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<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Changelog • CRE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<img src="" class="logo" alt=""><h1>Changelog</h1>
<small>Source: <a href="https://github.com/NSAPH-Software/CRE/blob/HEAD/NEWS.md"><code>NEWS.md</code></a></small>
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="0.2.5" id="cre-025-2024-4-21">CRE 0.2.5 (2024-4-21)<a class="anchor" aria-label="anchor" href="#cre-025-2024-4-21"></a></h2><p class="text-muted">CRAN release: 2023-12-06</p>
<div class="section level3">
<h3 id="added-0-2-5">Added<a class="anchor" aria-label="anchor" href="#added-0-2-5"></a></h3>
<ul><li>A copy of inTrees package source code.</li>
</ul></div>
<div class="section level3">
<h3 id="removed-0-2-5">Removed<a class="anchor" aria-label="anchor" href="#removed-0-2-5"></a></h3>
<ul><li>The inTrees package dependency</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="0.2.5" id="cre-025-2023-12-6">CRE 0.2.5 (2023-12-6)<a class="anchor" aria-label="anchor" href="#cre-025-2023-12-6"></a></h2><p class="text-muted">CRAN release: 2023-12-06</p>
<div class="section level3">
<h3 id="added-0-2-5-1">Added<a class="anchor" aria-label="anchor" href="#added-0-2-5-1"></a></h3>
<ul><li>Add (vanilla) Stability Selection (without Error Control).</li>
<li>
<code>max_rules</code> hyper parameters for max rules filtering.</li>
<li>Uncertainty Quantification in estimation by bootstrapping.</li>
<li>
<code>B</code> hyper-parameter,</li>
<li>
<code>subsample</code> hyper-parameter.</li>
<li>
<code>rules</code>(implicit form) in cre() function return.</li>
<li>predict() function for ITE estimation via CRE.</li>
</ul></div>
<div class="section level3">
<h3 id="changed-0-2-5">Changed<a class="anchor" aria-label="anchor" href="#changed-0-2-5"></a></h3>
<ul><li>Type <code>stability_selection</code> binary -> string (‘no’,‘vanilla’,‘error_control’).</li>
<li>Unify <code>ntrees_gbm</code> hyper-parameter and <code>ntrees_gbm</code> hyper-parameter in <code>ntrees</code> hyper-parameter.</li>
<li>In rules generation retrieve decision rules also from internal nodes, and not just from terminal nodes.</li>
<li>
<code>ite_method_dis</code>, <code>ite_method_inf</code> method-parameter -> <code>ite_method</code>.</li>
<li>
<code>ps_method_dis</code>, <code>ps_method_inf</code> method-parameter -> <code>learner_ps</code>.</li>
<li>
<code>oreg_method_dis</code>, <code>oreg_method_inf</code> method-parameter -> <code>learner_y</code>.</li>
</ul></div>
<div class="section level3">
<h3 id="removed-0-2-5-1">Removed<a class="anchor" aria-label="anchor" href="#removed-0-2-5-1"></a></h3>
<ul><li>
<code>max_nodes</code> hyper-parameter.</li>
<li>Remove rules generation by Generalized Boosted Regression.</li>
<li>
<code>replace</code> hyper-parameter.</li>
<li>
<code>penalty_rl</code> hyper-parameter.</li>
<li>
<code>t_pvalue</code> hyper-parameter.</li>
<li>
<code>ite_pred</code> from cre() function return.</li>
</ul></div>
<div class="section level3">
<h3 id="bug-fixes-0-2-5">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-2-5"></a></h3>
<ul><li>Error saving covariates name in CRE result when using <code>intervention_vars</code>.</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="0.2.4" id="cre-024-2023-6-14">CRE 0.2.4 (2023-6-14)<a class="anchor" aria-label="anchor" href="#cre-024-2023-6-14"></a></h2><p class="text-muted">CRAN release: 2023-06-14</p>
<div class="section level3">
<h3 id="changed-0-2-4">Changed<a class="anchor" aria-label="anchor" href="#changed-0-2-4"></a></h3>
