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<!DOCTYPE HTML>
<html lang="en">
<head>
<!-- Generated by javadoc (25) on Mon Jan 12 19:25:19 EST 2026 -->
<title>Index</title>
<meta name="viewport" content="width=device-width, initial-scale=1">
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<h1>Index</h1>
</div>
<a href="#I:A">A</a> <a href="#I:B">B</a> <a href="#I:C">C</a> <a href="#I:D">D</a> <a href="#I:E">E</a> <a href="#I:F">F</a> <a href="#I:G">G</a> <a href="#I:H">H</a> <a href="#I:I">I</a> <a href="#I:J">J</a> <a href="#I:L">L</a> <a href="#I:M">M</a> <a href="#I:N">N</a> <a href="#I:O">O</a> <a href="#I:P">P</a> <a href="#I:R">R</a> <a href="#I:S">S</a> <a href="#I:T">T</a> <a href="#I:U">U</a> <a href="#I:V">V</a> <a href="#I:W">W</a> <a href="#I:X">X</a> <a href="#I:Y">Y</a> <br><a href="allclasses-index.html">All Classes and Interfaces</a><span class="vertical-separator">|</span><a href="allpackages-index.html">All Packages</a><span class="vertical-separator">|</span><a href="constant-values.html">Constant Field Values</a><span class="vertical-separator">|</span><a href="serialized-form.html">Serialized Form</a>
<h2 class="title" id="I:A">A</h2>
<dl class="index">
<dt><a href="OpenSourceExtensions/MersenneTwisterFast.html#about-the-mersenne-twister-heading" class="search-tag-link">About the Mersenne Twister</a> - Section in class OpenSourceExtensions.MersenneTwisterFast</dt>
<dd> </dd>
<dt><a href="OpenSourceExtensions/MersenneTwisterFast.html#about-this-version-heading" class="search-tag-link">About this Version</a> - Section in class OpenSourceExtensions.MersenneTwisterFast</dt>
<dd> </dd>
<dt><a href="bartMachine/TreeIllustration.ImageFileFilter.html#accept(java.io.File,java.lang.String)" class="member-name-link">accept(File, String)</a> - Method in class bartMachine.<a href="bartMachine/TreeIllustration.ImageFileFilter.html" title="class in bartMachine">TreeIllustration.ImageFileFilter</a></dt>
<dd>
<div class="block">Given a file, returns true if it is an image</div>
</dd>
<dt><a href="bartMachine/bartMachine_a_base.html#accept_reject_mh" class="member-name-link">accept_reject_mh</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_a_base.html" title="class in bartMachine">bartMachine_a_base</a></dt>
<dd>
<div class="block">a record of whether each Gibbs sample accepted or rejected the MH step within each of the <code>num_trees</code> trees</div>
</dd>
<dt><a href="bartMachine/bartMachine_a_base.html#accept_reject_mh_steps" class="member-name-link">accept_reject_mh_steps</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_a_base.html" title="class in bartMachine">bartMachine_a_base</a></dt>
<dd>
<div class="block">a record of the proposal of each Gibbs sample within each of the <code>m</code> trees: G, P or C for "grow", "prune", "change"</div>
</dd>
<dt><a href="OpenSourceExtensions/TDoubleHashSetAndArray.html#add(double)" class="member-name-link">add(double)</a> - Method in class OpenSourceExtensions.<a href="OpenSourceExtensions/TDoubleHashSetAndArray.html" title="class in OpenSourceExtensions">TDoubleHashSetAndArray</a></dt>
<dd> </dd>
<dt><a href="bartMachine/Tools.html#add_arrays(double%5B%5D,double%5B%5D)" class="member-name-link">add_arrays(double[], double[])</a> - Static method in class bartMachine.<a href="bartMachine/Tools.html" title="class in bartMachine">Tools</a></dt>
<dd>
<div class="block">Adds one array to another</div>
</dd>
<dt><a href="bartMachine/Tools.html#add_arrays(double%5B%5D,int%5B%5D)" class="member-name-link">add_arrays(double[], int[])</a> - Static method in class bartMachine.<a href="bartMachine/Tools.html" title="class in bartMachine">Tools</a></dt>
<dd>
<div class="block">Adds one array to another</div>
</dd>
<dt><a href="bartMachine/Tools.html#add_arrays(int%5B%5D,int%5B%5D)" class="member-name-link">add_arrays(int[], int[])</a> - Static method in class bartMachine.<a href="bartMachine/Tools.html" title="class in bartMachine">Tools</a></dt>
<dd>
<div class="block">Adds one array to another</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#addInteractionConstraint(int,int%5B%5D)" class="member-name-link">addInteractionConstraint(int, int[])</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd> </dd>
<dt><a href="bartMachine/TreeArrayIllustration.html#addLikelihood(double)" class="member-name-link">addLikelihood(double)</a> - Method in class bartMachine.<a href="bartMachine/TreeArrayIllustration.html" title="class in bartMachine">TreeArrayIllustration</a></dt>
<dd> </dd>
<dt><a href="bartMachine/Classifier.html#addTrainingDataRow(java.lang.String%5B%5D)" class="member-name-link">addTrainingDataRow(String[])</a> - Method in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">Adds an observation / record to the training data array.</div>
</dd>
<dt><a href="bartMachine/TreeArrayIllustration.html#AddTree(bartMachine.bartMachineTreeNode)" class="member-name-link">AddTree(bartMachineTreeNode)</a> - Method in class bartMachine.<a href="bartMachine/TreeArrayIllustration.html" title="class in bartMachine">TreeArrayIllustration</a></dt>
<dd> </dd>
<dt><a href="AlgorithmTesting/package-summary.html">AlgorithmTesting</a> - package AlgorithmTesting</dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#alpha" class="member-name-link">alpha</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd>
<div class="block">A hyperparameter that controls how easy it is to grow new nodes in a tree independent of depth</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#alpha" class="member-name-link">alpha</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">A hyperparameter that controls how easy it is to grow new nodes in a tree independent of depth</div>
</dd>
<dt><a href="bartMachine/bartMachine_e_gibbs_base.html#assignLeafValsBySamplingFromPosteriorMeanAndSigsqAndUpdateYhats(bartMachine.bartMachineTreeNode,double)" class="member-name-link">assignLeafValsBySamplingFromPosteriorMeanAndSigsqAndUpdateYhats(bartMachineTreeNode, double)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_e_gibbs_base.html" title="class in bartMachine">bartMachine_e_gibbs_base</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_f_gibbs_internal.html#assignLeafValsBySamplingFromPosteriorMeanAndSigsqAndUpdateYhats(bartMachine.bartMachineTreeNode,double)" class="member-name-link">assignLeafValsBySamplingFromPosteriorMeanAndSigsqAndUpdateYhats(bartMachineTreeNode, double)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_f_gibbs_internal.html" title="class in bartMachine">bartMachine_f_gibbs_internal</a></dt>
<dd>
<div class="block">Assigns a value to this terminal node; the value is the prediction at this corner of X space.</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#attributeSplitCounts()" class="member-name-link">attributeSplitCounts()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">A wrapper to find the attributes used</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#attributeSplitCountsInner(int%5B%5D)" class="member-name-link">attributeSplitCountsInner(int[])</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#avg_response_untransformed()" class="member-name-link">avg_response_untransformed()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Find the average repsonse in this node and then transform it back to the original response scale</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#avgResponse()" class="member-name-link">avgResponse()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">The sample average response value at this node</div>
</dd>
</dl>
<h2 class="title" id="I:B">B</h2>
<dl class="index">
<dt><a href="bartMachine/bartMachineTreeNode.html#BAD_FLAG_double" class="member-name-link">BAD_FLAG_double</a> - Static variable in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">a flag that represents an invalid double value</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#BAD_FLAG_int" class="member-name-link">BAD_FLAG_int</a> - Static variable in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">a flag that represents an invalid integer value</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#bart_gibbs_chain_threads" class="member-name-link">bart_gibbs_chain_threads</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">the collection of <code>num_cores</code> BART models which will run separate Gibbs chains</div>
</dd>
<dt><a href="bartMachine/package-summary.html">bartMachine</a> - package bartMachine</dt>
<dd>
<div class="block">The code for the implementation of the BART algorithm as described in detail in:
See Kapelner, A and Bleich, J.</div>
</dd>
<dt><a href="bartMachine/bartMachine_a_base.html" class="type-name-link" title="class in bartMachine">bartMachine_a_base</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">The base class for any BART implementation.</div>
</dd>
<dt><a href="bartMachine/bartMachine_a_base.html#%3Cinit%3E()" class="member-name-link">bartMachine_a_base()</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachine_a_base.html" title="class in bartMachine">bartMachine_a_base</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html" class="type-name-link" title="class in bartMachine">bartMachine_b_hyperparams</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">This portion of the code controls hyperparameters for the BART
algorithm as well as properties and transformations of the response variable.</div>
</dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#%3Cinit%3E()" class="member-name-link">bartMachine_b_hyperparams()</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_c_debug.html" class="type-name-link" title="class in bartMachine">bartMachine_c_debug</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">This portion of the code used to have many debug functions.</div>
