diff --git a/404.html b/404.html index c49ea32..8f98ce0 100644 --- a/404.html +++ b/404.html @@ -4,113 +4,87 @@ - + Page not found (404) • stochtree - - - + + + - - + - + + Skip to contents -
-
-
-
-

Page not found (404)

Content not found. Please use links in the navbar. -
- - - +
- -
- diff --git a/LICENSE-text.html b/LICENSE-text.html index 8801364..9a13e48 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -1,91 +1,72 @@ -License • stochtreeLicense • stochtree + + Skip to contents -
-
-
-
-

License

+ +
+
+
+
+

License

+ 
YEAR: 2024
 COPYRIGHT HOLDER: stochtree authors
-
- - - -
+
- -
-

Developed by Drew Herren, Richard Hahn, Jared Murray, Carlos Carvalho, Jingyu He.

+
+

Developed by Drew Herren, Richard Hahn, Jared Murray, Carlos Carvalho, Jingyu He.

-
-

Site built with pkgdown 2.0.9.

+
+

Site built with pkgdown 2.0.9.

-
+
- diff --git a/LICENSE.html b/LICENSE.html index fd501cb..f4bf5bd 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -1,62 +1,51 @@ -MIT License • stochtreeMIT License • stochtree + + Skip to contents -
-
-
-
-

MIT License

+ +
+
+
+
+

MIT License

+
@@ -67,29 +56,21 @@

MIT License

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

-
- - - -
- +
-
-

Developed by Drew Herren, Richard Hahn, Jared Murray, Carlos Carvalho, Jingyu He.

+
+

Developed by Drew Herren, Richard Hahn, Jared Murray, Carlos Carvalho, Jingyu He.

-
-

Site built with pkgdown 2.0.9.

+
+

Site built with pkgdown 2.0.9.

-
+
- diff --git a/articles/BayesianSupervisedLearning.html b/articles/BayesianSupervisedLearning.html index a82881e..53e6cce 100644 --- a/articles/BayesianSupervisedLearning.html +++ b/articles/BayesianSupervisedLearning.html @@ -4,88 +4,75 @@ - + + Bayesian Supervised Learning in StochTree • stochtree - - - + + + - - + - + + Skip to contents -
-
-
-
-

Bayesian Supervised Learning in StochTree

+
+
+

Bayesian Supervised Learning in StochTree

- - +
BayesianSupervisedLearning.Rmd
@@ -94,7 +81,7 @@

Bayesian Supervised Learning in StochTree

function for Bayesian supervised learning (Chipman, George, and McCulloch (2010)). To begin, we load the stochtree package.

+library(stochtree)

Demo 1: Step Function

@@ -408,34 +395,25 @@

References - - -

- +
-
- diff --git a/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot-1.png b/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot-1.png index 3e21df7..127d085 100644 Binary files a/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot-1.png and b/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot-1.png differ diff --git a/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot-2.png b/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot-2.png index eedc64b..87d30c1 100644 Binary files a/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot-2.png and b/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot-2.png differ diff --git a/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm-1.png b/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm-1.png index 6149cd0..ce55d37 100644 Binary files a/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm-1.png and b/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm-1.png differ diff --git a/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm-2.png b/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm-2.png index 47ae4b9..91c1dcc 100644 Binary files a/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm-2.png and b/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm-2.png differ diff --git a/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm_rfx-1.png b/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm_rfx-1.png index 0017aad..629c28e 100644 Binary files a/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm_rfx-1.png and b/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm_rfx-1.png differ diff --git a/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm_rfx-2.png b/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm_rfx-2.png index 96aede5..e5ed0f7 100644 Binary files a/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm_rfx-2.png and b/articles/BayesianSupervisedLearning_files/figure-html/bart_root_plot_plm_rfx-2.png differ diff --git a/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot-1.png b/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot-1.png index 05cb8de..cebd87d 100644 Binary files a/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot-1.png and b/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot-1.png differ diff --git a/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot-2.png b/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot-2.png index 41a5249..7385803 100644 Binary files a/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot-2.png and b/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot-2.png differ diff --git a/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm-1.png b/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm-1.png index 301aff1..dcb8f4d 100644 Binary files a/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm-1.png and b/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm-1.png differ diff --git a/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm-2.png b/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm-2.png index fa5f987..19e7d74 100644 Binary files a/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm-2.png and b/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm-2.png differ diff --git a/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm_rfx-1.png b/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm_rfx-1.png index c8ee1ef..ea90be3 100644 Binary files a/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm_rfx-1.png and b/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm_rfx-1.png differ diff --git a/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm_rfx-2.png b/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm_rfx-2.png index ec7d9cd..22fe67c 100644 Binary files a/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm_rfx-2.png and b/articles/BayesianSupervisedLearning_files/figure-html/bart_warmstart_plot_plm_rfx-2.png differ diff --git a/articles/CausalInference.html b/articles/CausalInference.html index eda4d89..6923b8e 100644 --- a/articles/CausalInference.html +++ b/articles/CausalInference.html @@ -4,88 +4,75 @@ - + + Causal Machine Learning in StochTree • stochtree - - - + + + - - + - + + Skip to contents -
-
-
-
-

