class magpie.attributes.generators.prototype.PairSiteAttributeGenerator: Information of this particular prototype
SiteInfo - Variable in class magpie.data.materials.PrototypeDataset: Stores information about each site
SiteInfo - Variable in class magpie.data.materials.PrototypeEntry: Link to site information from corresponding dataset
SiteInfo - Variable in class magpie.data.utilities.generators.PrototypeEntryGenerator: Description of sites on prototype
siteIsIncludedInAttributes(int) - Method in class magpie.data.materials.util.PrototypeSiteInformation
size - Variable in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator: Either number of stops in each direction or max denominator
SmoothParameter - Variable in class magpie.attributes.generators.crystal.APRDFAttributeGenerator: Smoothing parameter for AP-RDF
SoftmaxNormalizer - Class in magpie.data.utilities.normalizers: Normalization using the "softmax" method.
SoftmaxNormalizer() - Constructor for class magpie.data.utilities.normalizers.SoftmaxNormalizer
sortAndGetRanks(double[], boolean) - Static method in class magpie.utility.UtilityOperations: Sort an array and return the original indices of the each value.
sortAndGetRanks(double[], Comparator<Double>) - Static method in class magpie.utility.UtilityOperations: Sort an array and return the original index of each member.
sortByRanking(Dataset) - Method in class magpie.optimization.rankers.BaseEntryRanker: Sort entries in a dataset according to ranking
SortingOrder - Variable in class magpie.data.materials.CompositionDataset: Order in which elements are sorted (used when printing)
SortingOrder - Variable in class magpie.data.materials.CompositionEntry: Rank of each element (used in display order)
SortingOrder - Static variable in class magpie.data.materials.util.LookupData: Order in which to sort elements.
spawnStderrReader(Process) - Method in class magpie.attributes.selectors.PythonBasedAttributeSelector: Launch a thread that does nothing but read from the standard error of an external process.
SpearmansCorrelationEvaluator - Class in magpie.attributes.evaluators: Evaluate attributes based on Spearson's Correlation Coefficient, which is simply the Pearson's Correlation Coefficient between the measured and predicted ranks of entries.
SpearmansCorrelationEvaluator() - Constructor for class magpie.attributes.evaluators.SpearmansCorrelationEvaluator
Specificity - Variable in class magpie.statistics.performance.ClassificationStatistics: Specificity (True Negative Rate)
split(Dataset) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter: Splits a dataset into several partitions.
split(Dataset, boolean) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter: Split a dataset into several partitions.
SplitClassifier - Class in magpie.models.classification: Model that uses several other models to model different parts of a dataset.
SplitClassifier() - Constructor for class magpie.models.classification.SplitClassifier: Create a blank SplitClassifier
splitForThreading(int) - Method in class magpie.data.Dataset: Split for threading purposes.
splitIntoFolds(int) - Method in class magpie.data.Dataset: Split the dataset into multiple folds for cross-validation, empties the original test set
splitIntoFolds(int, long) - Method in class magpie.data.Dataset: Split the dataset into multiple folds for cross-validation, empties the original test set
SplitModel - Class in magpie.models: Abstract class for a model that splits the dataset and trains several submodels.
