Package index

Supervised learning

High-level functionality for training supervised Bayesian tree ensembles (BART, XBART)

bart()

Run BART for supervised learning

predict(<bartmodel>)

Predict from a BART model

print(<bartmodel>)

Print summary of BART model

summary(<bartmodel>)

Summarize BART model fit and parameters

plot(<bartmodel>)

Plot BART model fit

extractParameter(<bartmodel>)

Extract BART parameter samples

getRandomEffectSamples(<bartmodel>)

Extract random effects samples from BART model

computeBARTPosteriorInterval()

Compute BART posterior credible intervals

computeContrastBARTModel()

Compute contrast for BART model

sampleBARTPosteriorPredictive()

Sample BART posterior predictive

saveBARTModelToJson() saveBARTModelToJsonFile() saveBARTModelToJsonString() createBARTModelFromJson() createBARTModelFromJsonFile() createBARTModelFromJsonString() createBARTModelFromCombinedJson() createBARTModelFromCombinedJsonString()

BART Serialization Routines

Causal inference

High-level functionality for estimating causal effects using Bayesian tree ensembles (BCF, XBCF)

bcf()

Run BCF for causal effect estimation

predict(<bcfmodel>)

Predict from BCF model

print(<bcfmodel>)

Print summary of BCF model

summary(<bcfmodel>)

Summarize BCF model

plot(<bcfmodel>)

Plot BCF model

extractParameter(<bcfmodel>)

Extract BCF parameter samples

getRandomEffectSamples(<bcfmodel>)

Extract random effect samples from BCF model

computeBCFPosteriorInterval()

Compute BCF posterior credible intervals

computeContrastBCFModel()

Compute contrast for BCF model

sampleBCFPosteriorPredictive()

Sample BCF posterior predictive

saveBCFModelToJson() saveBCFModelToJsonFile() saveBCFModelToJsonString() createBCFModelFromJson() createBCFModelFromJsonFile() createBCFModelFromJsonString() createBCFModelFromCombinedJson() createBCFModelFromCombinedJsonString()

BCF Serialization Routines

Low-level functionality

Serialization

Classes and functions for converting sampling artifacts to JSON and saving to disk

CppJson

JSON C++ Object Wrapper

createCppJson() createCppJsonFile() createCppJsonString()

JSON Creation Routines

loadForestContainerJson() loadForestContainerCombinedJson() loadForestContainerCombinedJsonString()

Forest Container Serialization Routines

loadVectorJson()

Load vector from JSON

loadScalarJson()

Load scalar from JSON

loadRandomEffectSamplesJson() loadRandomEffectSamplesCombinedJson() loadRandomEffectSamplesCombinedJsonString()

Random Effects Container Serialization Routines

Data

Classes and functions for preparing data for sampling algorithms

ForestDataset

Forest Dataset C++ Wrapper

createForestDataset()

Create ForestDataset object

Outcome

Outcome Data C++ Wrapper

createOutcome()

Create outcome object

RandomEffectsDataset

Random Effects Dataset C++ Wrapper

createRandomEffectsDataset()

Create RandomEffectsDataset object

preprocessTrainData() preprocessPredictionData() savePreprocessorToJson() savePreprocessorToJsonString() createPreprocessorFromJson() createPreprocessorFromJsonString()

Data Preprocessing Routines

Forest

Classes and functions for constructing and persisting forests

Forest

Forest C++ Wrapper

createForest()

Create forest object

ForestModel

Forest Model C++ Wrapper

createForestModel()

Create ForestModel object

ForestSamples

Forest Container C++ Wrapper

createForestSamples()

Create ForestSamples object

print(<ForestSamples>)

Summarize a ForestSamples object

ForestModelConfig

Forest Model Configuration Object

createForestModelConfig()

Create ForestModelConfig object

GlobalModelConfig

Global Model Configuration Object

createGlobalModelConfig()

Create GlobalModelConfig object

CppRNG

Random Number Generator C++ Wrapper

createCppRNG()

Create CppRNG object

calibrateInverseGammaErrorVariance()

Calibrate inverse gamma prior

computeForestLeafIndices() computeForestLeafVariances() computeForestMaxLeafIndex()

Forest Kernel Computation Routines

resetActiveForest() resetForestModel()

Forest State Management Routines

Random Effects

Classes and functions for constructing and persisting random effects terms

RandomEffectSamples

Random Effect Container C++ Wrapper

createRandomEffectSamples()

Create RandomEffectSamples object

print(<RandomEffectSamples>)

Summarize a RandomEffectSamples object

RandomEffectsModel

Random Effects Model C++ Wrapper

createRandomEffectsModel()

Create RandomEffectsModel object

RandomEffectsTracker

Random Effects Tracker C++ Wrapper

createRandomEffectsTracker()

Create RandomEffectsTracker object

getRandomEffectSamples()

Extract random effect samples generic function

sampleGlobalErrorVarianceOneIteration()

Sample global error variance

sampleLeafVarianceOneIteration()

Sample leaf scale

resetRandomEffectsModel() resetRandomEffectsTracker() rootResetRandomEffectsModel() rootResetRandomEffectsTracker()

Random Effects State Management Routines

Utilities

Miscellaneous “utility” classes and functions

OutcomeModel()

Create a new outcome model object

sample_without_replacement()

Sample without replacement

extractParameter()

Extract parameter samples generic function

Package info

High-level package details

stochtree stochtree-package

stochtree: Stochastic Tree Ensembles (XBART and BART) for Supervised Learning and Causal Inference