<ul><li>Method paper description is updated.</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="0.2.3" id="cre-023-2023-4-27">CRE 0.2.3 (2023-4-27)<a class="anchor" aria-label="anchor" href="#cre-023-2023-4-27"></a></h2><p class="text-muted">CRAN release: 2023-04-27</p>
<div class="section level3">
<h3 id="removed-0-2-3">Removed<a class="anchor" aria-label="anchor" href="#removed-0-2-3"></a></h3>
<ul><li>Bayesian Causal Forest (<code>bcf</code>) ITE estimator is not supported.</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="0.2.2" id="cre-022-2023-4-17">CRE 0.2.2 (2023-4-17)<a class="anchor" aria-label="anchor" href="#cre-022-2023-4-17"></a></h2><p class="text-muted">CRAN release: 2023-04-17</p>
<div class="section level3">
<h3 id="changed-0-2-2">Changed<a class="anchor" aria-label="anchor" href="#changed-0-2-2"></a></h3>
<ul><li>Fixed failing unit tests on specific operating systems.</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="0.2.1" id="cre-021-2023-3-17">CRE 0.2.1 (2023-3-17)<a class="anchor" aria-label="anchor" href="#cre-021-2023-3-17"></a></h2><p class="text-muted">CRAN release: 2023-03-17</p>
<div class="section level3">
<h3 id="changed-0-2-1">Changed<a class="anchor" aria-label="anchor" href="#changed-0-2-1"></a></h3>
<ul><li>Replace BATE with ATE in CATE Linear Decomposition.</li>
<li>Update <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot()</a></code> function (remove ATE, old BATE, and explicit AATEs).</li>
</ul></div>
<div class="section level3">
<h3 id="added-0-2-1">Added<a class="anchor" aria-label="anchor" href="#added-0-2-1"></a></h3>
<ul><li>Code of Conduct.</li>
</ul></div>
<div class="section level3">
<h3 id="removed-0-2-1">Removed<a class="anchor" aria-label="anchor" href="#removed-0-2-1"></a></h3>
<ul><li>Causal Tree benchmark in functional tests.</li>
</ul></div>
<div class="section level3">
<h3 id="bug-fixes-0-2-1">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-2-1"></a></h3>
<ul><li>Rank-Deficient Rule Matrix Issue (redundant rules).</li>
<li>Intervention Variables Filtering (ordered filtering).</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="0.2.0" id="cre-020-2023-1-19">CRE 0.2.0 (2023-1-19)<a class="anchor" aria-label="anchor" href="#cre-020-2023-1-19"></a></h2><p class="text-muted">CRAN release: 2023-01-19</p>
<div class="section level3">
<h3 id="changed-0-2-0">Changed<a class="anchor" aria-label="anchor" href="#changed-0-2-0"></a></h3>
<ul><li>
<code>offset</code> method-parameter -> hyper-parameter</li>
<li>
<code>estimate_ite_poisson</code> function -> <code>estimate_ite_tpoisson</code>
</li>
<li>
<code>max_dacay</code> hyper-parameter -> <code>t_decay</code>.</li>
<li>
<code>interpret_select_rules</code> function -> <code>interpret_rules</code>.</li>
<li>
<code>generate_causal_rules</code> function -> <code>discover_rules</code>.</li>
<li>
<code>discover_causal_rules</code> function -><code>select_rules</code>.</li>
<li>
<code>offset_name</code> method parameter -> <code>offset</code>.</li>
<li>Hyper and method parameters are no more required arguments for <code>cre</code>.</li>
<li>
<code>cre</code> object: added parameters and ite estimation.</li>
</ul></div>
<div class="section level3">
<h3 id="added-0-2-0">Added<a class="anchor" aria-label="anchor" href="#added-0-2-0"></a></h3>
<ul><li>Synthetic data set with 1 or 3 rules (<code>generate_cre_dataset</code>).</li>
<li>S-Learner (<code>slearner</code>) method for ITE estimation.</li>
<li>T-Learner (<code>tlearner</code>) method for ITE estimation.</li>