Causal Machine Learning in StochTree

+
+
+

Causal Machine Learning in StochTree

- - +
CausalInference.Rmd
@@ -93,7 +80,7 @@

Causal Machine Learning in StochTree

This vignette demonstrates how to use the bcf() function for supervised learning. To begin, we load the stochtree package.

+library(stochtree)

We also define several simple functions that configure the data generating processes used in this vignette.

@@ -265,7 +252,7 @@ 
BART MCMC without Warmstart(test_ub >= tau_x[test_inds])
 )
 mean(cover)
-#> [1] 0.96
+#> [1] 0.87
@@ -383,7 +370,7 @@
Warmstart(test_ub >= tau_x[test_inds]) ) mean(cover) -#> [1] 0.89
+#> [1] 0.8
BART MCMC without Warmstart @@ -429,7 +416,7 @@
BART MCMC without Warmstart(test_ub >= tau_x[test_inds]) ) mean(cover) -#> [1] 0.82
+#> [1] 0.96
@@ -707,7 +694,7 @@
Warmstart(test_ub >= tau_x[test_inds]) ) mean(cover) -#> [1] 0.99 +#> [1] 1
BART MCMC without Warmstart @@ -753,7 +740,7 @@
BART MCMC without Warmstart(test_ub >= tau_x[test_inds]) ) mean(cover) -#> [1] 0.98
+#> [1] 0.975 @@ -880,7 +867,7 @@
Warmstart(test_ub >= tau_x[test_inds]) ) mean(cover) -#> [1] 0.94 +#> [1] 0.96

It is clear that causal inference is much more difficult in the presence of both strong covariate-dependent prognostic effects and strong group-level random effects. In this sense, proper @@ -998,7 +985,7 @@

MCMC, full covariate set in 
 test_mean <- rowMeans(bcf_model_mcmc$tau_hat_test)
 sqrt(mean((test_mean - tau_test)^2))
-#> [1] 0.3537478
+#> [1] 0.3602501
MCMC, covariate subset in \(\tau(X)\) @@ -1051,7 +1038,7 @@
MCMC, covariate subset in 
 test_mean <- rowMeans(bcf_model_mcmc$tau_hat_test)
 sqrt(mean((test_mean - tau_test)^2))
-#> [1] 0.3634036
+#> [1] 0.3682418
Warmstart, full covariate set in \(\tau(X)\) @@ -1103,7 +1090,7 @@
Warmstart, full covariate set in < 
 test_mean <- apply(bcf_model_warmstart$tau_hat_test, 1, mean)
 sqrt(mean((tau_x[test_inds] - test_mean)^2))
-#> [1] 0.3707581
+#> [1] 0.3825377
Warmstart, covariate subset in \(\tau(X)\) @@ -1157,7 +1144,7 @@
Warmstart, covariate subset in 
 test_mean <- apply(bcf_model_warmstart$tau_hat_test, 1, mean)
 sqrt(mean((tau_x[test_inds] - test_mean)^2))
-#> [1] 0.3568036
+#> [1] 0.3445904 @@ -1274,7 +1261,7 @@
Warmstart(test_ub >= tau_x[test_inds]) ) mean(cover) -#> [1] 0.89 +#> [1] 0.87
BART MCMC without Warmstart @@ -1320,7 +1307,7 @@
BART MCMC without Warmstart(test_ub >= tau_x[test_inds]) ) mean(cover) -#> [1] 0.85
+#> [1] 0.84 @@ -1343,34 +1330,25 @@

