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<!DOCTYPE HTML>
<html lang="en">
<head>
<!-- Generated by javadoc (25) on Mon Jan 12 19:25:19 EST 2026 -->
<title>Serialized Form</title>
<meta name="viewport" content="width=device-width, initial-scale=1">
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<h1 title="Serialized Form" class="title">Serialized Form</h1>
</div>
<ul class="block-list">
<li>
<section class="serialized-package-container">
<h2 title="Package">Package <a href="bartMachine/package-summary.html">bartMachine</a></h2>
<ul class="block-list">
<li>
<section class="serialized-class-details" id="bartMachine.bartMachine_a_base">
<h3>Class <a href="bartMachine/bartMachine_a_base.html" title="class in bartMachine">bartMachine.bartMachine_a_base</a></h3>
<div class="type-signature">class bartMachine_a_base extends <a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
<ul class="block-list">
<li>
<section class="detail">
<h4>Serialized Fields</h4>
<ul class="block-list">
<li class="block-list">
<h5>accept_reject_mh</h5>
<pre>boolean[][] accept_reject_mh</pre>
<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>
</li>
<li class="block-list">
<h5>accept_reject_mh_steps</h5>
<pre>char[][] accept_reject_mh_steps</pre>
<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>
</li>
<li class="block-list">
<h5>flush_indices_to_save_ram</h5>
<pre>boolean flush_indices_to_save_ram</pre>
<div class="block">saves indices in nodes (useful for computing weights)</div>
</li>
<li class="block-list">
<h5>gibbs_samples_of_bart_trees</h5>
<pre><a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a>[][] gibbs_samples_of_bart_trees</pre>
<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>
</li>
<li class="block-list">
<h5>gibbs_samples_of_bart_trees_after_burn_in</h5>
<pre><a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a>[][] gibbs_samples_of_bart_trees_after_burn_in</pre>
<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>
</li>
<li class="block-list">
<h5>gibbs_samples_of_sigsq</h5>
<pre>double[] gibbs_samples_of_sigsq</pre>
<div class="block">Gibbs samples for burn-in and post burn-in of the variances</div>
</li>
<li class="block-list">
<h5>gibbs_samples_of_sigsq_after_burn_in</h5>
<pre>double[] gibbs_samples_of_sigsq_after_burn_in</pre>
<div class="block">Gibbs samples for post burn-in of the variances</div>
</li>
<li class="block-list">
<h5>mem_cache_for_speed</h5>
<pre>boolean mem_cache_for_speed</pre>
<div class="block">whether or not we use the memory cache feature
See Section 3.1 of Kapelner, A and Bleich, J. bartMachine: A Powerful Tool for Machine Learning in R. ArXiv e-prints, 2013</div>
</li>
<li class="block-list">
<h5>num_cores</h5>
<pre>int num_cores</pre>
<div class="block">how many CPU cores to use during model creation</div>
</li>
<li class="block-list">
<h5>num_gibbs_burn_in</h5>
<pre>int num_gibbs_burn_in</pre>
<div class="block">how many Gibbs samples we burn-in for</div>
</li>
<li class="block-list">
<h5>num_gibbs_total_iterations</h5>
<pre>int num_gibbs_total_iterations</pre>
<div class="block">how many total Gibbs samples in a BART model creation</div>
</li>
<li class="block-list">
<h5>num_trees</h5>
<pre>int num_trees</pre>
<div class="block">the number of trees in our sum-of-trees model</div>
</li>
<li class="block-list">
<h5>seed</h5>
<pre><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Long.html" title="class or interface in java.lang" class="external-link">Long</a> seed</pre>
<div class="block">the seed for the random number generator</div>
</li>
<li class="block-list">
<h5>threadNum</h5>
<pre>int threadNum</pre>
<div class="block">the current thread being used to run this Gibbs sampler</div>
</li>
<li class="block-list">
<h5>use_xoshiro</h5>
<pre>boolean use_xoshiro</pre>
<div class="block">whether or not to use the Xoshiro256PlusPlus random number generator</div>
</li>
<li class="block-list">
<h5>verbose</h5>
<pre>boolean verbose</pre>
<div class="block">should we print stuff out to screen?</div>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
<li>
<section class="serialized-class-details" id="bartMachine.bartMachine_b_hyperparams">
<h3>Class <a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine.bartMachine_b_hyperparams</a></h3>