<li>X-Learner (<code>xlearner</code>) method for ITE estimation.</li>
<li>Rules Selection description in <code>summary.cre</code>.</li>
<li>
<code>verbose</code> parameter in <code>summary.cre</code>.</li>
<li>
<code>ite</code>, additional <code>cre</code> input parameter to use personalized ite estimations.</li>
<li>Default values for hyper parameters.</li>
<li>Default values for method parameters.</li>
<li>Simulation experiments for estimation (<code>estimation.R</code>).</li>
<li>Simulation experiments for discovery (<code>discovery.R</code>).</li>
<li>
<code>extract_effect_modifiers</code> function (utility for performance evaluation).</li>
<li>
<code>evaluate</code> function for discovery evaluation.</li>
<li>
<code>confounding</code> parameter in <code>generate_cre_dataset</code> to set confounding type.</li>
<li>
<code>ite_pred</code> and <code>model</code> in CRE results.</li>
<li>
<code>binary_covariates</code> parameter in <code>generate_cre_dataset</code> to set covariates domain.</li>
</ul></div>
<div class="section level3">
<h3 id="removed-0-2-0">Removed<a class="anchor" aria-label="anchor" href="#removed-0-2-0"></a></h3>
<ul><li>
<code>include_ps_inf</code> method-parameter.</li>
<li>
<code>include_ps_dis</code> method-parameter.</li>
<li>
<code>oreg</code> method for ITE estimation.</li>
<li>
<code>ipw</code> method for ITE estimation.</li>
<li>
<code>sipw</code> method for ITE estimation.</li>
<li>ITE standard deviation estimation.</li>
<li>
<code>type_decay</code> hyper-parameter.</li>
<li>Keep only <code>linreg</code> for CATE estimation (remove <code>cate_method</code> and <code>cate_SL_library</code> parameters).</li>
<li>
<code>method_params</code> and <code>hyper_params</code> additional parameters in <code>summary.cre</code>.</li>
<li>ite standardization for Rules Generation.</li>
<li>
<code>random_state</code> parameter.</li>
<li>
<code>include_offset</code> method parameter.</li>
</ul></div>
<div class="section level3">
<h3 id="bug-fixes-0-2-0">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-2-0"></a></h3>
<ul><li>Rules Generation Issue (set rules length and fix bootstrapping).</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="0.1.1" id="cre-011-2022-10-18">CRE 0.1.1 (2022-10-18)<a class="anchor" aria-label="anchor" href="#cre-011-2022-10-18"></a></h2><p class="text-muted">CRAN release: 2022-10-22</p>
<div class="section level3">
<h3 id="changed-0-1-1">Changed<a class="anchor" aria-label="anchor" href="#changed-0-1-1"></a></h3>
<ul><li>
<code>binary</code> parameter in <code>generate_cre_dataset</code> -> <code>binary_outcome</code> .</li>
<li>
<code>filter_cate</code> hyper-parameter -> <code>t_pvalue</code>.</li>
<li>
<code>t_anom</code> hyper-parameter -> <code>t_ext</code>.</li>
<li>
<code>effect_modifier</code> hyper-parameter -> <code>intervention_vars</code>.</li>
<li>
<code>lasso_rules_filter</code> function -> <code>discover_causal_rules</code>.</li>
<li>
<code>split_data</code> function -> <code>honest_splitting</code>.</li>
<li>
<code>prune_rules</code> function -> `<code>filter_irrelevant_rules</code>.</li>
<li>
<code>discard_correlated_rules</code> function -> <code>filter_correlated_rules</code>.</li>
<li>
<code>discard_anomalous_rules</code> function -> <code>filter_extreme_rules</code>.</li>
</ul></div>
<div class="section level3">
<h3 id="added-0-1-1">Added<a class="anchor" aria-label="anchor" href="#added-0-1-1"></a></h3>