References - - - - + - - diff --git a/articles/CausalInference_files/figure-html/bart_root_plot-1.png b/articles/CausalInference_files/figure-html/bart_root_plot-1.png index 74c5593..b4955b5 100644 Binary files a/articles/CausalInference_files/figure-html/bart_root_plot-1.png and b/articles/CausalInference_files/figure-html/bart_root_plot-1.png differ diff --git a/articles/CausalInference_files/figure-html/bart_root_plot-2.png b/articles/CausalInference_files/figure-html/bart_root_plot-2.png index 223aaed..9ddfae5 100644 Binary files a/articles/CausalInference_files/figure-html/bart_root_plot-2.png and b/articles/CausalInference_files/figure-html/bart_root_plot-2.png differ diff --git a/articles/CausalInference_files/figure-html/bart_root_plot-3.png b/articles/CausalInference_files/figure-html/bart_root_plot-3.png index 970b818..02e8ffb 100644 Binary files a/articles/CausalInference_files/figure-html/bart_root_plot-3.png and b/articles/CausalInference_files/figure-html/bart_root_plot-3.png differ diff --git a/articles/CausalInference_files/figure-html/bart_root_plot_2-1.png b/articles/CausalInference_files/figure-html/bart_root_plot_2-1.png index b5defb1..ea28b0e 100644 Binary files a/articles/CausalInference_files/figure-html/bart_root_plot_2-1.png and b/articles/CausalInference_files/figure-html/bart_root_plot_2-1.png differ diff --git a/articles/CausalInference_files/figure-html/bart_root_plot_2-2.png b/articles/CausalInference_files/figure-html/bart_root_plot_2-2.png index 966cc26..7d5c8f0 100644 Binary files a/articles/CausalInference_files/figure-html/bart_root_plot_2-2.png and b/articles/CausalInference_files/figure-html/bart_root_plot_2-2.png differ diff --git a/articles/CausalInference_files/figure-html/bart_root_plot_2-3.png b/articles/CausalInference_files/figure-html/bart_root_plot_2-3.png index 590f190..c600a33 100644 Binary files a/articles/CausalInference_files/figure-html/bart_root_plot_2-3.png and b/articles/CausalInference_files/figure-html/bart_root_plot_2-3.png differ diff --git a/articles/CausalInference_files/figure-html/bart_root_plot_3-1.png b/articles/CausalInference_files/figure-html/bart_root_plot_3-1.png index 75bdb20..11fa356 100644 Binary files a/articles/CausalInference_files/figure-html/bart_root_plot_3-1.png and b/articles/CausalInference_files/figure-html/bart_root_plot_3-1.png differ diff --git a/articles/CausalInference_files/figure-html/bart_root_plot_3-2.png b/articles/CausalInference_files/figure-html/bart_root_plot_3-2.png index d1f7085..b317763 100644 Binary files a/articles/CausalInference_files/figure-html/bart_root_plot_3-2.png and b/articles/CausalInference_files/figure-html/bart_root_plot_3-2.png differ diff --git a/articles/CausalInference_files/figure-html/bart_root_plot_3-3.png b/articles/CausalInference_files/figure-html/bart_root_plot_3-3.png index ccf92e2..e74033a 100644 Binary files a/articles/CausalInference_files/figure-html/bart_root_plot_3-3.png and b/articles/CausalInference_files/figure-html/bart_root_plot_3-3.png differ diff --git a/articles/CausalInference_files/figure-html/bart_root_plot_4-1.png b/articles/CausalInference_files/figure-html/bart_root_plot_4-1.png index 5286f77..8cf43ac 100644 Binary files a/articles/CausalInference_files/figure-html/bart_root_plot_4-1.png and b/articles/CausalInference_files/figure-html/bart_root_plot_4-1.png differ diff --git a/articles/CausalInference_files/figure-html/bart_root_plot_4-2.png b/articles/CausalInference_files/figure-html/bart_root_plot_4-2.png index f0dc06e..d8471b7 100644 Binary files a/articles/CausalInference_files/figure-html/bart_root_plot_4-2.png and b/articles/CausalInference_files/figure-html/bart_root_plot_4-2.png differ diff --git a/articles/CausalInference_files/figure-html/bart_root_plot_4-3.png b/articles/CausalInference_files/figure-html/bart_root_plot_4-3.png index f2ef599..e6ffb67 100644 Binary files a/articles/CausalInference_files/figure-html/bart_root_plot_4-3.png and b/articles/CausalInference_files/figure-html/bart_root_plot_4-3.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot-1.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot-1.png index 2ffbad1..6326b26 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot-1.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot-1.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot-2.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot-2.png index 66e8d1b..96bf8f7 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot-2.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot-2.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot-3.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot-3.png index 17f8b23..2eeb0a8 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot-3.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot-3.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot_2-1.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot_2-1.png index 8afe916..b0d8d0b 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot_2-1.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot_2-1.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot_2-2.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot_2-2.png index a62da49..4af8299 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot_2-2.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot_2-2.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot_2-3.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot_2-3.png index 6e17333..4b86b41 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot_2-3.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot_2-3.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot_3-1.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot_3-1.png index a4ae8d8..558e195 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot_3-1.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot_3-1.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot_3-2.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot_3-2.png index 174a5fe..1cfd0aa 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot_3-2.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot_3-2.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot_3-3.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot_3-3.png index ecaa392..d8a1ca9 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot_3-3.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot_3-3.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot_4-1.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot_4-1.png index ff6196c..0e3479f 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot_4-1.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot_4-1.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot_4-2.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot_4-2.png index 8a10932..5299180 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot_4-2.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot_4-2.