<div class="type-signature">class bartMachine_b_hyperparams extends <a href="bartMachine/bartMachine_a_base.html" title="class in bartMachine">bartMachine_a_base</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
<ul class="block-list">
<li>
<section class="detail">
<h4>Serialized Fields</h4>
<ul class="block-list">
<li class="block-list">
<h5>alpha</h5>
<pre>double alpha</pre>
<div class="block">A hyperparameter that controls how easy it is to grow new nodes in a tree independent of depth</div>
</li>
<li class="block-list">
<h5>beta</h5>
<pre>double beta</pre>
<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>
</li>
<li class="block-list">
<h5>hyper_k</h5>
<pre>double hyper_k</pre>
<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>
</li>
<li class="block-list">
<h5>hyper_lambda</h5>
<pre>double hyper_lambda</pre>
<div class="block">the multiplier of the scale parameter of the inverse gamma prior on the variance</div>
</li>
<li class="block-list">
<h5>hyper_mu_mu</h5>
<pre>double hyper_mu_mu</pre>
<div class="block">the center of the prior of the terminal node prediction distribution</div>
</li>
<li class="block-list">
<h5>hyper_nu</h5>
<pre>double hyper_nu</pre>
<div class="block">half the shape parameter and half the multiplicand of the scale parameter of the inverse gamma prior on the variance</div>
</li>
<li class="block-list">
<h5>hyper_q</h5>
<pre>double hyper_q</pre>
<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>
</li>
<li class="block-list">
<h5>hyper_sigsq_mu</h5>
<pre>double hyper_sigsq_mu</pre>
<div class="block">the variance of the prior of the terminal node prediction distribution</div>
</li>
<li class="block-list">
<h5>interaction_constraints</h5>
<pre><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/util/HashMap.html" title="class or interface in java.util" class="external-link">HashMap</a><<a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Integer.html" title="class or interface in java.lang" class="external-link">Integer</a>, it.unimi.dsi.fastutil.ints.IntOpenHashSet> interaction_constraints</pre>
<div class="block">if a covariate is a key here, the value defines interaction between the variables that are legal</div>
</li>
<li class="block-list">
<h5>sample_var_y</h5>
<pre><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Double.html" title="class or interface in java.lang" class="external-link">Double</a> sample_var_y</pre>
<div class="block">the sample variance of the response variable on its original scale</div>
</li>
<li class="block-list">
<h5>y_max</h5>
<pre>double y_max</pre>
<div class="block">the maximum of the response variable on its original scale</div>
</li>
<li class="block-list">
<h5>y_min</h5>
<pre>double y_min</pre>
<div class="block">the minimum of the response variable on its original scale</div>
</li>
<li class="block-list">
<h5>y_range_sq</h5>
<pre>double y_range_sq</pre>
<div class="block">the minimum of the response variable on its original scale</div>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
<li>
<section class="serialized-class-details" id="bartMachine.bartMachine_c_debug">
<h3>Class <a href="bartMachine/bartMachine_c_debug.html" title="class in bartMachine">bartMachine.bartMachine_c_debug</a></h3>
<div class="type-signature">class bartMachine_c_debug extends <a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
<ul class="block-list">
<li>
<section class="detail">
<h4>Serialized Fields</h4>
<ul class="block-list">
<li class="block-list">
<h5>tree_illust</h5>
<pre>boolean tree_illust</pre>
<div class="block">should we create illustrations of the trees and save the images to the debug directory?</div>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
<li>
<section class="serialized-class-details" id="bartMachine.bartMachine_d_init">
<h3>Class <a href="bartMachine/bartMachine_d_init.html" title="class in bartMachine">bartMachine.bartMachine_d_init</a></h3>
<div class="type-signature">class bartMachine_d_init extends <a href="bartMachine/bartMachine_c_debug.html" title="class in bartMachine">bartMachine_c_debug</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
<ul class="block-list">
<li>
<section class="detail">
<h4>Serialized Fields</h4>
<ul class="block-list">
<li class="block-list">
<h5>gibbs_sample_num</h5>
<pre>int gibbs_sample_num</pre>
<div class="block">the number of the current Gibbs sample</div>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
<li>