<ul><li>Weighted LASSO for Causal Rules Discovery (by <code>penalty_rl</code> hyper-parameter).</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="0.1.0" id="cre-010-2022-10-17">CRE 0.1.0 (2022-10-17)<a class="anchor" aria-label="anchor" href="#cre-010-2022-10-17"></a></h2><p class="text-muted">CRAN release: 2022-10-18</p>
<div class="section level3">
<h3 id="changed-0-1-0">Changed<a class="anchor" aria-label="anchor" href="#changed-0-1-0"></a></h3>
<ul><li>Update examples and tests for all functions.</li>
<li>
<code>q</code> hyper-parameter -> <code>cutoff</code>.</li>
<li>
<code>pfer_val</code> hyper-parameter -> <code>pfer</code>.</li>
<li>
<code>select_causal_rules</code> function -> <code>lasso_rules_filter</code>.</li>
<li>
<code>t</code> hyper-parameter -> <code>t_anom</code>.</li>
<li>Separate standardization, and remove filtering from <code>generate_rules_matrix</code> function.</li>
<li>
<code>summary.cre</code> function to describe results.</li>
<li>
<code>min_nodes</code> hyper-parameter -> <code>node_size</code> (<code>randomForest</code> convention).</li>
<li>
<code>cre</code> returns an S3 object.</li>
</ul></div>
<div class="section level3">
<h3 id="added-0-1-0">Added<a class="anchor" aria-label="anchor" href="#added-0-1-0"></a></h3>
<ul><li>Examples and tests for all functions.</li>
<li>
<code>prune_rules</code> function to discard un-predictive rules.</li>
<li>
<code>discard_anomalous_rules</code> function to discard anomalous rules (see <code>t_corr</code> hyper-parameter.).</li>
<li>
<code>discard_correlated_rules</code> function to discard correlated rules (see <code>t_anom</code> hyper-parameter).</li>
<li>
<code>effect_modifiers</code> parameter in <code>generate_rules</code> function for covariates filtering.</li>
<li>
<code>generate_causal_rules</code> function.</li>
<li>Helper function with <code>SuperLearner</code> package for propensity score estimation in <code>estimate_ite_xyz</code>.</li>
<li>Five methods for CATE estimation (<code>poisson</code>, <code>DRLearner</code>, <code>bart-baggr</code>, <code>cf-means</code>, <code>linreg</code>) in <code>estimate_cate</code> function.</li>
<li>(<code>ps_method_dis</code>, <code>ps_method_inf</code>, <code>or_method_dis</code>, <code>or_method_inf</code>, <code>cate_SL_library</code>) method-parameters to complement <code>SuperLearner</code> package.</li>
<li>
<code>cate_method</code> method-parameter to select CATE estimation method.</li>
<li>
<code>filter_cate</code> method-parameter for estimation filtering.</li>
<li>
<code>p</code> parameter (in <code>generate_cre_dataset</code> function) to set the number of covariates.</li>
<li>
<code>replace</code> parameter (in <code>generate_rules</code> function) to allow bootstrapping.</li>
<li>
<code>cre.print</code> generic function to print <code>cre</code> S3 object results.</li>
<li>
<code>cre.summary</code> generic functions to summarize <code>cre</code> S3 object Results.</li>
<li>
<code>check_input</code> function to isolate input checks.</li>
<li>
<code>estimate_ite_aipw</code> function for augmented inverse propensity weighting.</li>
<li>
<code>plot.cre</code> generic function to plot <code>cre</code> S3 object results.</li>
<li>
<code>test-cre_functional.R</code> to test the functionality of the package.</li>
<li>
<code>stability_selection</code> function for causal rules selection.</li>
</ul></div>
<div class="section level3">
<h3 id="removed-0-1-0">Removed<a class="anchor" aria-label="anchor" href="#removed-0-1-0"></a></h3>
<ul><li>
<code>estimate_ite_blp</code> function.</li>
<li>
<code>take1()</code> function.</li>
</ul></div>
<div class="section level3">