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot_4-3.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot_4-3.png index 2e5fab2..45f52b6 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot_4-3.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot_4-3.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-1.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-1.png index 838d014..1749670 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-1.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-1.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-2.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-2.png index cda60d5..224286d 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-2.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-2.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-3.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-3.png index d123a75..3a7fef6 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-3.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-3.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-4.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-4.png index f15404d..00a7bd5 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-4.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-4.png differ diff --git a/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-5.png b/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-5.png index 79e2913..063933f 100644 Binary files a/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-5.png and b/articles/CausalInference_files/figure-html/bart_warmstart_plot_rfx-5.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-23-1.png b/articles/CausalInference_files/figure-html/unnamed-chunk-23-1.png index cdbbd0d..6a832a6 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-23-1.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-23-1.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-23-2.png b/articles/CausalInference_files/figure-html/unnamed-chunk-23-2.png index 29657e0..1b3795f 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-23-2.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-23-2.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-23-3.png b/articles/CausalInference_files/figure-html/unnamed-chunk-23-3.png index a79efae..6cc88ab 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-23-3.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-23-3.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-27-1.png b/articles/CausalInference_files/figure-html/unnamed-chunk-27-1.png index 8cbc2da..c92e248 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-27-1.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-27-1.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-27-2.png b/articles/CausalInference_files/figure-html/unnamed-chunk-27-2.png index 2f3b82c..4195d9a 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-27-2.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-27-2.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-27-3.png b/articles/CausalInference_files/figure-html/unnamed-chunk-27-3.png index c174200..db405bf 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-27-3.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-27-3.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-31-1.png b/articles/CausalInference_files/figure-html/unnamed-chunk-31-1.png index 373cbeb..eff5305 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-31-1.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-31-1.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-31-2.png b/articles/CausalInference_files/figure-html/unnamed-chunk-31-2.png index 71f86f9..37b0759 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-31-2.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-31-2.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-31-3.png b/articles/CausalInference_files/figure-html/unnamed-chunk-31-3.png index 7718dae..a9da42c 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-31-3.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-31-3.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-35-1.png b/articles/CausalInference_files/figure-html/unnamed-chunk-35-1.png index 4b847e3..0b0633d 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-35-1.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-35-1.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-35-2.png b/articles/CausalInference_files/figure-html/unnamed-chunk-35-2.png index ca56be2..3bfca8c 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-35-2.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-35-2.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-35-3.png b/articles/CausalInference_files/figure-html/unnamed-chunk-35-3.png index 589f3c5..8d927b1 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-35-3.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-35-3.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-40-1.png b/articles/CausalInference_files/figure-html/unnamed-chunk-40-1.png index cc78587..d2c2cdc 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-40-1.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-40-1.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-40-2.png b/articles/CausalInference_files/figure-html/unnamed-chunk-40-2.png index 1c8c8a4..ff62719 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-40-2.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-40-2.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-40-3.png b/articles/CausalInference_files/figure-html/unnamed-chunk-40-3.png index bbbf72b..9093f67 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-40-3.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-40-3.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-43-1.png b/articles/CausalInference_files/figure-html/unnamed-chunk-43-1.png index 1537897..52b1184 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-43-1.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-43-1.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-43-2.png b/articles/CausalInference_files/figure-html/unnamed-chunk-43-2.png index 1b16a65..c942028 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-43-2.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-43-2.png differ diff --git a/articles/CausalInference_files/figure-html/unnamed-chunk-43-3.png b/articles/CausalInference_files/figure-html/unnamed-chunk-43-3.png index 206cbb0..74dda12 100644 Binary files a/articles/CausalInference_files/figure-html/unnamed-chunk-43-3.png and b/articles/CausalInference_files/figure-html/unnamed-chunk-43-3.png differ diff --git a/articles/CustomSamplingRoutine.html b/articles/CustomSamplingRoutine.html index 1579f47..9345d17 100644 --- a/articles/CustomSamplingRoutine.html +++ b/articles/CustomSamplingRoutine.html @@ -4,88 +4,75 @@ - + + Custom Sampling Routines in StochTree • stochtree - - - + + + - - + - + + Skip to contents -
-
-
-
-