<section class="serialized-class-details" id="bartMachine.bartMachine_e_gibbs_base">
<h3>Class <a href="bartMachine/bartMachine_e_gibbs_base.html" title="class in bartMachine">bartMachine.bartMachine_e_gibbs_base</a></h3>
<div class="type-signature">class bartMachine_e_gibbs_base extends <a href="bartMachine/bartMachine_d_init.html" title="class in bartMachine">bartMachine_d_init</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
</section>
</li>
<li>
<section class="serialized-class-details" id="bartMachine.bartMachine_f_gibbs_internal">
<h3>Class <a href="bartMachine/bartMachine_f_gibbs_internal.html" title="class in bartMachine">bartMachine.bartMachine_f_gibbs_internal</a></h3>
<div class="type-signature">class bartMachine_f_gibbs_internal extends <a href="bartMachine/bartMachine_e_gibbs_base.html" title="class in bartMachine">bartMachine_e_gibbs_base</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
</section>
</li>
<li>
<section class="serialized-class-details" id="bartMachine.bartMachine_g_mh">
<h3>Class <a href="bartMachine/bartMachine_g_mh.html" title="class in bartMachine">bartMachine.bartMachine_g_mh</a></h3>
<div class="type-signature">class bartMachine_g_mh extends <a href="bartMachine/bartMachine_f_gibbs_internal.html" title="class in bartMachine">bartMachine_f_gibbs_internal</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
<ul class="block-list">
<li>
<section class="detail">
<h4>Serialized Fields</h4>
<ul class="block-list">
<li class="block-list">
<h5>prob_grow</h5>
<pre>double prob_grow</pre>
<div class="block">the hyperparameter of the probability of picking a grow step during the Metropolis-Hastings tree proposal</div>
</li>
<li class="block-list">
<h5>prob_prune</h5>
<pre>double prob_prune</pre>
<div class="block">the hyperparameter of the probability of picking a prune step during the Metropolis-Hastings tree proposal</div>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
<li>
<section class="serialized-class-details" id="bartMachine.bartMachine_h_eval">
<h3>Class <a href="bartMachine/bartMachine_h_eval.html" title="class in bartMachine">bartMachine.bartMachine_h_eval</a></h3>
<div class="type-signature">class bartMachine_h_eval extends <a href="bartMachine/bartMachine_g_mh.html" title="class in bartMachine">bartMachine_g_mh</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
</section>
</li>
<li>
<section class="serialized-class-details" id="bartMachine.bartMachine_i_prior_cov_spec">
<h3>Class <a href="bartMachine/bartMachine_i_prior_cov_spec.html" title="class in bartMachine">bartMachine.bartMachine_i_prior_cov_spec</a></h3>
<div class="type-signature">class bartMachine_i_prior_cov_spec extends <a href="bartMachine/bartMachine_h_eval.html" title="class in bartMachine">bartMachine_h_eval</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
<ul class="block-list">
<li>
<section class="detail">
<h4>Serialized Fields</h4>
<ul class="block-list">
<li class="block-list">
<h5>cov_split_prior</h5>
<pre>double[] cov_split_prior</pre>
<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>
</li>
<li class="block-list">
<h5>use_prior_cov_spec</h5>
<pre>boolean use_prior_cov_spec</pre>
<div class="block">Do we use this feature in this BART model?</div>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
<li>
<section class="serialized-class-details" id="bartMachine.bartMachineClassification">
<h3>Class <a href="bartMachine/bartMachineClassification.html" title="class in bartMachine">bartMachine.bartMachineClassification</a></h3>
<div class="type-signature">class bartMachineClassification extends <a href="bartMachine/bartMachineRegression.html" title="class in bartMachine">bartMachineRegression</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
</section>
</li>
<li>
<section class="serialized-class-details" id="bartMachine.bartMachineClassificationMultThread">
<h3>Class <a href="bartMachine/bartMachineClassificationMultThread.html" title="class in bartMachine">bartMachine.bartMachineClassificationMultThread</a></h3>
<div class="type-signature">class bartMachineClassificationMultThread extends <a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachineRegressionMultThread</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
<ul class="block-list">
<li>
<section class="detail">
<h4>Serialized Fields</h4>
<ul class="block-list">
<li class="block-list">
<h5>classification_rule</h5>