SplitModel() - Constructor for class magpie.models.SplitModel
SplitRegression - Class in magpie.models.regression: Abstract class for models that use multiple submodels.
SplitRegression() - Constructor for class magpie.models.regression.SplitRegression: Create a blank split regression model
StabilityCalculationModifier - Class in magpie.data.utilities.modifiers: Use GCLP compute the stability with respect to other phases.
StabilityCalculationModifier() - Constructor for class magpie.data.utilities.modifiers.StabilityCalculationModifier
StabilityFilter - Class in magpie.data.utilities.filters: Filter based on computed stability.
StabilityFilter() - Constructor for class magpie.data.utilities.filters.StabilityFilter
StagedAttributeSelector - Class in magpie.attributes.selectors: Selector that uses multiple selection strategies in series.
StagedAttributeSelector() - Constructor for class magpie.attributes.selectors.StagedAttributeSelector
StagedRegression - Class in magpie.models.regression: Composite regression where the error signal from a model is used to train the next.
StagedRegression() - Constructor for class magpie.models.regression.StagedRegression
StartDate - Static variable in class magpie.user.server.ServerLauncher: Time server was launched
startReader(InputStream, OutputStream) - Static method in class magpie.models.utility.ExternalModelUtility: Launch a thread that does nothing but read from the output of another process.
startServer() - Method in class magpie.models.classification.ScikitLearnClassifier
startServer() - Method in interface magpie.models.interfaces.ExternalModel: Start the server hosting the model.
startServer() - Method in class magpie.models.regression.ScikitLearnRegression
startServer() - Static method in class magpie.user.server.ServerLauncher: Given the current settings, start the Magpie server
StartTime - Variable in class magpie.user.CommandHandler: Holds start time of default timer
StepFraction - Variable in class magpie.data.utilities.generators.CompositionRangeEntryGenerator: Fraction step size of certain element.
Stiochiometries - Variable in class magpie.data.utilities.generators.FixedStoichiometryCompositionEntryGenerator: List of stiochiometries.
StoichiometricAttributeGenerator - Class in magpie.attributes.generators.composition: Generate attributes based on stoichiometry of material.
StoichiometricAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
stopServer(ExternalModel) - Static method in class magpie.models.utility.ExternalModelUtility: Send the "exit" command and stop a server
StructuralHeterogeneityAttributeGenerator - Class in magpie.attributes.generators.crystal: Compute attributes based on heterogeneity in structure.
StructuralHeterogeneityAttributeGenerator() - Constructor for class magpie.attributes.generators.crystal.StructuralHeterogeneityAttributeGenerator
StructureKRRBasedRegression - Class in magpie.models.regression.crystal: Abstract class for methods that predict properties of crystal structures with KKR-based schemes.
StructureKRRBasedRegression() - Constructor for class magpie.models.regression.crystal.StructureKRRBasedRegression
StructureProbability - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics: For each composition, probability of each structure existing in a phase diagram.
subtract(Dataset) - Method in class magpie.data.Dataset: Remove all entries that are in another dataset from this dataset