Custom Sampling Routines in StochTree

+
+
+

Custom Sampling Routines in StochTree

- - +
CustomSamplingRoutine.Rmd
@@ -142,7 +129,7 @@

Motivation
-library(stochtree)

+library(stochtree)

Demo 1: Supervised Learning @@ -1080,7 +1067,7 @@

Results

 mean((rowMeans(tau_hat[,1:num_gfr]) - tau_x)^2)
-#> [1] 0.2619911
+#> [1] 0.2827006

Inspect the warm start BART results

 plot(sigma_samples[(num_gfr+1):num_samples], ylab="sigma^2")
@@ -1097,7 +1084,7 @@

Results

 mean((rowMeans(tau_hat[,(num_gfr+1):num_samples]) - tau_x)^2)
-#> [1] 0.2149971
+#> [1] 0.3012734

Inspect the “adaptive coding” parameters \(b_0\) and \(b_1\).

 plot(b_0_samples, col = "blue", ylab = "Coding parameter draws", 
@@ -1144,34 +1131,25 @@ 
References
-
-        
-
- +
- - diff --git a/articles/CustomSamplingRoutine_files/figure-html/adaptive_coding-1.png b/articles/CustomSamplingRoutine_files/figure-html/adaptive_coding-1.png index f324add..547d866 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/adaptive_coding-1.png and b/articles/CustomSamplingRoutine_files/figure-html/adaptive_coding-1.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/bcf_warm_start_plot-1.png b/articles/CustomSamplingRoutine_files/figure-html/bcf_warm_start_plot-1.png index 048f406..47c2695 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/bcf_warm_start_plot-1.png and b/articles/CustomSamplingRoutine_files/figure-html/bcf_warm_start_plot-1.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/bcf_warm_start_plot-2.png b/articles/CustomSamplingRoutine_files/figure-html/bcf_warm_start_plot-2.png index b6df255..3856dac 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/bcf_warm_start_plot-2.png and b/articles/CustomSamplingRoutine_files/figure-html/bcf_warm_start_plot-2.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/bcf_warm_start_plot-3.png b/articles/CustomSamplingRoutine_files/figure-html/bcf_warm_start_plot-3.png index 62844a4..b91632d 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/bcf_warm_start_plot-3.png and b/articles/CustomSamplingRoutine_files/figure-html/bcf_warm_start_plot-3.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/bcf_xbcf_plot-1.png b/articles/CustomSamplingRoutine_files/figure-html/bcf_xbcf_plot-1.png index 194ba55..373f460 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/bcf_xbcf_plot-1.png and b/articles/CustomSamplingRoutine_files/figure-html/bcf_xbcf_plot-1.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/bcf_xbcf_plot-2.png b/articles/CustomSamplingRoutine_files/figure-html/bcf_xbcf_plot-2.png index af39c8f..f4f9d3a 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/bcf_xbcf_plot-2.png and b/articles/CustomSamplingRoutine_files/figure-html/bcf_xbcf_plot-2.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/bcf_xbcf_plot-3.png b/articles/CustomSamplingRoutine_files/figure-html/bcf_xbcf_plot-3.png index 9f7415a..6aed77a 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/bcf_xbcf_plot-3.png and b/articles/CustomSamplingRoutine_files/figure-html/bcf_xbcf_plot-3.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-11-1.png b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-11-1.png index 90bf714..d6f42f0 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-11-1.png and b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-11-1.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-11-2.png b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-11-2.png index 4099b4e..3acce86 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-11-2.png and b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-11-2.