<pre>double classification_rule</pre>
<div class="block">The value of the classification rule which if the probability estimate of Y = 1 is greater than, we predict 1</div>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
<li>
<section class="serialized-class-details" id="bartMachine.bartMachineRegression">
<h3>Class <a href="bartMachine/bartMachineRegression.html" title="class in bartMachine">bartMachine.bartMachineRegression</a></h3>
<div class="type-signature">class bartMachineRegression extends <a href="bartMachine/bartMachine_i_prior_cov_spec.html" title="class in bartMachine">bartMachine_i_prior_cov_spec</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
</section>
</li>
<li>
<section class="serialized-class-details" id="bartMachine.bartMachineRegressionMultThread">
<h3>Class <a href="bartMachine/bartMachineRegressionMultThread.html" title="class in bartMachine">bartMachine.bartMachineRegressionMultThread</a></h3>
<div class="type-signature">class bartMachineRegressionMultThread extends <a href="bartMachine/Classifier.html" title="class in bartMachine">Classifier</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
<ul class="block-list">
<li>
<section class="detail">
<h4>Serialized Fields</h4>
<ul class="block-list">
<li class="block-list">
<h5>alpha</h5>
<pre><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Double.html" title="class or interface in java.lang" class="external-link">Double</a> alpha</pre>
<div class="block">A hyperparameter that controls how easy it is to grow new nodes in a tree independent of depth</div>
</li>
<li class="block-list">
<h5>bart_gibbs_chain_threads</h5>
<pre><a href="bartMachine/bartMachineRegression.html" title="class in bartMachine">bartMachineRegression</a>[] bart_gibbs_chain_threads</pre>
<div class="block">the collection of <code>num_cores</code> BART models which will run separate Gibbs chains</div>
</li>
<li class="block-list">
<h5>beta</h5>
<pre><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Double.html" title="class or interface in java.lang" class="external-link">Double</a> beta</pre>
<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>
</li>
<li class="block-list">
<h5>cov_split_prior</h5>
<pre>double[] cov_split_prior</pre>
<div class="block">The probability vector that samples covariates for selecting split rules</div>
</li>
<li class="block-list">
<h5>flush_indices_to_save_ram</h5>
<pre>boolean flush_indices_to_save_ram</pre>
<div class="block">saves indices in nodes (useful for computing weights)</div>
</li>
<li class="block-list">
<h5>gibbs_samples_of_bart_trees_after_burn_in</h5>
<pre><a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a>[][] gibbs_samples_of_bart_trees_after_burn_in</pre>
<div class="block">this is the combined gibbs samples after burn in from all of the <code>num_cores</code> chains</div>
</li>
<li class="block-list">
<h5>hyper_k</h5>
<pre><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Double.html" title="class or interface in java.lang" class="external-link">Double</a> hyper_k</pre>
<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>
</li>
<li class="block-list">
<h5>hyper_nu</h5>
<pre><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Double.html" title="class or interface in java.lang" class="external-link">Double</a> hyper_nu</pre>
<div class="block">half the shape parameter and half the multiplicand of the scale parameter of the inverse gamma prior on the variance</div>
</li>
<li class="block-list">
<h5>hyper_q</h5>
<pre><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Double.html" title="class or interface in java.lang" class="external-link">Double</a> hyper_q</pre>
<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>
</li>
<li class="block-list">
<h5>interaction_constraints</h5>
<pre><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/util/HashMap.html" title="class or interface in java.util" class="external-link">HashMap</a><<a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Integer.html" title="class or interface in java.lang" class="external-link">Integer</a>, it.unimi.dsi.fastutil.ints.IntOpenHashSet> interaction_constraints</pre>
</li>
<li class="block-list">
<h5>mem_cache_for_speed</h5>
<pre>boolean mem_cache_for_speed</pre>
<div class="block">whether or not we use the memory cache feature
See Section 3.1 of Kapelner, A and Bleich, J. bartMachine: A Powerful Tool for Machine Learning in R. ArXiv e-prints, 2013</div>