T

Target - Variable in class magpie.optimization.rankers.TargetEntryRanker: Target value of class
Target - Variable in class magpie.statistics.performance.TargetRegressionStatistics: Target value of class variable
TargetAttribute - Variable in class magpie.data.utilities.filters.AttributeFilter: Name of feature to base filter on
TargetEntryRanker - Class in magpie.optimization.rankers: Rank entries based on the distance of their class variable from a target.
TargetEntryRanker(double) - Constructor for class magpie.optimization.rankers.TargetEntryRanker: Create a new instance while specifying the target
TargetEntryRanker() - Constructor for class magpie.optimization.rankers.TargetEntryRanker: Create a new instance the target set to 0.0
TargetRegressionStatistics - Class in magpie.statistics.performance: Statistics for the ability of a model to find entries with a class near a target value.
TargetRegressionStatistics() - Constructor for class magpie.statistics.performance.TargetRegressionStatistics
Tau - Variable in class magpie.statistics.performance.RegressionStatistics: Kendall's rank correlation coefficient
TermNames - Variable in class magpie.models.regression.LASSORegression: Names of terms used in the model
Terms - Variable in class magpie.models.regression.LASSORegression: Terms used in the model
test(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer: Check whether the normalize/restore operations are reversible.
testCriteria(double[]) - Method in class magpie.data.utilities.filters.ComparisonOperatorFilter: Evaluate the filtering criteria on each member of an array
TestFraction - Variable in class magpie.statistics.utility.RobustRegressionUtility: What fraction of the population to test
TestMethod - Variable in class magpie.attributes.selectors.ExhaustiveAttributeSelector: Method used to evaluate models
ThreadCount - Static variable in class magpie.user.server.ServerLauncher: Number of allowed threads
ThreadPool - Static variable in class magpie.user.server.ServerLauncher: Executor used to prevent too many complex calculations at once.
Threshold - Variable in class magpie.attributes.selectors.RemoveCorrelatedAttributeSelector: Threshold at which attributes are marked as correlated.
Threshold - Variable in class magpie.data.utilities.filters.ComparisonOperatorFilter: Threshold value
Title - Variable in class magpie.utility.interfaces.Citation: Title of resource being cited.
TN - Variable in class magpie.statistics.performance.ClassificationStatistics: Number of True Negatives
toExclude() - Method in class magpie.data.utilities.filters.BaseDatasetFilter
toHTMLString() - Method in class magpie.data.BaseEntry: Print entry in a HTML-friendly format.
toHTMLString() - Method in class magpie.data.materials.CompositionEntry
toHTMLString() - Method in class magpie.data.materials.ElementEntry
toHTMLString() - Method in class magpie.data.materials.PrototypeEntry
toJSON() - Method in class magpie.data.BaseEntry: Print entry as a JSON object
toJSON() - Method in class magpie.data.Dataset: Print dataset to JSON format
toJSON() - Method in class magpie.data.materials.CompositionEntry
toJSON() - Method in class magpie.data.materials.CrystalStructureEntry
toJSON() - Method in class magpie.data.materials.ElementEntry
toJSON() - Method in class magpie.data.materials.PrototypeEntry
toJSON() - Method in class magpie.data.MultiPropertyDataset
toJSON() - Method in class magpie.data.MultiPropertyEntry
toJSON() - Method in class magpie.user.server.ModelPackage: Render the model information as a JSON file
toJSON() - Method in class magpie.utility.interfaces.Citation: Return citation into JSON.
toJSONArray(double[]) - Static method in class magpie.utility.UtilityOperations: Convert an array of doubles into a JSON array.
Tolerance - Variable in class magpie.attributes.selectors.RemoveDuplicateAttributeSelector: Maximum absolute difference at which to declare two floats equal
Tolerance - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter: Number of standard deviation away from mean used when defining outliers
Tolerance - Variable in class magpie.statistics.performance.TargetRegressionStatistics: Tolerance for successful prediction
toString() - Method in class magpie.data.BaseEntry
toString() - Method in class magpie.data.Dataset
toString() - Method in class magpie.data.materials.CompositionEntry
toString() - Method in class magpie.data.materials.CrystalStructureEntry
toString() - Method in class magpie.data.materials.ElementEntry
toString() - Method in class magpie.data.materials.PrototypeEntry
toString() - Method in class magpie.data.MultiPropertyDataset
toString() - Method in class magpie.models.classification.WekaClassifier
toString() - Method in class magpie.models.regression.WekaRegression
toString() - Method in class magpie.statistics.performance.ClassificationStatistics
toString() - Method in class magpie.statistics.performance.RegressionStatistics
toString() - Method in class magpie.utility.interfaces.Citation