</dd>
<dt><a href="bartMachine/bartMachine_c_debug.html#%3Cinit%3E()" class="member-name-link">bartMachine_c_debug()</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachine_c_debug.html" title="class in bartMachine">bartMachine_c_debug</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_d_init.html" class="type-name-link" title="class in bartMachine">bartMachine_d_init</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">This portion of the code initializes the Gibbs sampler</div>
</dd>
<dt><a href="bartMachine/bartMachine_d_init.html#%3Cinit%3E()" class="member-name-link">bartMachine_d_init()</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachine_d_init.html" title="class in bartMachine">bartMachine_d_init</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_e_gibbs_base.html" class="type-name-link" title="class in bartMachine">bartMachine_e_gibbs_base</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">This portion of the code performs everything in
the Gibbs sampling except for the posterior sampling itself</div>
</dd>
<dt><a href="bartMachine/bartMachine_e_gibbs_base.html#%3Cinit%3E()" class="member-name-link">bartMachine_e_gibbs_base()</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachine_e_gibbs_base.html" title="class in bartMachine">bartMachine_e_gibbs_base</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_f_gibbs_internal.html" class="type-name-link" title="class in bartMachine">bartMachine_f_gibbs_internal</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">This portion of the code that performs the posterior sampling
in the Gibbs sampler except for the Metropolis-Hastings tree search step</div>
</dd>
<dt><a href="bartMachine/bartMachine_f_gibbs_internal.html#%3Cinit%3E()" class="member-name-link">bartMachine_f_gibbs_internal()</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachine_f_gibbs_internal.html" title="class in bartMachine">bartMachine_f_gibbs_internal</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_g_mh.html" class="type-name-link" title="class in bartMachine">bartMachine_g_mh</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">This portion of the code performs the Metropolis-Hastings tree search step</div>
</dd>
<dt><a href="bartMachine/bartMachine_g_mh.html#%3Cinit%3E()" class="member-name-link">bartMachine_g_mh()</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachine_g_mh.html" title="class in bartMachine">bartMachine_g_mh</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_g_mh.Steps.html" class="type-name-link" title="enum class in bartMachine">bartMachine_g_mh.Steps</a> - Enum Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">the types of steps in the Metropolis-Hastings tree search</div>
</dd>
<dt><a href="bartMachine/bartMachine_h_eval.html" class="type-name-link" title="class in bartMachine">bartMachine_h_eval</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">This portion of the code performs the evaluation / prediction on the BART model</div>
</dd>
<dt><a href="bartMachine/bartMachine_h_eval.html#%3Cinit%3E()" class="member-name-link">bartMachine_h_eval()</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachine_h_eval.html" title="class in bartMachine">bartMachine_h_eval</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_i_prior_cov_spec.html" class="type-name-link" title="class in bartMachine">bartMachine_i_prior_cov_spec</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">This portion of the code implements the informed prior information on covariates feature.</div>
</dd>
<dt><a href="bartMachine/bartMachine_i_prior_cov_spec.html#%3Cinit%3E()" class="member-name-link">bartMachine_i_prior_cov_spec()</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachine_i_prior_cov_spec.html" title="class in bartMachine">bartMachine_i_prior_cov_spec</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineClassification.html" class="type-name-link" title="class in bartMachine">bartMachineClassification</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">The class that is instantiated to build a binary classification BART model</div>
</dd>
<dt><a href="bartMachine/bartMachineClassification.html#%3Cinit%3E()" class="member-name-link">bartMachineClassification()</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachineClassification.html" title="class in bartMachine">bartMachineClassification</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineClassificationMultThread.html" class="type-name-link" title="class in bartMachine">bartMachineClassificationMultThread</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">This class handles the parallelization of many Gibbs chains over many CPU cores
to create one BART regression model.</div>
</dd>
<dt><a href="bartMachine/bartMachineClassificationMultThread.html#%3Cinit%3E()" class="member-name-link">bartMachineClassificationMultThread()</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachineClassificationMultThread.html" title="class in bartMachine">bartMachineClassificationMultThread</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineRegression.html" class="type-name-link" title="class in bartMachine">bartMachineRegression</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">The class that is instantiated to build a Regression BART model</div>
</dd>
<dt><a href="bartMachine/bartMachineRegression.html#%3Cinit%3E()" class="member-name-link">bartMachineRegression()</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachineRegression.html" title="class in bartMachine">bartMachineRegression</a></dt>
<dd>
<div class="block">Constructs the BART classifier for regression.</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html" class="type-name-link" title="class in bartMachine">bartMachineRegressionMultThread</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">This class handles the parallelization of many Gibbs chains over many CPU cores
to create one BART regression model.</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#%3Cinit%3E()" class="member-name-link">bartMachineRegressionMultThread()</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">the default constructor sets the number of total iterations each Gibbs chain is charged with sampling</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html" class="type-name-link" title="class in bartMachine">bartMachineTreeNode</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">The class that stores all the information in one node of the BART trees</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#%3Cinit%3E()" class="member-name-link">bartMachineTreeNode()</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#%3Cinit%3E(bartMachine.bartMachine_b_hyperparams)" class="member-name-link">bartMachineTreeNode(bartMachine_b_hyperparams)</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Creates a new node</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#%3Cinit%3E(bartMachine.bartMachineTreeNode)" class="member-name-link">bartMachineTreeNode(bartMachineTreeNode)</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Creates a new node</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#%3Cinit%3E(bartMachine.bartMachineTreeNode,bartMachine.bartMachine_b_hyperparams)" class="member-name-link">bartMachineTreeNode(bartMachineTreeNode, bartMachine_b_hyperparams)</a> - Constructor for class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Creates a new node</div>
</dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#beta" class="member-name-link">beta</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd>
<div class="block">A hyperparameter that controls how easy it is to grow new nodes in a tree dependent on depth which makes it more difficult as the tree gets deeper</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#beta" class="member-name-link">beta</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">A hyperparameter that controls how easy it is to grow new nodes in a tree dependent on depth which makes it more difficult as the tree gets deeper</div>
</dd>
<dt><a href="bartMachine/Tools.html#binary_add_arrays(int%5B%5D,int%5B%5D)" class="member-name-link">binary_add_arrays(int[], int[])</a> - Static method in class bartMachine.<a href="bartMachine/Tools.html" title="class in bartMachine">Tools</a></dt>
<dd>
<div class="block">Adds one array to another after first converting each addend to binary
(1 if the value > 0, 0 otherwise)</div>
</dd>
<dt><a href="bartMachine/bartMachine_e_gibbs_base.html#Build()" class="member-name-link">Build()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_e_gibbs_base.html" title="class in bartMachine">bartMachine_e_gibbs_base</a></dt>
<dd>
<div class="block">Builds a BART model by unleashing the Gibbs sampler</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#Build()" class="member-name-link">Build()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">This function actually initiates the Gibbs sampling to build all the BART models</div>
</dd>
<dt><a href="bartMachine/Classifier.html#Build()" class="member-name-link">Build()</a> - Method in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">build the machine learning classifier (implemented by a daughter class), you must <a href="bartMachine/Classifier.html#setData(java.util.ArrayList)"><code>set the data</code></a> first</div>
</dd>
</dl>
<h2 class="title" id="I:C">C</h2>
<dl class="index">
<dt><a href="bartMachine/bartMachine_f_gibbs_internal.html#calcLeafPosteriorMean(bartMachine.bartMachineTreeNode,double,double)" class="member-name-link">calcLeafPosteriorMean(bartMachineTreeNode, double, double)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_f_gibbs_internal.html" title="class in bartMachine">bartMachine_f_gibbs_internal</a></dt>