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-12-1.png b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-12-1.png index 02b7d5c..f098b88 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-12-1.png and b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-12-1.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-12-2.png b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-12-2.png index c19afd7..92784ae 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-12-2.png and b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-12-2.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-13-1.png b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-13-1.png index 3e0fada..72b3733 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-13-1.png and b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-13-1.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-22-1.png b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-22-1.png index b4ede52..379968b 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-22-1.png and b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-22-1.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-22-2.png b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-22-2.png index 81954d1..8690999 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-22-2.png and b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-22-2.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-23-1.png b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-23-1.png index c82cfc4..2a9c109 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-23-1.png and b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-23-1.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-23-2.png b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-23-2.png index 9477831..93b313a 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-23-2.png and b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-23-2.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-24-1.png b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-24-1.png index 07ef059..dce804b 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-24-1.png and b/articles/CustomSamplingRoutine_files/figure-html/unnamed-chunk-24-1.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/warm_start_plot-1.png b/articles/CustomSamplingRoutine_files/figure-html/warm_start_plot-1.png index 42bb13f..52e6950 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/warm_start_plot-1.png and b/articles/CustomSamplingRoutine_files/figure-html/warm_start_plot-1.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/warm_start_plot-2.png b/articles/CustomSamplingRoutine_files/figure-html/warm_start_plot-2.png index 19abef4..f062ee1 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/warm_start_plot-2.png and b/articles/CustomSamplingRoutine_files/figure-html/warm_start_plot-2.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/xbart_plot-1.png b/articles/CustomSamplingRoutine_files/figure-html/xbart_plot-1.png index 22f34bf..751ebd9 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/xbart_plot-1.png and b/articles/CustomSamplingRoutine_files/figure-html/xbart_plot-1.png differ diff --git a/articles/CustomSamplingRoutine_files/figure-html/xbart_plot-2.png b/articles/CustomSamplingRoutine_files/figure-html/xbart_plot-2.png index e6018e0..ec32b38 100644 Binary files a/articles/CustomSamplingRoutine_files/figure-html/xbart_plot-2.png and b/articles/CustomSamplingRoutine_files/figure-html/xbart_plot-2.png differ diff --git a/articles/EnsembleKernel.html b/articles/EnsembleKernel.html index bfd242a..b34b4b0 100644 --- a/articles/EnsembleKernel.html +++ b/articles/EnsembleKernel.html @@ -4,89 +4,75 @@ - + + Kernel Methods from Tree Ensembles in StochTree • stochtree - - - + + + - - + - + + Skip to contents -
-
-
-
-