</li>
<li class="block-list">
<h5>num_cores</h5>
<pre>int num_cores</pre>
<div class="block">the number of CPU cores to build many different Gibbs chain within a BART model</div>
</li>
<li class="block-list">
<h5>num_gibbs_burn_in</h5>
<pre>int num_gibbs_burn_in</pre>
<div class="block">the number of burn-in samples in each Gibbs chain</div>
</li>
<li class="block-list">
<h5>num_gibbs_total_iterations</h5>
<pre>int num_gibbs_total_iterations</pre>
<div class="block">the total number of gibbs samples where each chain gets a number of burn-in and then the difference from the total divided by <code>num_cores</code></div>
</li>
<li class="block-list">
<h5>num_trees</h5>
<pre>int num_trees</pre>
<div class="block">the number of trees in this BART model on all Gibbs chains</div>
</li>
<li class="block-list">
<h5>prob_grow</h5>
<pre><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Double.html" title="class or interface in java.lang" class="external-link">Double</a> prob_grow</pre>
<div class="block">the hyperparameter of the probability of picking a grow step during the Metropolis-Hastings tree proposal</div>
</li>
<li class="block-list">
<h5>prob_prune</h5>
<pre><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Double.html" title="class or interface in java.lang" class="external-link">Double</a> prob_prune</pre>
<div class="block">the hyperparameter of the probability of picking a prune step during the Metropolis-Hastings tree proposal</div>
</li>
<li class="block-list">
<h5>sample_var_y</h5>
<pre><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Double.html" title="class or interface in java.lang" class="external-link">Double</a> sample_var_y</pre>
<div class="block">the estimate of some upper limit of the variance of the response which is usually the MSE from a a linear regression</div>
</li>
<li class="block-list">
<h5>seed</h5>
<pre><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Integer.html" title="class or interface in java.lang" class="external-link">Integer</a> seed</pre>
<div class="block">the seed for the random number generator</div>
</li>
<li class="block-list">
<h5>total_iterations_multithreaded</h5>
<pre>int total_iterations_multithreaded</pre>
<div class="block">the total number of Gibbs samples for each of the <code>num_cores</code> chains</div>
</li>
<li class="block-list">
<h5>tree_illust</h5>
<pre>boolean tree_illust</pre>
</li>
<li class="block-list">
<h5>use_xoshiro</h5>
<pre>boolean use_xoshiro</pre>
<div class="block">whether or not to use the Xoshiro256PlusPlus random number generator</div>
</li>
<li class="block-list">
<h5>verbose</h5>
<pre>boolean verbose</pre>
<div class="block">should we print select messages to the screen</div>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
<li>
<section class="serialized-class-details" id="bartMachine.bartMachineTreeNode">
<h3>Class <a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachine.bartMachineTreeNode</a></h3>
<div class="type-signature">class bartMachineTreeNode extends <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Object.html" title="class or interface in java.lang" class="external-link">Object</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
<ul class="block-list">
<li>
<section class="detail">
<h4>Serialized Fields</h4>
<ul class="block-list">
<li class="block-list">
<h5>attribute_split_counts</h5>
<pre>int[] attribute_split_counts</pre>
<div class="block">a tabulation of the counts of attributes being used in split points in this tree</div>
</li>
<li class="block-list">
<h5>bart</h5>
<pre><a href="bartMachine/bartMachine_b_hyperparams.html" title="class in bartMachine">bartMachine_b_hyperparams</a> bart</pre>
<div class="block">a link back to the overall bart model</div>
</li>
<li class="block-list">
<h5>depth</h5>
<pre>int depth</pre>
<div class="block">the generation of this node from the top node (root note has generation = 0 by definition)</div>
</li>
<li class="block-list">
<h5>indicies</h5>
<pre>int[] indicies</pre>
<div class="block">the indices in {0, 1, ..., n-1} of the data records in this node</div>
</li>
<li class="block-list">
<h5>isLeaf</h5>
<pre>boolean isLeaf</pre>
<div class="block">is this node a terminal node?</div>
</li>
<li class="block-list">
<h5>left</h5>
<pre><a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a> left</pre>