<dd>
<div class="block">Calculate the posterior mean of the prediction distribution at a certain node</div>
</dd>
<dt><a href="bartMachine/bartMachine_f_gibbs_internal.html#calcLeafPosteriorVar(bartMachine.bartMachineTreeNode,double)" class="member-name-link">calcLeafPosteriorVar(bartMachineTreeNode, double)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_f_gibbs_internal.html" title="class in bartMachine">bartMachine_f_gibbs_internal</a></dt>
<dd>
<div class="block">Calculate the posterior variance of the prediction distribution at a certain node</div>
</dd>
<dt><a href="bartMachine/bartMachine_g_mh.html#calcLnLikRatioGrow(bartMachine.bartMachineTreeNode)" class="member-name-link">calcLnLikRatioGrow(bartMachineTreeNode)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_g_mh.html" title="class in bartMachine">bartMachine_g_mh</a></dt>
<dd>
<div class="block">Calculates the log of the likelihood ratio for a grow step</div>
</dd>
<dt><a href="bartMachine/bartMachine_g_mh.html#calcLnTransRatioGrow(bartMachine.bartMachineTreeNode,bartMachine.bartMachineTreeNode,bartMachine.bartMachineTreeNode)" class="member-name-link">calcLnTransRatioGrow(bartMachineTreeNode, bartMachineTreeNode, bartMachineTreeNode)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_g_mh.html" title="class in bartMachine">bartMachine_g_mh</a></dt>
<dd>
<div class="block">Calculates the log transition ratio for a grow step</div>
</dd>
<dt><a href="bartMachine/bartMachine_g_mh.html#calcLnTransRatioPrune(bartMachine.bartMachineTreeNode,bartMachine.bartMachineTreeNode,bartMachine.bartMachineTreeNode)" class="member-name-link">calcLnTransRatioPrune(bartMachineTreeNode, bartMachineTreeNode, bartMachineTreeNode)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_g_mh.html" title="class in bartMachine">bartMachine_g_mh</a></dt>
<dd>
<div class="block">This calculates the log transition ratio for the prune step.</div>
</dd>
<dt><a href="bartMachine/bartMachine_g_mh.html#calcLnTreeStructureRatioGrow(bartMachine.bartMachineTreeNode)" class="member-name-link">calcLnTreeStructureRatioGrow(bartMachineTreeNode)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_g_mh.html" title="class in bartMachine">bartMachine_g_mh</a></dt>
<dd>
<div class="block">Calculates the log transition ratio for a grow step</div>
</dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#calculateHyperparameters()" class="member-name-link">calculateHyperparameters()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd>
<div class="block">Computes <code>hyper_sigsq_mu</code> and <code>hyper_lambda</code>.</div>
</dd>
<dt><a href="bartMachine/bartMachineClassification.html#calculateHyperparameters()" class="member-name-link">calculateHyperparameters()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineClassification.html" title="class in bartMachine">bartMachineClassification</a></dt>
<dd>
<div class="block">Calculates the hyperparameters needed for binary classifcation BART.</div>
</dd>
<dt><a href="bartMachine/Classifier.html#calculateInSampleLoss(bartMachine.Classifier.ErrorTypes,int)" class="member-name-link">calculateInSampleLoss(Classifier.ErrorTypes, int)</a> - Method in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">Calculates the in-sample error based on a specified error metric</div>
</dd>
<dt><a href="bartMachine/bartMachine_g_mh.Steps.html#CHANGE" class="member-name-link">CHANGE</a> - Enum constant in enum class bartMachine.<a href="bartMachine/bartMachine_g_mh.Steps.html" title="enum class in bartMachine">bartMachine_g_mh.Steps</a></dt>
<dd> </dd>
<dt><a href="bartMachine/Classifier.html" class="type-name-link" title="class in bartMachine">Classifier</a> - Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">The base class for all machine learning / statistical-learning
algorithms.</div>
</dd>
<dt><a href="bartMachine/Classifier.html#%3Cinit%3E()" class="member-name-link">Classifier()</a> - Constructor for class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">A dummy constructor which keeps <code>Serializable</code> happy</div>
</dd>
<dt><a href="bartMachine/Classifier.ErrorTypes.html" class="type-name-link" title="enum class in bartMachine">Classifier.ErrorTypes</a> - Enum Class in <a href="bartMachine/package-summary.html">bartMachine</a></dt>
<dd>
<div class="block">a variable that represents the different error calculation types</div>
</dd>
<dt><a href="OpenSourceExtensions/MersenneTwisterFast.html#clearGaussian()" class="member-name-link">clearGaussian()</a> - Method in class OpenSourceExtensions.<a href="OpenSourceExtensions/MersenneTwisterFast.html" title="class in OpenSourceExtensions">MersenneTwisterFast</a></dt>
<dd>
<div class="block">Clears the internal gaussian variable from the RNG.</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#clearRulesAndSplitCache()" class="member-name-link">clearRulesAndSplitCache()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">When <code>mem_cache_for_speed</code> is set in the BART model, running this function will reset the caches for this node's valid predictors and valid split values</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#clone()" class="member-name-link">clone()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Creates a cloned copy of the tree beginning at this node by recursing cloning its children.</div>
</dd>
<dt><a href="bartMachine/Classifier.html#clone()" class="member-name-link">clone()</a> - Method in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd> </dd>
<dt><a href="OpenSourceExtensions/MersenneTwisterFast.html#clone()" class="member-name-link">clone()</a> - Method in class OpenSourceExtensions.<a href="OpenSourceExtensions/MersenneTwisterFast.html" title="class in OpenSourceExtensions">MersenneTwisterFast</a></dt>
<dd> </dd>
<dt><a href="OpenSourceExtensions/UnorderedPair.html#compareTo(OpenSourceExtensions.UnorderedPair)" class="member-name-link">compareTo(UnorderedPair)</a> - Method in record class OpenSourceExtensions.<a href="OpenSourceExtensions/UnorderedPair.html" title="class in OpenSourceExtensions">UnorderedPair</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#ConstructBurnedChainForTreesAndOtherInformation()" class="member-name-link">ConstructBurnedChainForTreesAndOtherInformation()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">Create a post burn-in chain for ease of manipulation later</div>
</dd>
<dt><a href="OpenSourceExtensions/TDoubleHashSetAndArray.html#contains(double)" class="member-name-link">contains(double)</a> - Method in class OpenSourceExtensions.<a href="OpenSourceExtensions/TDoubleHashSetAndArray.html" title="class in OpenSourceExtensions">TDoubleHashSetAndArray</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_i_prior_cov_spec.html#cov_split_prior" class="member-name-link">cov_split_prior</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_i_prior_cov_spec.html" title="class in bartMachine">bartMachine_i_prior_cov_spec</a></dt>
<dd>
<div class="block">This is a probability vector which is the prior on which covariates to split instead of the uniform discrete distribution by default</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#cov_split_prior" class="member-name-link">cov_split_prior</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">The probability vector that samples covariates for selecting split rules</div>
</dd>
<dt><a href="bartMachine/TreeArrayIllustration.html#CreateIllustrationAndSaveImage()" class="member-name-link">CreateIllustrationAndSaveImage()</a> - Method in class bartMachine.<a href="bartMachine/TreeArrayIllustration.html" title="class in bartMachine">TreeArrayIllustration</a></dt>
<dd> </dd>
<dt><a href="CustomLogging/package-summary.html">CustomLogging</a> - package CustomLogging</dt>
<dd>
<div class="block">This is for debugging only, please ignore.</div>
</dd>
</dl>
<h2 class="title" id="I:D">D</h2>
<dl class="index">
<dt><a href="AlgorithmTesting/DataAnalysis.html" class="type-name-link" title="class in AlgorithmTesting">DataAnalysis</a> - Class in <a href="AlgorithmTesting/package-summary.html">AlgorithmTesting</a></dt>
<dd> </dd>
<dt><a href="AlgorithmTesting/DataAnalysis.html#%3Cinit%3E()" class="member-name-link">DataAnalysis()</a> - Constructor for class AlgorithmTesting.<a href="AlgorithmTesting/DataAnalysis.html" title="class in AlgorithmTesting">DataAnalysis</a></dt>
<dd> </dd>
<dt><a href="AlgorithmTesting/DataSetupForCSVFile.html" class="type-name-link" title="class in AlgorithmTesting">DataSetupForCSVFile</a> - Class in <a href="AlgorithmTesting/package-summary.html">AlgorithmTesting</a></dt>
<dd> </dd>
<dt><a href="AlgorithmTesting/DataSetupForCSVFile.html#%3Cinit%3E(java.io.File,boolean)" class="member-name-link">DataSetupForCSVFile(File, boolean)</a> - Constructor for class AlgorithmTesting.<a href="AlgorithmTesting/DataSetupForCSVFile.html" title="class in AlgorithmTesting">DataSetupForCSVFile</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#DEBUG_NODES" class="member-name-link">DEBUG_NODES</a> - Static variable in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Setting this to true will print out debug information at the node level during Gibbs sampling</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#deepestNode()" class="member-name-link">deepestNode()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Find the terminal node at the largest depth from this point in the tree and down</div>
</dd>
<dt><a href="bartMachine/TreeIllustration.html#DeletePreviousTreeIllustrations()" class="member-name-link">DeletePreviousTreeIllustrations()</a> - Static method in class bartMachine.<a href="bartMachine/TreeIllustration.html" title="class in bartMachine">TreeIllustration</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#depth" class="member-name-link">depth</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">the generation of this node from the top node (root note has generation = 0 by definition)</div>
</dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#depth_prior_log_ratio_table" class="member-name-link">depth_prior_log_ratio_table</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd>
<div class="block">A cached table of the depth-dependent part of the tree prior log-ratio</div>
</dd>
<dt><a href="bartMachine/bartMachine_e_gibbs_base.html#DoGibbsSampling()" class="member-name-link">DoGibbsSampling()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_e_gibbs_base.html" title="class in bartMachine">bartMachine_e_gibbs_base</a></dt>
<dd>
<div class="block">Run the Gibbs sampler for the total number of samples prespecified while flushing unneeded memory from the previous sample</div>
</dd>
<dt><a href="bartMachine/bartMachine_g_mh.html#doMHChangeAndCalcLnR(bartMachine.bartMachineTreeNode,bartMachine.bartMachineTreeNode)" class="member-name-link">doMHChangeAndCalcLnR(bartMachineTreeNode, bartMachineTreeNode)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_g_mh.html" title="class in bartMachine">bartMachine_g_mh</a></dt>
<dd>
<div class="block">Perform the change step on a tree and return the log Metropolis-Hastings ratio</div>
</dd>
<dt><a href="bartMachine/bartMachine_g_mh.html#doMHGrowAndCalcLnR(bartMachine.bartMachineTreeNode,bartMachine.bartMachineTreeNode)" class="member-name-link">doMHGrowAndCalcLnR(bartMachineTreeNode, bartMachineTreeNode)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_g_mh.html" title="class in bartMachine">bartMachine_g_mh</a></dt>
<dd>
<div class="block">Perform the grow step on a tree and return the log Metropolis-Hastings ratio</div>
</dd>
<dt><a href="bartMachine/bartMachine_g_mh.html#doMHPruneAndCalcLnR(bartMachine.bartMachineTreeNode,bartMachine.bartMachineTreeNode)" class="member-name-link">doMHPruneAndCalcLnR(bartMachineTreeNode, bartMachineTreeNode)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_g_mh.html" title="class in bartMachine">bartMachine_g_mh</a></dt>
<dd>
<div class="block">Perform the prune step on a tree and return the log Metropolis-Hastings ratio</div>
</dd>
<dt><a href="bartMachine/bartMachine_e_gibbs_base.html#DoOneGibbsSample()" class="member-name-link">DoOneGibbsSample()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_e_gibbs_base.html" title="class in bartMachine">bartMachine_e_gibbs_base</a></dt>
<dd>
<div class="block">Run one Gibbs sample at the current sample number</div>
</dd>
<dt><a href="bartMachine/bartMachineClassification.html#DoOneGibbsSample()" class="member-name-link">DoOneGibbsSample()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineClassification.html" title="class in bartMachine">bartMachineClassification</a></dt>
<dd>
<div class="block">A Gibbs sample for binary classification BART is a little different
than for regression BART.</div>
</dd>
<dt><a href="bartMachine/bartMachine_e_gibbs_base.html#drawSigsqFromPosterior(int,double%5B%5D)" class="member-name-link">drawSigsqFromPosterior(int, double[])</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_e_gibbs_base.html" title="class in bartMachine">bartMachine_e_gibbs_base</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_f_gibbs_internal.html#drawSigsqFromPosterior(int,double%5B%5D)" class="member-name-link">drawSigsqFromPosterior(int, double[])</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_f_gibbs_internal.html" title="class in bartMachine">bartMachine_f_gibbs_internal</a></dt>
<dd>
<div class="block">Draws one variance from the posterior distribution</div>
</dd>
<dt><a href="bartMachine/Classifier.html#dumpDataToFile(java.lang.String)" class="member-name-link">dumpDataToFile(String)</a> - Method in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">Useful for debugging.</div>
</dd>
</dl>
<h2 class="title" id="I:E">E</h2>
<dl class="index">
<dt><a href="OpenSourceExtensions/UnorderedPair.html#equals(java.lang.Object)" class="member-name-link">equals(Object)</a> - Method in record class OpenSourceExtensions.<a href="OpenSourceExtensions/UnorderedPair.html" title="class in OpenSourceExtensions">UnorderedPair</a></dt>
<dd>
<div class="block">Indicates whether some other object is "equal to" this one.</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#Evaluate(double%5B%5D)" class="member-name-link">Evaluate(double[])</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">The default BART evaluation of a new observations is done via sample average of the
posterior predictions.</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#Evaluate(double%5B%5D)" class="member-name-link">Evaluate(double[])</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Evaluate a record recursively accounting for split rules and the presence of missing data</div>
</dd>
<dt><a href="bartMachine/Classifier.html#Evaluate(double%5B%5D)" class="member-name-link">Evaluate(double[])</a> - Method in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">A wrapper for <a href="bartMachine/Classifier.html#Evaluate(double%5B%5D,int)"><code>Classifier.Evaluate(double[], int)</code></a> where one processor core is used</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#Evaluate(double%5B%5D%5B%5D,int)" class="member-name-link">Evaluate(double[][], int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd> </dd>
<dt><a href="bartMachine/Classifier.html#Evaluate(double%5B%5D%5B%5D,int)" class="member-name-link">Evaluate(double[][], int)</a> - Method in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">Evaluate multiple records at once.</div>
</dd>
<dt><a href="bartMachine/bartMachine_h_eval.html#Evaluate(double%5B%5D,int)" class="member-name-link">Evaluate(double[], int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_h_eval.html" title="class in bartMachine">bartMachine_h_eval</a></dt>
<dd>
<div class="block">The default BART evaluation of a new observations is done via sample average of the
posterior predictions.</div>
</dd>
<dt><a href="bartMachine/bartMachineClassificationMultThread.html#Evaluate(double%5B%5D,int)" class="member-name-link">Evaluate(double[], int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineClassificationMultThread.html" title="class in bartMachine">bartMachineClassificationMultThread</a></dt>
<dd>
<div class="block">Predicts the best guess of the class for an observation</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#Evaluate(double%5B%5D,int)" class="member-name-link">Evaluate(double[], int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">The default BART evaluation of a new observations is done via sample average of the
posterior predictions.</div>
</dd>
<dt><a href="bartMachine/Classifier.html#Evaluate(double%5B%5D,int)" class="member-name-link">Evaluate(double[], int)</a> - Method in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">After the classifier has been built, new records can be evaluated / predicted
(implemented by a daughter class)</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#evaluateBatch(double%5B%5D%5B%5D,int%5B%5D,double%5B%5D)" class="member-name-link">evaluateBatch(double[][], int[], double[])</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Legacy support or convenient entry point for evaluateBatch.</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#evaluateBatch(double%5B%5D%5B%5D,int%5B%5D,int,int,double%5B%5D)" class="member-name-link">evaluateBatch(double[][], int[], int, int, double[])</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Evaluate a batch of records and add their predictions to the results array.</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#EvaluateNode(double%5B%5D)" class="member-name-link">EvaluateNode(double[])</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_h_eval.html#EvaluateViaSampAvg(double%5B%5D,int)" class="member-name-link">EvaluateViaSampAvg(double[], int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_h_eval.html" title="class in bartMachine">bartMachine_h_eval</a></dt>
<dd>
<div class="block">Evaluates a new observations via sample average of the posterior predictions.</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#EvaluateViaSampAvg(double%5B%5D,int)" class="member-name-link">EvaluateViaSampAvg(double[], int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">Evaluates a new observations via sample average of the posterior predictions.</div>
</dd>
<dt><a href="bartMachine/bartMachine_h_eval.html#EvaluateViaSampMed(double%5B%5D,int)" class="member-name-link">EvaluateViaSampMed(double[], int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_h_eval.html" title="class in bartMachine">bartMachine_h_eval</a></dt>
<dd>
<div class="block">Evaluates a new observations via sample median of the posterior predictions.</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#EvaluateViaSampMed(double%5B%5D,int)" class="member-name-link">EvaluateViaSampMed(double[], int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">Evaluates a new observations via sample median of the posterior predictions.</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#extractRawNodeInformation(int)" class="member-name-link">extractRawNodeInformation(int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd> </dd>
</dl>
<h2 class="title" id="I:F">F</h2>
<dl class="index">
<dt><a href="bartMachine/Classifier.html#finalizeTrainingData()" class="member-name-link">finalizeTrainingData()</a> - Method in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">This method finalizes the training data after all