TP - Variable in class magpie.statistics.performance.ClassificationStatistics: Number of True Positives.
train(Dataset) - Method in class magpie.attributes.selectors.BaseAttributeSelector: Train an attribute selection algorithm on a dataset.
train(Dataset) - Method in class magpie.cluster.BaseClusterer: Train the clusterer
train(Dataset) - Method in class magpie.data.utilities.filters.AllMetalsFilter
train(Dataset) - Method in class magpie.data.utilities.filters.AttributeFilter
train(Dataset) - Method in class magpie.data.utilities.filters.BaseDatasetFilter: Train a dataset splitter, if necessary
train(Dataset) - Method in class magpie.data.utilities.filters.BestInAlloySystemFilter
train(Dataset) - Method in class magpie.data.utilities.filters.ClassFilter
train(Dataset) - Method in class magpie.data.utilities.filters.ClassProbabilityFilter
train(Dataset) - Method in class magpie.data.utilities.filters.ClassRangeFilter
train(Dataset) - Method in class magpie.data.utilities.filters.CompositionDistanceFilter
train(Dataset) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
train(Dataset) - Method in class magpie.data.utilities.filters.ContainsElementFilter
train(Dataset) - Method in class magpie.data.utilities.filters.EntryRankerFilter
train(Dataset) - Method in class magpie.data.utilities.filters.IQROutlierFilter
train(Dataset) - Method in class magpie.data.utilities.filters.MultiFilter
train(Dataset) - Method in class magpie.data.utilities.filters.PredictionOutlierFilter
train(Dataset) - Method in class magpie.data.utilities.filters.PropertyRangeFilter
train(Dataset) - Method in class magpie.data.utilities.filters.RegressionErrorFilter
train(Dataset) - Method in class magpie.data.utilities.filters.StabilityFilter
train(Dataset) - Method in class magpie.data.utilities.filters.ZScoreOutlierFilter
train(Dataset) - Method in class magpie.data.utilities.generators.BaseEntryGenerator: Define any settings based on a dataset
train(Dataset) - Method in class magpie.data.utilities.generators.IonicCompoundGenerator
train(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer: Train the normalizer.
train(Dataset) - Method in class magpie.data.utilities.splitters.AllMetalsSplitter
train(Dataset) - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
train(Dataset) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter: Train a dataset splitter, if necessary
train(Dataset) - Method in class magpie.data.utilities.splitters.ClustererSplitter
train(Dataset) - Method in class magpie.data.utilities.splitters.FilterSplitter
train(Dataset) - Method in class magpie.data.utilities.splitters.MeasuredClassSplitter
train(Dataset) - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter: Train a classifier for determining which entries have a non-zero class
train(Dataset) - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
train(Dataset) - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
train(Dataset) - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
train(Dataset) - Method in class magpie.models.BaseModel: Train a model on a specified training set and then evaluate performance on the training set.
train(Dataset, boolean) - Method in class magpie.models.BaseModel: Train a model on a specified training set and then evaluate performance on the training set, if desired
train(Dataset, boolean) - Method in class magpie.models.classification.BaseClassifier
train(MultiPropertyDataset) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
train(Dataset) - Method in class magpie.optimization.rankers.BaseEntryRanker: Train ranker.
train(Dataset) - Method in class magpie.optimization.rankers.ClassProbabilityRanker
train(Dataset) - Method in class magpie.optimization.rankers.CompositionDistanceRanker
train(MultiPropertyDataset) - Method in class magpie.optimization.rankers.MultiObjectiveEntryRanker: Train the entry ranker.
train(Dataset) - Method in class magpie.optimization.rankers.MultiObjectiveEntryRanker
train(MultiPropertyDataset) - Method in class magpie.optimization.rankers.PropertyFormulaRanker
train(Dataset) - Method in class magpie.optimization.rankers.PropertyRanker
train(Dataset) - Method in class magpie.optimization.rankers.SimpleEntryRanker
train(Dataset) - Method in class magpie.optimization.rankers.TargetEntryRanker
train_protected(Dataset) - Method in class magpie.attributes.selectors.BaseAttributeSelector: Operation that actually does the work for training.
train_protected(Dataset) - Method in class magpie.attributes.selectors.BestIndividualSelector
train_protected(Dataset) - Method in class magpie.attributes.selectors.ExhaustiveAttributeSelector
train_protected(Dataset) - Method in class magpie.attributes.selectors.MeredigAttributeSelector
train_protected(Dataset) - Method in class magpie.attributes.selectors.PythonBasedAttributeSelector
train_protected(Dataset) - Method in class magpie.attributes.selectors.RegexAttributeSelector
train_protected(Dataset) - Method in class magpie.attributes.selectors.RemoveCorrelatedAttributeSelector