<div class="block">the left daughter node</div>
</li>
<li class="block-list">
<h5>parent</h5>
<pre><a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a> parent</pre>
<div class="block">the parent node of this node</div>
</li>
<li class="block-list">
<h5>posterior_mean</h5>
<pre>double posterior_mean</pre>
<div class="block">the posterior mean in the conditional distribution if applicable (for research purposes only)</div>
</li>
<li class="block-list">
<h5>posterior_var</h5>
<pre>double posterior_var</pre>
<div class="block">the posterior variance in the conditional distribution if applicable (for research purposes only)</div>
</li>
<li class="block-list">
<h5>right</h5>
<pre><a href="bartMachine/bartMachineTreeNode.html" title="class in bartMachine">bartMachineTreeNode</a> right</pre>
<div class="block">the right daughter node</div>
</li>
<li class="block-list">
<h5>sendMissingDataRight</h5>
<pre>boolean sendMissingDataRight</pre>
<div class="block">send missing data to the right?</div>
</li>
<li class="block-list">
<h5>splitAttributeM</h5>
<pre>int splitAttributeM</pre>
<div class="block">the attribute this node makes a decision on</div>
</li>
<li class="block-list">
<h5>splitValue</h5>
<pre>double splitValue</pre>
<div class="block">the value this node makes a decision on</div>
</li>
<li class="block-list">
<h5>y_avg</h5>
<pre>double y_avg</pre>
<div class="block">the average of the node responses if applicable (for research purposes only)</div>
</li>
<li class="block-list">
<h5>y_pred</h5>
<pre>double y_pred</pre>
<div class="block">if this is a leaf node, then the result of the prediction for regression, otherwise null</div>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
<li>
<section class="serialized-class-details" id="bartMachine.Classifier">
<h3>Class <a href="bartMachine/Classifier.html" title="class in bartMachine">bartMachine.Classifier</a></h3>
<div class="type-signature">class Classifier extends <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Object.html" title="class or interface in java.lang" class="external-link">Object</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
<dl class="name-value">
<dt>serialVersionUID:</dt>
<dd>-7470305759402002995L</dd>
</dl>
<ul class="block-list">
<li>
<section class="detail">
<h4>Serialized Fields</h4>
<ul class="block-list">
<li class="block-list">
<h5>n</h5>
<pre>int n</pre>
<div class="block">the number of records in the training set</div>
</li>
<li class="block-list">
<h5>p</h5>
<pre>int p</pre>
<div class="block">the number of features / predictors in the training set</div>
</li>
<li class="block-list">
<h5>unique_name</h5>
<pre><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a> unique_name</pre>
<div class="block">the name of this classifier (useful for debugging)</div>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
<li>
<section class="serialized-package-container">
<h2 title="Package">Package <a href="CustomLogging/package-summary.html">CustomLogging</a></h2>
<ul class="block-list">
<li>
<section class="serialized-class-details" id="CustomLogging.StdOutErrLevel">
<h3>Class <a href="CustomLogging/StdOutErrLevel.html" title="class in CustomLogging">CustomLogging.StdOutErrLevel</a></h3>
<div class="type-signature">class StdOutErrLevel extends <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.logging/java/util/logging/Level.html" title="class or interface in java.util.logging" class="external-link">Level</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
<dl class="name-value">
<dt>serialVersionUID:</dt>
<dd>-9122466300490214950L</dd>
</dl>
<ul class="block-list">
<li>
<section class="detail">
<h4>Serialization Methods</h4>
<ul class="block-list">
<li>
<h5>readResolve</h5>
<div class="member-signature"><span class="modifiers">protected</span> <span class="return-type"><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Object.html" title="class or interface in java.lang" class="external-link">Object</a></span> <span class="element-name">readResolve</span>()
throws <span class="exceptions"><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/ObjectStreamException.html" title="class or interface in java.io" class="external-link">ObjectStreamException</a></span></div>
<div class="block">\* Method to avoid creating duplicate instances when deserializing the
\* object.