records have been added via the method <a href="bartMachine/Classifier.html#addTrainingDataRow(java.lang.String%5B%5D)"><code>Classifier.addTrainingDataRow(String[])</code></a>.</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#findInteractions(java.util.HashSet)" class="member-name-link">findInteractions(HashSet)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">A wrapper to find all interactions recursively by checking all splits underneath this node</div>
</dd>
<dt><a href="bartMachine/StatToolbox.html#FindMaxIndex(int%5B%5D)" class="member-name-link">FindMaxIndex(int[])</a> - Static method in class bartMachine.<a href="bartMachine/StatToolbox.html" title="class in bartMachine">StatToolbox</a></dt>
<dd>
<div class="block">Given an array, return the index of the maximum value</div>
</dd>
<dt><a href="OpenSourceExtensions/UnorderedPair.html#first()" class="member-name-link">first()</a> - Method in record class OpenSourceExtensions.<a href="OpenSourceExtensions/UnorderedPair.html" title="class in OpenSourceExtensions">UnorderedPair</a></dt>
<dd>
<div class="block">Returns the value of the <code>first</code> record component.</div>
</dd>
<dt><a href="bartMachine/bartMachine_d_init.html#fixed_sigsq" class="member-name-link">fixed_sigsq</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_d_init.html" title="class in bartMachine">bartMachine_d_init</a></dt>
<dd>
<div class="block">during debugging, we may want to fix sigsq</div>
</dd>
<dt><a href="CustomLogging/LoggingOutputStream.html#flush()" class="member-name-link">flush()</a> - Method in class CustomLogging.<a href="CustomLogging/LoggingOutputStream.html" title="class in CustomLogging">LoggingOutputStream</a></dt>
<dd>
<div class="block">\* upon flush() write the existing contents of the OutputStream
\* to the logger as a log record.</div>
</dd>
<dt><a href="bartMachine/bartMachine_a_base.html#flush_indices_to_save_ram" class="member-name-link">flush_indices_to_save_ram</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_a_base.html" title="class in bartMachine">bartMachine_a_base</a></dt>
<dd>
<div class="block">saves indices in nodes (useful for computing weights)</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#flush_indices_to_save_ram" class="member-name-link">flush_indices_to_save_ram</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">saves indices in nodes (useful for computing weights)</div>
</dd>
<dt><a href="bartMachine/bartMachine_a_base.html#FlushData()" class="member-name-link">FlushData()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_a_base.html" title="class in bartMachine">bartMachine_a_base</a></dt>
<dd>
<div class="block">Remove unnecessary data from the Gibbs chain to conserve RAM</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#FlushData()" class="member-name-link">FlushData()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">Flush all unnecessary data from the Gibbs chains to conserve RAM</div>
</dd>
<dt><a href="bartMachine/Classifier.html#FlushData()" class="member-name-link">FlushData()</a> - Method in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">deletes all data that's unneeded at this point in runtime in order to save memory</div>
</dd>
<dt><a href="bartMachine/bartMachine_a_base.html#FlushDataForSample(bartMachine.bartMachineTreeNode%5B%5D)" class="member-name-link">FlushDataForSample(bartMachineTreeNode[])</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_a_base.html" title="class in bartMachine">bartMachine_a_base</a></dt>
<dd>
<div class="block">Remove unnecessary data from an individual Gibbs sample</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#flushNodeData()" class="member-name-link">flushNodeData()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Remove all the data in this node and its children recursively to save memory</div>
</dd>
<dt><a href="CustomLogging/SuperSimpleFormatter.html#format(java.util.logging.LogRecord)" class="member-name-link">format(LogRecord)</a> - Method in class CustomLogging.<a href="CustomLogging/SuperSimpleFormatter.html" title="class in CustomLogging">SuperSimpleFormatter</a></dt>
<dd>
<div class="block">Format the given LogRecord.</div>
</dd>
</dl>
<h2 class="title" id="I:G">G</h2>
<dl class="index">
<dt><a href="bartMachine/bartMachine_h_eval.html#get95PctPostPredictiveIntervalForPrediction(double%5B%5D,int)" class="member-name-link">get95PctPostPredictiveIntervalForPrediction(double[], int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_h_eval.html" title="class in bartMachine">bartMachine_h_eval</a></dt>
<dd>
<div class="block">For each sum-of-trees in each psoterior of the Gibbs samples, evaluate / predict these new records by summing over
the prediction for each tree then order these by value and create a 95% uncertainty interval</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#get95PctPostPredictiveIntervalForPrediction(double%5B%5D,int)" class="member-name-link">get95PctPostPredictiveIntervalForPrediction(double[], int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">Using the <a href="bartMachine/bartMachineRegressionMultThread.html#getPostPredictiveIntervalForPrediction(double%5B%5D,double,int)"><code>bartMachineRegressionMultThread.getPostPredictiveIntervalForPrediction(double[], double, int)</code></a> function, return a 95\% credible interval</div>
</dd>
<dt><a href="bartMachine/bartMachine_d_init.html#getAcceptRejectMH()" class="member-name-link">getAcceptRejectMH()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_d_init.html" title="class in bartMachine">bartMachine_d_init</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getAcceptRejectMHsAfterBurnIn(int)" class="member-name-link">getAcceptRejectMHsAfterBurnIn(int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">Returns a record of Metropolis-Hastings acceptances or rejections for all trees after burn-in</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getAcceptRejectMHsBurnin()" class="member-name-link">getAcceptRejectMHsBurnin()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">Returns a record of Metropolis-Hastings acceptances or rejections for all trees during burn-in</div>
</dd>
<dt><a href="OpenSourceExtensions/TDoubleHashSetAndArray.html#getAtIndex(int)" class="member-name-link">getAtIndex(int)</a> - Method in class OpenSourceExtensions.<a href="OpenSourceExtensions/TDoubleHashSetAndArray.html" title="class in OpenSourceExtensions">TDoubleHashSetAndArray</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getAttributeProps(java.lang.String)" class="member-name-link">getAttributeProps(String)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">Return the proportion of times each of the attributes were used (count over total number of splits)
during the construction of the sum-of-trees by Gibbs sample.</div>
</dd>
<dt><a href="bartMachine/TreeIllustration.html#getCanvas()" class="member-name-link">getCanvas()</a> - Method in class bartMachine.<a href="bartMachine/TreeIllustration.html" title="class in bartMachine">TreeIllustration</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getCountsForAllAttribute(java.lang.String)" class="member-name-link">getCountsForAllAttribute(String)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">Return the number of times each of the attributes were used during the construction of the sum-of-trees
by Gibbs sample.</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getCredibleIntervalsForPrediction(double%5B%5D%5B%5D,double,int)" class="member-name-link">getCredibleIntervalsForPrediction(double[][], double, int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">Return credible interval bounds for each record.</div>
</dd>
<dt><a href="bartMachine/bartMachine_c_debug.html#getDepthsForTrees(int,int)" class="member-name-link">getDepthsForTrees(int, int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_c_debug.html" title="class in bartMachine">bartMachine_c_debug</a></dt>
<dd>
<div class="block">Queries the depths of the <code>num_trees</code> trees between a range of Gibbs samples</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getDepthsForTreesInGibbsSampAfterBurnIn(int)" class="member-name-link">getDepthsForTreesInGibbsSampAfterBurnIn(int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">After burn in, find the depth (greatest generation of a terminal node) of each tree for each Gibbs sample</div>
</dd>
<dt><a href="OpenSourceExtensions/UnorderedPair.html#getFirst()" class="member-name-link">getFirst()</a> - Method in record class OpenSourceExtensions.<a href="OpenSourceExtensions/UnorderedPair.html" title="class in OpenSourceExtensions">UnorderedPair</a></dt>
<dd>
<div class="block">Gets the smallest element of the pair (according to its <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Comparable.html" title="class or interface in java.lang" class="external-link"><code>Comparable</code></a> implementation).</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#getGeneration()" class="member-name-link">getGeneration()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineClassificationMultThread.html#getGibbsSamplesForPrediction(double%5B%5D%5B%5D,int)" class="member-name-link">getGibbsSamplesForPrediction(double[][], int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineClassificationMultThread.html" title="class in bartMachine">bartMachineClassificationMultThread</a></dt>
<dd>
<div class="block">This returns the Gibbs sample predictions for all trees and all posterior samples.</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getGibbsSamplesForPrediction(double%5B%5D%5B%5D,int)" class="member-name-link">getGibbsSamplesForPrediction(double[][], int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">Return the predictions from each tree for each burned-in Gibbs sample</div>
</dd>