train_protected(Dataset) - Method in class magpie.attributes.selectors.RemoveDuplicateAttributeSelector
train_protected(Dataset) - Method in class magpie.attributes.selectors.RemoveNaNAttributeSelector
train_protected(Dataset) - Method in class magpie.attributes.selectors.StagedAttributeSelector
train_protected(Dataset) - Method in class magpie.attributes.selectors.UserSpecifiedAttributeSelector
train_protected(Dataset) - Method in class magpie.attributes.selectors.UserSpecifiedExcludingAttributeSelector
train_protected(Dataset) - Method in class magpie.attributes.selectors.WekaAttributeSelector
train_protected(Dataset) - Method in class magpie.cluster.BaseClusterer: Perform the actual training.
train_protected(Dataset) - Method in class magpie.cluster.WekaClusterer
train_protected(Dataset) - Method in class magpie.models.BaseModel: Train a model without evaluating performance
train_protected(Dataset) - Method in class magpie.models.classification.CumulantExpansionClassifier
train_protected(Dataset) - Method in class magpie.models.classification.ScikitLearnClassifier
train_protected(Dataset) - Method in class magpie.models.classification.SplitClassifier
train_protected(Dataset) - Method in class magpie.models.classification.WekaClassifier
train_protected(Dataset) - Method in class magpie.models.regression.AbstractNonlinearRegression
train_protected(Dataset) - Method in class magpie.models.regression.ClassificationRegression
train_protected(Dataset) - Method in class magpie.models.regression.CompositeRegression
train_protected(Dataset) - Method in class magpie.models.regression.crystal.StructureKRRBasedRegression
train_protected(Dataset) - Method in class magpie.models.regression.GuessMeanRegression
train_protected(Dataset) - Method in class magpie.models.regression.LASSORegression
train_protected(Dataset) - Method in class magpie.models.regression.LinearCorrectedRegression
train_protected(Dataset) - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
train_protected(Dataset) - Method in class magpie.models.regression.MixingRuleRegression
train_protected(Dataset) - Method in class magpie.models.regression.MultiObjectiveRegression
train_protected(Dataset) - Method in class magpie.models.regression.PolynomialRegression
train_protected(Dataset) - Method in class magpie.models.regression.RandomGuessRegression
train_protected(Dataset) - Method in class magpie.models.regression.ScikitLearnRegression
train_protected(Dataset) - Method in class magpie.models.regression.SingleGuessRegression
train_protected(Dataset) - Method in class magpie.models.regression.StagedRegression
train_protected(Dataset) - Method in class magpie.models.regression.WekaRegression
train_protected(Dataset) - Method in class magpie.models.SplitModel
trained - Variable in class magpie.attributes.selectors.BaseAttributeSelector: Whether this BaseAttributeSelector has been trained
Trained - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter: Whether this class has been trained
trained - Variable in class magpie.models.BaseModel: Records whether model has been trained
TrainingSet - Variable in class magpie.user.server.ModelPackage: Training set description
TrainingStats - Variable in class magpie.models.BaseModel: Statistics about performance on training set
TrainingStatsPtr - Variable in class magpie.models.classification.SplitClassifier: Pointer to ClassificationStatistics interface of TrainingStats
trainModel(ExternalModel, Dataset) - Static method in class magpie.models.utility.ExternalModelUtility: Make a call to the model server to train a model
trainOnAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer: Perform the actual training work for attributes.
trainOnAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
trainOnAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
trainOnAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.MultiNormalizer
trainOnAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
trainOnMeasuredClass(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer: Perform the actual training work for the class variable.
trainOnMeasuredClass(Dataset) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
trainOnMeasuredClass(Dataset) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
trainOnMeasuredClass(Dataset) - Method in class magpie.data.utilities.normalizers.MultiNormalizer
trainOnMeasuredClass(Dataset) - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
transferToWeka(boolean, boolean) - Method in class magpie.data.Dataset: Convert to Weka Instances object, delete attribute information in each entry.
transform(Dataset) - Method in class magpie.data.utilities.modifiers.BaseDatasetModifier: Apply some change to the dataset and all of its entries
transpose(double[][]) - Static method in class magpie.utility.MathUtils: Transpose a rectangular array
Type - Variable in class magpie.utility.interfaces.Citation: Type of resource being cited.