Kernel Methods from Tree Ensembles in -StochTree

+
+
+

Kernel Methods from Tree Ensembles in StochTree

- - +
EnsembleKernel.Rmd
@@ -126,7 +112,7 @@

Motivation
-library(stochtree)
+library(stochtree)
 library(tgp)
 library(MASS)
 library(mvtnorm)

@@ -203,7 +189,7 @@

BART-based Gaussian process
 sqrt(mean((yhat_mean_test - y_test)^2))
-#> [1] 0.08843715

+#> [1] 0.09763591
@@ -274,7 +260,7 @@

BART-based Gaussian process
 sqrt(mean((yhat_mean_test - y_test)^2))
-#> [1] 5.834927

+#> [1] 4.92703

While the use case of a BART kernel for classical kriging is perhaps unclear without more empirical investigation, we will see in a later vignette that the kernel approach can be very beneficial for causal @@ -293,34 +279,25 @@

References - - - - + - - diff --git a/articles/EnsembleKernel_files/figure-html/unnamed-chunk-4-1.png b/articles/EnsembleKernel_files/figure-html/unnamed-chunk-4-1.png index 427d41b..01fcb44 100644 Binary files a/articles/EnsembleKernel_files/figure-html/unnamed-chunk-4-1.png and b/articles/EnsembleKernel_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/articles/EnsembleKernel_files/figure-html/unnamed-chunk-8-1.png b/articles/EnsembleKernel_files/figure-html/unnamed-chunk-8-1.png index d62570c..2523106 100644 Binary files a/articles/EnsembleKernel_files/figure-html/unnamed-chunk-8-1.png and b/articles/EnsembleKernel_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/articles/ModelSerialization.html b/articles/ModelSerialization.html index 666bc33..3fb337a 100644 --- a/articles/ModelSerialization.html +++ b/articles/ModelSerialization.html @@ -4,88 +4,75 @@ - + + Model Serialization in StochTree • stochtree - - - + + + - - + - + + Skip to contents -
-
-
-
-

Model Serialization in StochTree

+ + +
+
+

Model Serialization in StochTree

- - +
ModelSerialization.Rmd
@@ -94,7 +81,7 @@

Model Serialization in StochTree

files and deserialize back to an R session, where the forests and other parameters can be used for prediction and further analysis.

+library(stochtree)

We also define several simple functions that configure the data generating processes used in this vignette.

@@ -223,34 +210,25 @@ 
References
-
-        
-
- +
-
- diff --git a/articles/ModelSerialization_files/figure-html/bcf_roundtrip-1.png b/articles/ModelSerialization_files/figure-html/bcf_roundtrip-1.png index 1dcbbf2..9b912ba 100644 Binary files a/articles/ModelSerialization_files/figure-html/bcf_roundtrip-1.png and b/articles/ModelSerialization_files/figure-html/bcf_roundtrip-1.png differ diff --git a/articles/ModelSerialization_files/figure-html/bcf_roundtrip-2.png b/articles/ModelSerialization_files/figure-html/bcf_roundtrip-2.png index 16c0dbd..ba021cf 100644 Binary files a/articles/ModelSerialization_files/figure-html/bcf_roundtrip-2.png and b/articles/ModelSerialization_files/figure-html/bcf_roundtrip-2.png differ diff --git a/articles/ModelSerialization_files/figure-html/bcf_roundtrip-3.png b/articles/ModelSerialization_files/figure-html/bcf_roundtrip-3.png index 5a47480..f39926a 100644 Binary files a/articles/ModelSerialization_files/figure-html/bcf_roundtrip-3.png and b/articles/ModelSerialization_files/figure-html/bcf_roundtrip-3.png differ diff --git a/articles/index.html b/articles/index.html index 19009c0..1f23b14 100644 --- a/articles/index.html +++ b/articles/index.html @@ -1,96 +1,88 @@ -Articles • stochtreeArticles • stochtree + + Skip to contents -
-
-
-
-