<dt><a href="bartMachine/bartMachine_h_eval.html#getGibbsSamplesForPrediction(double%5B%5D,int)" class="member-name-link">getGibbsSamplesForPrediction(double[], int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_h_eval.html" title="class in bartMachine">bartMachine_h_eval</a></dt>
<dd>
<div class="block">For each sum-of-trees in each psoterior of the Gibbs samples, evaluate / predict these new records by summing over
the prediction for each tree</div>
</dd>
<dt><a href="bartMachine/bartMachine_c_debug.html#getGibbsSamplesSigsqs()" class="member-name-link">getGibbsSamplesSigsqs()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_c_debug.html" title="class in bartMachine">bartMachine_c_debug</a></dt>
<dd>
<div class="block">Get the untransformed samples of the sigsqs from the Gibbs chaing</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getGibbsSamplesSigsqs()" class="member-name-link">getGibbsSamplesSigsqs()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#getHyper_lambda()" class="member-name-link">getHyper_lambda()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#getHyper_mu_mu()" class="member-name-link">getHyper_mu_mu()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#getHyper_nu()" class="member-name-link">getHyper_nu()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#getHyper_sigsq_mu()" class="member-name-link">getHyper_sigsq_mu()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getInteractionCounts()" class="member-name-link">getInteractionCounts()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">For all Gibbs samples after burn in, calculate the set of interaction counts (consider a split on x_j
and a daughter node splits on x_k and that would be considered an "interaction")</div>
</dd>
<dt><a href="OpenSourceExtensions/StatUtil.html#getInvCDF(double)" class="member-name-link">getInvCDF(double)</a> - Static method in class OpenSourceExtensions.<a href="OpenSourceExtensions/StatUtil.html" title="class in OpenSourceExtensions">StatUtil</a></dt>
<dd> </dd>
<dt><a href="AlgorithmTesting/DataSetupForCSVFile.html#getK()" class="member-name-link">getK()</a> - Method in class AlgorithmTesting.<a href="AlgorithmTesting/DataSetupForCSVFile.html" title="class in AlgorithmTesting">DataSetupForCSVFile</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#getLeft()" class="member-name-link">getLeft()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd> </dd>
<dt><a href="bartMachine/Classifier.html#getN()" class="member-name-link">getN()</a> - Method in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">How many observations are in the training data set?</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getNodePredictionTrainingIndicies(double%5B%5D%5B%5D)" class="member-name-link">getNodePredictionTrainingIndicies(double[][])</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_c_debug.html#getNumNodesAndLeavesForTrees(int,int)" class="member-name-link">getNumNodesAndLeavesForTrees(int, int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_c_debug.html" title="class in bartMachine">bartMachine_c_debug</a></dt>
<dd>
<div class="block">Queries the number of nodes (terminal and non-terminal) in the <code>num_trees</code> trees between a range of Gibbs samples</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getNumNodesAndLeavesForTreesInGibbsSampAfterBurnIn(int)" class="member-name-link">getNumNodesAndLeavesForTreesInGibbsSampAfterBurnIn(int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">After burn in, return the number of total nodes (internal plus terminal) of each tree for each Gibbs sample</div>
</dd>
<dt><a href="bartMachine/Classifier.html#getP()" class="member-name-link">getP()</a> - Method in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">How many features are in the training data set?</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getPosteriorMeanForPrediction(double%5B%5D%5B%5D,int)" class="member-name-link">getPosteriorMeanForPrediction(double[][], int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">Return posterior mean predictions for each record without storing all Gibbs samples.</div>
</dd>
<dt><a href="bartMachine/bartMachine_h_eval.html#getPostPredictiveIntervalForPrediction(double%5B%5D,double,int)" class="member-name-link">getPostPredictiveIntervalForPrediction(double[], double, int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_h_eval.html" title="class in bartMachine">bartMachine_h_eval</a></dt>
<dd>
<div class="block">For each sum-of-trees in each psoterior of the Gibbs samples, evaluate / predict these new records by summing over
the prediction for each tree then order these by value and create an uncertainty interval</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getPostPredictiveIntervalForPrediction(double%5B%5D,double,int)" class="member-name-link">getPostPredictiveIntervalForPrediction(double[], double, int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">Using the <a href="bartMachine/bartMachineRegressionMultThread.html#getGibbsSamplesForPrediction(double%5B%5D%5B%5D,int)"><code>bartMachineRegressionMultThread.getGibbsSamplesForPrediction(double[][], int)</code></a> function, return a credible interval at a specified
level of coverage</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getPredictionIntervalsForPrediction(double%5B%5D%5B%5D,double,int,int)" class="member-name-link">getPredictionIntervalsForPrediction(double[][], double, int, int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">Return prediction interval bounds for each record.</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#getProjectionWeights(double%5B%5D%5B%5D)" class="member-name-link">getProjectionWeights(double[][])</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#getPrunableAndChangeableNodes()" class="member-name-link">getPrunableAndChangeableNodes()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Find a list of prunable and changeable nodes (ie singly internal nodes)
from this point in the tree and below</div>
</dd>
<dt><a href="bartMachine/bartMachine_e_gibbs_base.html#getResidualsFromFullSumModel(int,double%5B%5D)" class="member-name-link">getResidualsFromFullSumModel(int, double[])</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_e_gibbs_base.html" title="class in bartMachine">bartMachine_e_gibbs_base</a></dt>
<dd>
<div class="block">This function calculates the residuals from the sum-of-trees model using the diff trick explained in the paper</div>
</dd>
<dt><a href="bartMachine/Classifier.html#getResponseFromRecord(double%5B%5D)" class="member-name-link">getResponseFromRecord(double[])</a> - Method in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">Given a data record, return the Y (response) value i.e.</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#getRight()" class="member-name-link">getRight()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd> </dd>
<dt><a href="OpenSourceExtensions/UnorderedPair.html#getSecond()" class="member-name-link">getSecond()</a> - Method in record class OpenSourceExtensions.<a href="OpenSourceExtensions/UnorderedPair.html" title="class in OpenSourceExtensions">UnorderedPair</a></dt>
<dd>
<div class="block">Gets the largest element of the pair (according to its <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Comparable.html" title="class or interface in java.lang" class="external-link"><code>Comparable</code></a> implementation).</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#getSplitAttributeM()" class="member-name-link">getSplitAttributeM()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#getSplitValue()" class="member-name-link">getSplitValue()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#getTerminalNodes()" class="member-name-link">getTerminalNodes()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Return all terminal nodes under this node</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#getTerminalNodesWithDataAboveOrEqualToN(int)" class="member-name-link">getTerminalNodesWithDataAboveOrEqualToN(int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Search the tree below this current node for terminal nodes that have more than <code>n_rule</code>
data records</div>
</dd>
<dt><a href="AlgorithmTesting/DataSetupForCSVFile.html#getX_y()" class="member-name-link">getX_y()</a> - Method in class AlgorithmTesting.<a href="AlgorithmTesting/DataSetupForCSVFile.html" title="class in AlgorithmTesting">DataSetupForCSVFile</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#getY_max()" class="member-name-link">getY_max()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#getY_min()" class="member-name-link">getY_min()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#getY_range_sq()" class="member-name-link">getY_range_sq()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_d_init.html#gibbs_sample_num" class="member-name-link">gibbs_sample_num</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_d_init.html" title="class in bartMachine">bartMachine_d_init</a></dt>
<dd>
<div class="block">the number of the current Gibbs sample</div>
</dd>
<dt><a href="bartMachine/bartMachine_a_base.html#gibbs_samples_of_bart_trees" class="member-name-link">gibbs_samples_of_bart_trees</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_a_base.html" title="class in bartMachine">bartMachine_a_base</a></dt>
<dd>
<div class="block">all Gibbs samples for burn-in and post burn-in where each entry is a vector of pointers to the <code>num_trees</code> trees in the sum-of-trees model</div>
</dd>
<dt><a href="bartMachine/bartMachine_a_base.html#gibbs_samples_of_bart_trees_after_burn_in" class="member-name-link">gibbs_samples_of_bart_trees_after_burn_in</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_a_base.html" title="class in bartMachine">bartMachine_a_base</a></dt>
<dd>