U

Units - Variable in class magpie.user.server.ModelPackage: Units for property
useAbsoluteError() - Method in class magpie.data.utilities.modifiers.ErrorSignalModifier: Set filter to compute absolute error.
useAbsoluteError() - Method in class magpie.models.regression.StagedRegression: Set to train subsequent models on absolute error from previous.
UseClass - Variable in class magpie.attributes.selectors.RemoveCorrelatedAttributeSelector: Whether to pick the attribute most strongly correlated with the class variable
useCompositionAsAttributes(boolean) - Method in class magpie.data.materials.CompositionDataset: Set whether to use composition (i.e.
UseCorrection - Variable in class magpie.models.regression.MixingRuleRegression: Whether to apply correction factors
UseInverse - Variable in class magpie.models.regression.MixingRuleRegression: Whether to compute harmonic mean.
UseManhattan - Variable in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier: Whether to use Manhattan distance (vs Euclidean)
UseMeasured - Variable in class magpie.data.utilities.filters.ClassFilter: Whether to use measured class variable
UseMeasured - Variable in class magpie.data.utilities.filters.PropertyFilter: Whether to use measured or predicted property values
useRelativeError() - Method in class magpie.data.utilities.modifiers.ErrorSignalModifier: Set filter to computer relative error.
useRelativeError() - Method in class magpie.models.regression.StagedRegression: Set model to train subsequent models on relative error from previous.
UserFormula - Variable in class magpie.models.regression.AbstractParsedNonlinearRegression: Stores the user-provided formula
UserSpecifiedAttributeSelector - Class in magpie.attributes.selectors: Use only attributes with a specified name or ID number.
UserSpecifiedAttributeSelector() - Constructor for class magpie.attributes.selectors.UserSpecifiedAttributeSelector
UserSpecifiedExcludingAttributeSelector - Class in magpie.attributes.selectors: Exclude attributes with a certain name
UserSpecifiedExcludingAttributeSelector() - Constructor for class magpie.attributes.selectors.UserSpecifiedExcludingAttributeSelector
usingPropertyAsClass() - Method in class magpie.data.MultiPropertyDataset
usingPropertyAsClass() - Method in class magpie.data.MultiPropertyEntry
UtilityOperations - Class in magpie.utility: This is only a class full of useful static methods.
UtilityOperations() - Constructor for class magpie.utility.UtilityOperations

V

ValenceShellAttributeGenerator - Class in magpie.attributes.generators.composition: Generate attributes based on fraction of electrons in valence shell of constituent elements.
ValenceShellAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.ValenceShellAttributeGenerator
validated - Variable in class magpie.models.BaseModel: Records whether model has been validated
ValidationStats - Variable in class magpie.models.BaseModel: Statistics generated during model validation
ValidationStatsPtr - Variable in class magpie.models.classification.SplitClassifier: Pointer to ClassificationStatistics interface of ValidationStates
value(double[]) - Method in class magpie.utility.ParsedFunction
valueOf(String) - Static method in enum magpie.attributes.selectors.ExhaustiveAttributeSelector.EvaluationMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum magpie.attributes.selectors.RemoveCorrelatedAttributeSelector.CorrelationMeasure: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum magpie.data.utilities.generators.CombinatorialSubstitutionGenerator.EnumerationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum magpie.data.utilities.output.CompositionOutput.ElementSelectionMethod: Returns the enum constant of this type with the specified name.
values() - Static method in enum magpie.attributes.selectors.ExhaustiveAttributeSelector.EvaluationMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum magpie.attributes.selectors.RemoveCorrelatedAttributeSelector.CorrelationMeasure: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum magpie.data.utilities.generators.CombinatorialSubstitutionGenerator.EnumerationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum magpie.data.utilities.output.CompositionOutput.ElementSelectionMethod: Returns an array containing the constants of this enum type, in the order they are declared.
Variables - Variable in class magpie.user.Workspace: Map of variable name to object
VolumeToLatticeParamModifier - Class in magpie.data.utilities.modifiers: Add a new property to a CompositionDataset that represents a cubic lattice parameter.
VolumeToLatticeParamModifier() - Constructor for class magpie.data.utilities.modifiers.VolumeToLatticeParamModifier