<h3 id="bug-fixes-0-1-0">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-1-0"></a></h3>
<ul><li>Undesired ‘All’ Decision Rule Issue.</li>
<li>No Causal Rule Selected Issue.</li>
</ul></div>
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="0.0.1" id="cre-001-2021-10-20">CRE 0.0.1 (2021-10-20)<a class="anchor" aria-label="anchor" href="#cre-001-2021-10-20"></a></h2>
<div class="section level3">
<h3 id="changed-0-0-1">Changed<a class="anchor" aria-label="anchor" href="#changed-0-0-1"></a></h3>
<ul><li>
<code>estimate_cate</code> include two methods for estimating the CATE values.</li>
<li>
<code>cre</code> added initial checks for binary outcome and whether to include the propensity score in the ITE estimation.</li>
<li>
<code>estimate_ite_xyz</code> conduct propensity score estimation using helper function.</li>
</ul></div>
<div class="section level3">
<h3 id="added-0-0-1">Added<a class="anchor" aria-label="anchor" href="#added-0-0-1"></a></h3>
<ul><li>Example for <code>generate_cre_dataset</code>.</li>
<li>
<code>set_logger</code> and <code>get_logger</code>.</li>
<li>
<code>check_input_data</code> function.</li>
<li>
<code>generate_cre_dataset</code> function to generate synthetic data for testing the package.</li>
<li>
<code>test-generate_cre_dataset</code> function test.</li>
<li>
<code>estimate_ps</code> function to estimate the propensity score.</li>
<li>
<code>estimate_ite_xbart</code> function to generate ITE estimates using accelerated BART.</li>
<li>
<code>estimate_ite_xbcf</code> function to generate ITE estimates using accelerated BCF.</li>
<li>
<code>analyze_sensitivity</code> function to conduct sensitivity analysis for unmeasured confounding.</li>
<li>
<code>cre</code> function to perform the entire Causal Rule Ensemble method.</li>
<li>
<code>estimate_cate</code> function to generate CATE estimates from the ITE estimates and select rules.</li>
<li>
<code>estimate_ite</code> function to generate ITE estimates using the user-specified method (calls the other <code>estimate_ite_xyz</code> functions).</li>
<li>
<code>estimate_ite_bart</code> function to generate ITE estimates using BART.</li>
<li>
<code>estimate_ite_bcf</code> function to generate ITE estimates using Bayesian Causal Forests.</li>
<li>
<code>estimate_ite_cf</code> function to generate ITE estimates using Causal Forests.</li>
<li>
<code>estimate_ite_ipw</code> function to generate ITE estimates using IPW.</li>
<li>
<code>estimate_ite_or</code> function to generate ITE estimates using Outcome Regression.</li>
<li>
<code>estimate_ite_sipw</code> function to generate ITE estimates using SIPW.</li>
<li>
<code>extract_rules</code> function to extract a list of causal rules from randomForest and GBM models.</li>
<li>
<code>generate_rules</code> function to generate causal rule models using randomForest and GBM methods.</li>
<li>
<code>generate_rules_matrix</code> function to convert a list of causal rules into a matrix.</li>
<li>
<code>select_causal_rules</code> function to apply penalized regression to causal rules. to select only the most important ones.</li>
<li>
<code>split_data</code> function to split input data into discovery and inference subsamples.</li>
<li>
<code>take1</code> function to create a subsample of indices.</li>
</ul></div>
<div class="section level3">
<h3 id="removed-0-0-1">Removed<a class="anchor" aria-label="anchor" href="#removed-0-0-1"></a></h3>
<ul><li>
<code>seed</code> argument in <code>generate_cre_datase</code> function.</li>
</ul></div>
</div>
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