<div class="block">Gibbs samples post burn-in where each entry is a vector of pointers to the <code>num_trees</code> trees in the sum-of-trees model</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#gibbs_samples_of_bart_trees_after_burn_in" class="member-name-link">gibbs_samples_of_bart_trees_after_burn_in</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">this is the combined gibbs samples after burn in from all of the <code>num_cores</code> chains</div>
</dd>
<dt><a href="bartMachine/bartMachine_a_base.html#gibbs_samples_of_sigsq" class="member-name-link">gibbs_samples_of_sigsq</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_a_base.html" title="class in bartMachine">bartMachine_a_base</a></dt>
<dd>
<div class="block">Gibbs samples for burn-in and post burn-in of the variances</div>
</dd>
<dt><a href="bartMachine/bartMachine_a_base.html#gibbs_samples_of_sigsq_after_burn_in" class="member-name-link">gibbs_samples_of_sigsq_after_burn_in</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_a_base.html" title="class in bartMachine">bartMachine_a_base</a></dt>
<dd>
<div class="block">Gibbs samples for post burn-in of the variances</div>
</dd>
<dt><a href="bartMachine/bartMachine_e_gibbs_base.html#GibbsSampleDebugMessage(int)" class="member-name-link">GibbsSampleDebugMessage(int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_e_gibbs_base.html" title="class in bartMachine">bartMachine_e_gibbs_base</a></dt>
<dd>
<div class="block">Print a Gibbs sample debug message</div>
</dd>
<dt><a href="bartMachine/bartMachine_g_mh.Steps.html#GROW" class="member-name-link">GROW</a> - Enum constant in enum class bartMachine.<a href="bartMachine/bartMachine_g_mh.Steps.html" title="enum class in bartMachine">bartMachine_g_mh.Steps</a></dt>
<dd> </dd>
</dl>
<h2 class="title" id="I:H">H</h2>
<dl class="index">
<dt><a href="OpenSourceExtensions/UnorderedPair.html#hashCode()" class="member-name-link">hashCode()</a> - Method in record class OpenSourceExtensions.<a href="OpenSourceExtensions/UnorderedPair.html" title="class in OpenSourceExtensions">UnorderedPair</a></dt>
<dd>
<div class="block">Returns a hash code value for this object.</div>
</dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#hyper_k" class="member-name-link">hyper_k</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd>
<div class="block">this controls where to set <code>hyper_sigsq_mu</code> by forcing the variance to be this number of standard deviations on the normal CDF</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#hyper_k" class="member-name-link">hyper_k</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">this controls where to set <code>hyper_sigsq_mu</code> by forcing the variance to be this number of standard deviations on the normal CDF</div>
</dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#hyper_lambda" class="member-name-link">hyper_lambda</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd>
<div class="block">the multiplier of the scale parameter of the inverse gamma prior on the variance</div>
</dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#hyper_mu_mu" class="member-name-link">hyper_mu_mu</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd>
<div class="block">the center of the prior of the terminal node prediction distribution</div>
</dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#hyper_nu" class="member-name-link">hyper_nu</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd>
<div class="block">half the shape parameter and half the multiplicand of the scale parameter of the inverse gamma prior on the variance</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#hyper_nu" class="member-name-link">hyper_nu</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">half the shape parameter and half the multiplicand of the scale parameter of the inverse gamma prior on the variance</div>
</dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#hyper_q" class="member-name-link">hyper_q</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd>
<div class="block">At a fixed <code>hyper_nu</code>, this controls where to set <code>hyper_lambda</code> by forcing q proportion to be at that value in the inverse gamma CDF</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#hyper_q" class="member-name-link">hyper_q</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">At a fixed <code>hyper_nu</code>, this controls where to set <code>hyper_lambda</code> by forcing q proportion to be at that value in the inverse gamma CDF</div>
</dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#hyper_sigsq_mu" class="member-name-link">hyper_sigsq_mu</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd>
<div class="block">the variance of the prior of the terminal node prediction distribution</div>
</dd>
</dl>
<h2 class="title" id="I:I">I</h2>
<dl class="index">
<dt><a href="bartMachine/StatToolbox.html#ILLEGAL_FLAG" class="member-name-link">ILLEGAL_FLAG</a> - Static variable in class bartMachine.<a href="bartMachine/StatToolbox.html" title="class in bartMachine">StatToolbox</a></dt>
<dd>
<div class="block">A flag that indicates an illegal value or failed operation</div>
</dd>
<dt><a href="bartMachine/bartMachine_c_debug.html#illustrate(bartMachine.TreeArrayIllustration)" class="member-name-link">illustrate(TreeArrayIllustration)</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_c_debug.html" title="class in bartMachine">bartMachine_c_debug</a></dt>
<dd>
<div class="block">the hook that gets called to save the tree illustrations for each Gibbs sample</div>
</dd>
<dt><a href="bartMachine/TreeIllustration.ImageFileFilter.html#%3Cinit%3E()" class="member-name-link">ImageFileFilter()</a> - Constructor for class bartMachine.<a href="bartMachine/TreeIllustration.ImageFileFilter.html" title="class in bartMachine">TreeIllustration.ImageFileFilter</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#indicies" class="member-name-link">indicies</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">the indices in {0, 1, ..., n-1} of the data records in this node</div>
</dd>
<dt><a href="bartMachine/bartMachine_d_init.html#InitGibbsSamplingData()" class="member-name-link">InitGibbsSamplingData()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_d_init.html" title="class in bartMachine">bartMachine_d_init</a></dt>
<dd>
<div class="block">Initializes the vectors that hold information across the Gibbs sampler</div>
</dd>
<dt><a href="bartMachine/bartMachine_d_init.html#InitializeMus()" class="member-name-link">InitializeMus()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_d_init.html" title="class in bartMachine">bartMachine_d_init</a></dt>
<dd>
<div class="block">Initializes the leaf structure (the mean predictions) by setting them to zero (in the transformed scale, this is the center of the range)</div>
</dd>
<dt><a href="bartMachine/bartMachine_d_init.html#InitializeTrees()" class="member-name-link">InitializeTrees()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_d_init.html" title="class in bartMachine">bartMachine_d_init</a></dt>
<dd>
<div class="block">Initializes the tree structures in the zeroth Gibbs sample to be merely stumps</div>
</dd>
<dt><a href="bartMachine/bartMachine_d_init.html#InitizializeSigsq()" class="member-name-link">InitizializeSigsq()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_d_init.html" title="class in bartMachine">bartMachine_d_init</a></dt>
<dd>
<div class="block">Initializes the first variance value by drawing from the prior</div>
</dd>
<dt><a href="bartMachine/bartMachine_c_debug.html#InitTreeIllustrations()" class="member-name-link">InitTreeIllustrations()</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_c_debug.html" title="class in bartMachine">bartMachine_c_debug</a></dt>
<dd>
<div class="block">the hook that gets called to save the tree illustrations when the Gibbs sampler begins</div>
</dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#interaction_constraints" class="member-name-link">interaction_constraints</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd>
<div class="block">if a covariate is a key here, the value defines interaction between the variables that are legal</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#intializeInteractionConstraints(int)" class="member-name-link">intializeInteractionConstraints(int)</a> - Method in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#isLeaf" class="member-name-link">isLeaf</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">is this node a terminal node?</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#isLeaf()" class="member-name-link">isLeaf()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd> </dd>
<dt><a href="bartMachine/Classifier.html#isMissing(double)" class="member-name-link">isMissing(double)</a> - Static method in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">Is this value missing?</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#isStump()" class="member-name-link">isStump()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Is this node a stump? That is, does it have no parents and no children?</div>
</dd>
<dt><a href="OpenSourceExtensions/TDoubleHashSetAndArray.html#iterator()" class="member-name-link">iterator()</a> - Method in class OpenSourceExtensions.<a href="OpenSourceExtensions/TDoubleHashSetAndArray.html" title="class in OpenSourceExtensions">TDoubleHashSetAndArray</a></dt>
<dd> </dd>
</dl>
<h2 class="title" id="I:J">J</h2>
<dl class="index">
<dt><a href="OpenSourceExtensions/MersenneTwisterFast.html#java-notes-heading" class="search-tag-link">Java notes</a> - Section in class OpenSourceExtensions.MersenneTwisterFast</dt>
<dd> </dd>
</dl>
<h2 class="title" id="I:L">L</h2>
<dl class="index">