W

WekaAttributeSelector - Class in magpie.attributes.selectors: Encapsulates Weka's ASSearch routines for attribute selection.
WekaAttributeSelector() - Constructor for class magpie.attributes.selectors.WekaAttributeSelector: Generates a WekaAttributeSelector with default methods
WekaClassifier - Class in magpie.models.classification: Classifier that uses algorithms from Weka.
WekaClassifier(String, String[]) - Constructor for class magpie.models.classification.WekaClassifier: Create a Weka model with a specified model and options
WekaClassifier() - Constructor for class magpie.models.classification.WekaClassifier: Create a WekaClassifier using a "rules.ZeroR" model
WekaClusterer - Class in magpie.cluster: Use Weka to cluster data.
WekaClusterer() - Constructor for class magpie.cluster.WekaClusterer
WekaModel - Interface in magpie.models.interfaces: Operations that a Weka-based model must implement.
WekaRegression - Class in magpie.models.regression: Implementation of WekaModel for regression purposes.
WekaRegression(String, String[]) - Constructor for class magpie.models.regression.WekaRegression: Create a Weka model with a specified model and options
WekaRegression() - Constructor for class magpie.models.regression.WekaRegression: Create a WekaRegression model based on the "rules.ZeroR" algorithm
WekaUtility - Class in magpie.utility: Holds static methods useful for Weka-based models/clusterers.
WekaUtility() - Constructor for class magpie.utility.WekaUtility
willNormalizeAttributes() - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
willNormalizeClass() - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
Workspace - Variable in class magpie.user.CommandHandler: Keep track of which variables have been created
Workspace - Class in magpie.user: Keeps track of variables produced by user interface.
Workspace() - Constructor for class magpie.user.Workspace: Create a Workspace with an empty variable list
writeDataset(Dataset, String) - Method in class magpie.data.utilities.output.BaseDatasetOutput: Write a dataset to disk
writeDataset(Dataset, File) - Method in class magpie.data.utilities.output.BaseDatasetOutput: Write dataset to disk
writeDataset(Dataset, OutputStream) - Method in class magpie.data.utilities.output.BaseDatasetOutput: Write a dataset to a output stream.
writeDataset(OutputStream) - Method in class magpie.user.server.ModelPackage: Write the dataset out via serialization
writeEntries(Dataset, OutputStream) - Method in class magpie.utility.tools.BatchAttributeGenerator: Write entries to output stream
writeModel(OutputStream) - Method in class magpie.models.classification.ScikitLearnClassifier: Write model to output stream
writeModel(OutputStream) - Method in interface magpie.models.interfaces.ExternalModel: Write model to an output stream
writeModel(OutputStream) - Method in class magpie.models.regression.ScikitLearnRegression: Write model to output stream
writeModel(OutputStream) - Method in class magpie.user.server.ModelPackage: Write the model out via serialization
writePOSCARs(String) - Method in class magpie.data.materials.CrystalStructureDataset: Save dataset as a directory full of POSCARs.

Y

YangOmegaAttributeGenerator - Class in magpie.attributes.generators.composition: Compute the Ω and δ parameters developed by Yang and Zhang.
YangOmegaAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.YangOmegaAttributeGenerator

Z

ZScoreNormalizer - Class in magpie.data.utilities.normalizers: Scale variables by calculating their Z scores.
ZScoreNormalizer() - Constructor for class magpie.data.utilities.normalizers.ZScoreNormalizer
ZScoreOutlierFilter - Class in magpie.data.utilities.filters: Remove entries that are outliers based on Z-score.
ZScoreOutlierFilter() - Constructor for class magpie.data.utilities.filters.ZScoreOutlierFilter

A B C D E F G H I J K L M N O P Q R S T U V W Y Z