Articles

+
  • + +
    +
    High-Level Interface
    + Bayesian Supervised Learning in StochTree + Causal Machine Learning in StochTree + Model Serialization in StochTree +
    +
    Prototype Interface
    + Custom Sampling Routines in StochTree + Kernel Methods from Tree Ensembles in StochTree +
    +
    • + + +
      + + +
      +
      +
      +
      +

      Articles

      -

      All vignettes

      -

      +

      High-Level Interface

      +
      Bayesian Supervised Learning in StochTree
      Causal Machine Learning in StochTree
      -
      Custom Sampling Routines in StochTree
      +
      Model Serialization in StochTree
      -
      Kernel Methods from Tree Ensembles in StochTree
      +
      +
      +

      Prototype Interface

      +
      + +
      Custom Sampling Routines in StochTree
      -
      Model Serialization in StochTree
      +
      Kernel Methods from Tree Ensembles in StochTree
      -
      -
      +
      -
      -

      Developed by Drew Herren, Richard Hahn, Jared Murray, Carlos Carvalho, Jingyu He.

      +
      +

      Developed by Drew Herren, Richard Hahn, Jared Murray, Carlos Carvalho, Jingyu He.

      -
      -

      Site built with pkgdown 2.0.9.

      +
      +

      Site built with pkgdown 2.0.9.

      -
      +
      - diff --git a/authors.html b/authors.html index d100fde..99b1c18 100644 --- a/authors.html +++ b/authors.html @@ -1,65 +1,54 @@ -Authors and Citation • stochtreeAuthors and Citation • stochtree + + Skip to contents -
      -
      -
      -
      -
      -

      Authors and Citation

      -
      + +
      +
      +
      +
      +

      Authors and Citation

      +
      +
      +

      Authors

      • Drew Herren. Author, maintainer. @@ -82,45 +71,39 @@

        Authors and Citation

      -
      -
      -

      Citation

      - -
      -
      +
      +

      Citation

      +

      -

      Herren D, Hahn R, Murray J, Carvalho C, He J (2024). +

      Herren D, Hahn R, Murray J, Carvalho C, He J (2024). stochtree: Stochastic tree ensembles (XBART and BART) for supervised learning and causal inference. -R package version 0.0.0.9000, https://stochastictree.github.io/stochtree-r/. +R package version 0.0.0.9000, https://stochastictree.github.io/stochtree-r/.

      - 
      @Manual{,
+      
      @Manual{,
   title = {stochtree: Stochastic tree ensembles (XBART and BART) for supervised learning and causal inference},
   author = {Drew Herren and Richard Hahn and Jared Murray and Carlos Carvalho and Jingyu He},
   year = {2024},
   note = {R package version 0.0.0.9000},
   url = {https://stochastictree.github.io/stochtree-r/},
 }
      
-
-
      - -
      - +
      +
      -
      -

      Developed by Drew Herren, Richard Hahn, Jared Murray, Carlos Carvalho, Jingyu He.

      +
      +

      Developed by Drew Herren, Richard Hahn, Jared Murray, Carlos Carvalho, Jingyu He.

      -
      -

      Site built with pkgdown 2.0.9.

      +
      +

      Site built with pkgdown 2.0.9.

      -
      +
      - diff --git a/index.html b/index.html index c382a25..eca01ba 100644 --- a/index.html +++ b/index.html @@ -4,86 +4,77 @@ - + + Stochastic tree ensembles (XBART and BART) for supervised learning and causal inference • stochtree - - - + + + - - + - + + Skip to contents -
      -
      -
      -Stochastic tree ensembles (XBART and BART) for supervised learning and causal inference. +
      - -