<dt><a href="bartMachine/Classifier.ErrorTypes.html#L1" class="member-name-link">L1</a> - Enum constant in enum class bartMachine.<a href="bartMachine/Classifier.ErrorTypes.html" title="enum class in bartMachine">Classifier.ErrorTypes</a></dt>
<dd> </dd>
<dt><a href="bartMachine/Classifier.ErrorTypes.html#L2" class="member-name-link">L2</a> - Enum constant in enum class bartMachine.<a href="bartMachine/Classifier.ErrorTypes.html" title="enum class in bartMachine">Classifier.ErrorTypes</a></dt>
<dd> </dd>
<dt><a href="bartMachine/TreeArrayIllustration.html#LeadingZeroes(double,int)" class="member-name-link">LeadingZeroes(double, int)</a> - Static method in class bartMachine.<a href="bartMachine/TreeArrayIllustration.html" title="class in bartMachine">TreeArrayIllustration</a></dt>
<dd> </dd>
<dt><a href="bartMachine/TreeArrayIllustration.html#LeadingZeroes(int,int)" class="member-name-link">LeadingZeroes(int, int)</a> - Static method in class bartMachine.<a href="bartMachine/TreeArrayIllustration.html" title="class in bartMachine">TreeArrayIllustration</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#left" class="member-name-link">left</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">the left daughter node</div>
</dd>
<dt><a href="OpenSourceExtensions/MersenneTwisterFast.html#license-heading" class="search-tag-link">License</a> - Section in class OpenSourceExtensions.MersenneTwisterFast</dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#log_sigsq" class="member-name-link">log_sigsq</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd>
<div class="block">Cached log(sigsq)</div>
</dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#log_sigsq_plus_n_sigsq_mu_table" class="member-name-link">log_sigsq_plus_n_sigsq_mu_table</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd>
<div class="block">A cached table of log(sigsq + n * hyper_sigsq_mu) for n = 0 to N</div>
</dd>
<dt><a href="bartMachine/bartMachine_b_hyperparams.html#log_table" class="member-name-link">log_table</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a></dt>
<dd>
<div class="block">A cached table of log(i) for i = 0 to max(N, P)</div>
</dd>
<dt><a href="CustomLogging/LoggingOutputStream.html" class="type-name-link" title="class in CustomLogging">LoggingOutputStream</a> - Class in <a href="CustomLogging/package-summary.html">CustomLogging</a></dt>
<dd>
<div class="block">\* An OutputStream that writes contents to a Logger upon each call to flush()
\</div>
</dd>
<dt><a href="CustomLogging/LoggingOutputStream.html#%3Cinit%3E(java.util.logging.Logger,java.util.logging.Level)" class="member-name-link">LoggingOutputStream(Logger, Level)</a> - Constructor for class CustomLogging.<a href="CustomLogging/LoggingOutputStream.html" title="class in CustomLogging">LoggingOutputStream</a></dt>
<dd>
<div class="block">\* Constructor
\* @param logger Logger to write to
\* @param level Level at which to write the log message
\</div>
</dd>
</dl>
<h2 class="title" id="I:M">M</h2>
<dl class="index">
<dt><a href="AlgorithmTesting/DataAnalysis.html#main(java.lang.String%5B%5D)" class="member-name-link">main(String[])</a> - Static method in class AlgorithmTesting.<a href="AlgorithmTesting/DataAnalysis.html" title="class in AlgorithmTesting">DataAnalysis</a></dt>
<dd> </dd>
<dt><a href="OpenSourceExtensions/MersenneTwisterFast.html#main(java.lang.String%5B%5D)" class="member-name-link">main(String[])</a> - Static method in class OpenSourceExtensions.<a href="OpenSourceExtensions/MersenneTwisterFast.html" title="class in OpenSourceExtensions">MersenneTwisterFast</a></dt>
<dd>
<div class="block">Tests the code.</div>
</dd>
<dt><a href="bartMachine/Tools.html#max(double%5B%5D)" class="member-name-link">max(double[])</a> - Static method in class bartMachine.<a href="bartMachine/Tools.html" title="class in bartMachine">Tools</a></dt>
<dd>
<div class="block">Returns the max of a vector</div>
</dd>
<dt><a href="bartMachine/bartMachine_a_base.html#mem_cache_for_speed" class="member-name-link">mem_cache_for_speed</a> - Variable in class bartMachine.<a href="bartMachine/bartMachine_a_base.html" title="class in bartMachine">bartMachine_a_base</a></dt>
<dd>
<div class="block">whether or not we use the memory cache feature
See Section 3.1 of Kapelner, A and Bleich, J.</div>
</dd>
<dt><a href="bartMachine/bartMachineRegressionMultThread.html#mem_cache_for_speed" class="member-name-link">mem_cache_for_speed</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a></dt>
<dd>
<div class="block">whether or not we use the memory cache feature
See Section 3.1 of Kapelner, A and Bleich, J.</div>
</dd>
<dt><a href="OpenSourceExtensions/MersenneTwisterFast.html#mersennetwister-and-mersennetwisterfast-heading" class="search-tag-link">MersenneTwister and MersenneTwisterFast</a> - Section in class OpenSourceExtensions.MersenneTwisterFast</dt>
<dd> </dd>
<dt><a href="OpenSourceExtensions/MersenneTwisterFast.html" class="type-name-link" title="class in OpenSourceExtensions">MersenneTwisterFast</a> - Class in <a href="OpenSourceExtensions/package-summary.html">OpenSourceExtensions</a></dt>
<dd>
<div class="block">MersenneTwister and MersenneTwisterFast</div>
</dd>
<dt><a href="OpenSourceExtensions/MersenneTwisterFast.html#%3Cinit%3E()" class="member-name-link">MersenneTwisterFast()</a> - Constructor for class OpenSourceExtensions.<a href="OpenSourceExtensions/MersenneTwisterFast.html" title="class in OpenSourceExtensions">MersenneTwisterFast</a></dt>
<dd>
<div class="block">Constructor using the default seed.</div>
</dd>
<dt><a href="OpenSourceExtensions/MersenneTwisterFast.html#%3Cinit%3E(int%5B%5D)" class="member-name-link">MersenneTwisterFast(int[])</a> - Constructor for class OpenSourceExtensions.<a href="OpenSourceExtensions/MersenneTwisterFast.html" title="class in OpenSourceExtensions">MersenneTwisterFast</a></dt>
<dd>
<div class="block">Constructor using an array of integers as seed.</div>
</dd>
<dt><a href="OpenSourceExtensions/MersenneTwisterFast.html#%3Cinit%3E(long)" class="member-name-link">MersenneTwisterFast(long)</a> - Constructor for class OpenSourceExtensions.<a href="OpenSourceExtensions/MersenneTwisterFast.html" title="class in OpenSourceExtensions">MersenneTwisterFast</a></dt>
<dd>
<div class="block">Constructor using a given seed.</div>
</dd>
<dt><a href="bartMachine/bartMachine_e_gibbs_base.html#metroHastingsPosteriorTreeSpaceIteration(bartMachine.bartMachineTreeNode,int,boolean%5B%5D%5B%5D,char%5B%5D%5B%5D)" class="member-name-link">metroHastingsPosteriorTreeSpaceIteration(bartMachineTreeNode, int, boolean[][], char[][])</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_e_gibbs_base.html" title="class in bartMachine">bartMachine_e_gibbs_base</a></dt>
<dd> </dd>
<dt><a href="bartMachine/bartMachine_g_mh.html#metroHastingsPosteriorTreeSpaceIteration(bartMachine.bartMachineTreeNode,int,boolean%5B%5D%5B%5D,char%5B%5D%5B%5D)" class="member-name-link">metroHastingsPosteriorTreeSpaceIteration(bartMachineTreeNode, int, boolean[][], char[][])</a> - Method in class bartMachine.<a href="bartMachine/bartMachine_g_mh.html" title="class in bartMachine">bartMachine_g_mh</a></dt>
<dd>
<div class="block">Performs one Metropolis-Hastings step for one tree</div>
</dd>
<dt><a href="bartMachine/Classifier.ErrorTypes.html#MISCLASSIFICATION" class="member-name-link">MISCLASSIFICATION</a> - Enum constant in enum class bartMachine.<a href="bartMachine/Classifier.ErrorTypes.html" title="enum class in bartMachine">Classifier.ErrorTypes</a></dt>
<dd> </dd>
<dt><a href="bartMachine/Classifier.html#MISSING_VALUE" class="member-name-link">MISSING_VALUE</a> - Static variable in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">The way we represent missing values from within our implementation</div>
</dd>
<dt><a href="bartMachine/StatToolbox.html#multinomial_sample(it.unimi.dsi.fastutil.ints.IntArrayList,double%5B%5D)" class="member-name-link">multinomial_sample(IntArrayList, double[])</a> - Static method in class bartMachine.<a href="bartMachine/StatToolbox.html" title="class in bartMachine">StatToolbox</a></dt>
<dd>
<div class="block">Sample from a multinomial distribution</div>
</dd>
</dl>
<h2 class="title" id="I:N">N</h2>
<dl class="index">
<dt><a href="bartMachine/Classifier.html#n" class="member-name-link">n</a> - Variable in class bartMachine.<a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a></dt>
<dd>
<div class="block">the number of records in the training set</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#n_eta" class="member-name-link">n_eta</a> - Variable in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">the number of data points in this node</div>
</dd>
<dt><a href="bartMachine/bartMachineTreeNode.html#nAdj()" class="member-name-link">nAdj()</a> - Method in class bartMachine.<a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a></dt>
<dd>
<div class="block">Gets the total number of valid split points that can be used for rules at this juncture
for the selected split rule predictor (it will be different for each predictor)</div>
</dd>
<dt><a href="OpenSourceExtensions/MersenneTwisterFast.html#nextBoolean()" class="member-name-link">nextBoolean()</a> - Method in class OpenSourceExtensions.<a href="OpenSourceExtensions/MersenneTwisterFast.html" title="class in OpenSourceExtensions">MersenneTwisterFast</a></dt>
<dd> </dd>
<dt><a href="OpenSourceExtensions/MersenneTwisterFast.html#nextBoolean(double)" class="member-name-link">nextBoolean(double)</a> - Method in class OpenSourceExtensions.<a href="OpenSourceExtensions/MersenneTwisterFast.html" title="class in OpenSourceExtensions">MersenneTwisterFast</a></dt>
<dd>
<div class="block">This generates a coin flip with a probability <tt>probability</tt>
of returning true, else returning false.</div>
</dd>