\* @return the singleton instance of this <code>Level</code> value in this
\* classloader
\* @throws ObjectStreamException If unable to deserialize
\</div>
<dl class="notes">
<dt>Throws:</dt>
<dd><code><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/ObjectStreamException.html" title="class or interface in java.io" class="external-link">ObjectStreamException</a></code></dd>
</dl>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
<li>
<section class="serialized-package-container">
<h2 title="Package">Package <a href="OpenSourceExtensions/package-summary.html">OpenSourceExtensions</a></h2>
<ul class="block-list">
<li>
<section class="serialized-class-details" id="OpenSourceExtensions.MersenneTwisterFast">
<h3>Class <a href="OpenSourceExtensions/MersenneTwisterFast.html" title="class in OpenSourceExtensions">OpenSourceExtensions.MersenneTwisterFast</a></h3>
<div class="type-signature">class MersenneTwisterFast extends <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Object.html" title="class or interface in java.lang" class="external-link">Object</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
<dl class="name-value">
<dt>serialVersionUID:</dt>
<dd>-8219700664442619525L</dd>
</dl>
<ul class="block-list">
<li>
<section class="detail">
<h4>Serialized Fields</h4>
<ul class="block-list">
<li class="block-list">
<h5>__haveNextNextGaussian</h5>
<pre>boolean __haveNextNextGaussian</pre>
</li>
<li class="block-list">
<h5>__nextNextGaussian</h5>
<pre>double __nextNextGaussian</pre>
</li>
<li class="block-list">
<h5>mag01</h5>
<pre>int[] mag01</pre>
</li>
<li class="block-list">
<h5>mt</h5>
<pre>int[] mt</pre>
</li>
<li class="block-list">
<h5>mti</h5>
<pre>int mti</pre>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
<li>
<section class="serialized-class-details" id="OpenSourceExtensions.TDoubleHashSetAndArray">
<h3>Class <a href="OpenSourceExtensions/TDoubleHashSetAndArray.html" title="class in OpenSourceExtensions">OpenSourceExtensions.TDoubleHashSetAndArray</a></h3>
<div class="type-signature">class TDoubleHashSetAndArray extends it.unimi.dsi.fastutil.doubles.AbstractDoubleSet implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Externalizable.html" title="class or interface in java.io" class="external-link">Externalizable</a></div>
<dl class="name-value">
<dt>serialVersionUID:</dt>
<dd>1L</dd>
</dl>
<ul class="block-list">
<li>
<section class="detail">
<h4>Serialization Methods</h4>
<ul class="block-list">
<li>
<h5>readExternal</h5>
<div class="member-signature"><span class="modifiers">public</span> <span class="return-type">void</span> <span class="element-name">readExternal</span><wbr><span class="parameters">(<a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/ObjectInput.html" title="class or interface in java.io" class="external-link">ObjectInput</a> in)</span>
throws <span class="exceptions"><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/IOException.html" title="class or interface in java.io" class="external-link">IOException</a>,
<a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/ClassNotFoundException.html" title="class or interface in java.lang" class="external-link">ClassNotFoundException</a></span></div>
<dl class="notes">
<dt>Throws:</dt>
<dd><code><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/IOException.html" title="class or interface in java.io" class="external-link">IOException</a></code></dd>
<dd><code><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/ClassNotFoundException.html" title="class or interface in java.lang" class="external-link">ClassNotFoundException</a></code></dd>
</dl>
</li>
<li>
<h5>writeExternal</h5>
<div class="member-signature"><span class="modifiers">public</span> <span class="return-type">void</span> <span class="element-name">writeExternal</span><wbr><span class="parameters">(<a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/ObjectOutput.html" title="class or interface in java.io" class="external-link">ObjectOutput</a> out)</span>
throws <span class="exceptions"><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/IOException.html" title="class or interface in java.io" class="external-link">IOException</a></span></div>
<dl class="notes">
<dt>Throws:</dt>
<dd><code><a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/IOException.html" title="class or interface in java.io" class="external-link">IOException</a></code></dd>
</dl>
</li>
</ul>
</section>
</li>
</ul>
</section>
</li>
<li>
<section class="serialized-class-details" id="OpenSourceExtensions.UnorderedPair">
<h3>Record Class <a href="OpenSourceExtensions/UnorderedPair.html" title="class in OpenSourceExtensions">OpenSourceExtensions.UnorderedPair</a></h3>
<div class="type-signature">class UnorderedPair extends <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/lang/Record.html" title="class or interface in java.lang" class="external-link">Record</a> implements <a href="https://docs.oracle.com/en/java/javase/25/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></div>
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<h4>Serialized Fields</h4>
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<h5>first</h5>
<pre><a href="OpenSourceExtensions/UnorderedPair.html#type-param-E" title="type parameter in UnorderedPair">E</a> extends <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">Comparable</a><<a href="OpenSourceExtensions/UnorderedPair.html#type-param-E" title="type parameter in UnorderedPair">E</a>> first</pre>
<div class="block">The field for the <code>first</code> record component.</div>
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<h5>second</h5>
<pre><a href="OpenSourceExtensions/UnorderedPair.html#type-param-E" title="type parameter in UnorderedPair">E</a> extends <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">Comparable</a><<a href="OpenSourceExtensions/UnorderedPair.html#type-param-E" title="type parameter in UnorderedPair">E</a>> second</pre>
<div class="block">The field for the <code>second</code> record component.</div>
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