diff --git a/404.html b/404.html index 90222d7..a8263d0 100644 --- a/404.html +++ b/404.html @@ -7,15 +7,15 @@ Page not found (404) • tidyhte - - + + - - + + + + +
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Attribution

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This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.

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Community Impact Guidelines were inspired by [Mozilla’s code of conduct enforcement ladder][https://github.com/mozilla/inclusion].

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For answers to common questions about this code of conduct, see the FAQ at https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.

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+ + + + + + + + diff --git a/LICENSE-text.html b/LICENSE-text.html index 4d57824..04e2b50 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/LICENSE.html b/LICENSE.html index 00083a3..66dfb06 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/articles/experimental_analysis.html b/articles/experimental_analysis.html index 5ece45e..8cd6d50 100644 --- a/articles/experimental_analysis.html +++ b/articles/experimental_analysis.html @@ -39,7 +39,7 @@ tidyhte - 1.0.1 + 1.0.2 @@ -94,7 +94,7 @@

HTE Analysis in an Experiment

Drew Dimmery (ddimmery@univie.ac.at)

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09 August, 2023

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14 August, 2023

Source: vignettes/experimental_analysis.Rmd @@ -259,7 +259,7 @@

Estimate Models## factor x2 has new levels 1 
 results
-
## # A tibble: 843 × 6
+
## # A tibble: 839 × 6
 ##    estimand term  value level estimate std_error
 ##    <chr>    <chr> <dbl> <chr>    <dbl>     <dbl>
 ##  1 MCATE    x1    -1.80 NA        3.22     0.173
@@ -272,7 +272,7 @@ 
Estimate Models##  8 MCATE    x1    -1.26 NA        2.65     0.137
 ##  9 MCATE    x1    -1.21 NA        2.60     0.135
 ## 10 MCATE    x1    -1.16 NA        2.56     0.134
-## # ℹ 833 more rows

+## # ℹ 829 more rows

ATEs @@ -462,34 +462,28 @@

Session Info## ## other attached packages: ## [1] nnls_1.4 SuperLearner_2.0-28.1 dplyr_1.1.2 -## [4] ggplot2_3.4.2 tidyhte_1.0.1 +## [4] ggplot2_3.4.2 tidyhte_1.0.2 ## ## loaded via a namespace (and not attached): -## [1] shape_1.4.6 gtable_0.3.3 xfun_0.39 -## [4] bslib_0.5.0 lattice_0.21-8 quadprog_1.5-8 -## [7] vctrs_0.6.3 tools_4.3.1 generics_0.1.3 -## [10] tibble_3.2.1 fansi_1.0.4 highr_0.10 -## [13] pkgconfig_2.0.3 Matrix_1.5-4.1 data.table_1.14.8 -## [16] checkmate_2.2.0 desc_1.4.2 lifecycle_1.0.3 -## [19] farver_2.1.1 compiler_4.3.1 stringr_1.5.0 -## [22] textshaping_0.3.6 progress_1.2.2 nprobust_0.4.0 -## [25] munsell_0.5.0 codetools_0.2-19 htmltools_0.5.5 -## [28] sass_0.4.7 yaml_2.3.7 glmnet_4.1-7 -## [31] pillar_1.9.0 pkgdown_2.0.7 crayon_1.5.2 -## [34] jquerylib_0.1.4 MASS_7.3-60 cachem_1.0.8 -## [37] iterators_1.0.14 boot_1.3-28.1 foreach_1.5.2 -## [40] tidyselect_1.2.0 digest_0.6.33 stringi_1.7.12 -## [43] purrr_1.0.1 labeling_0.4.2 splines_4.3.1 -## [46] distances_0.1.9 rprojroot_2.0.3 fastmap_1.1.1 -## [49] grid_4.3.1 colorspace_2.1-0 cli_3.6.1 -## [52] magrittr_2.0.3 survival_3.5-5 utf8_1.2.3 -## [55] withr_2.5.0 prettyunits_1.1.1 scales_1.2.1 -## [58] backports_1.4.1 vimp_2.3.1 rmarkdown_2.23 -## [61] WeightedROC_2020.1.31 ragg_1.2.5 hms_1.1.3 -## [64] gam_1.22-2 memoise_2.0.1 evaluate_0.21 -## [67] knitr_1.43 rlang_1.1.1 Rcpp_1.0.11 -## [70] glue_1.6.2 quickblock_0.2.0 jsonlite_1.8.7 -## [73] R6_2.5.1 systemfonts_1.0.4 fs_1.6.3 +## [1] shape_1.4.6 gtable_0.3.3 xfun_0.40 bslib_0.5.1 +## [5] lattice_0.21-8 quadprog_1.5-8 vctrs_0.6.3 tools_4.3.1 +## [9] generics_0.1.3 tibble_3.2.1 fansi_1.0.4 highr_0.10 +## [13] pkgconfig_2.0.3 Matrix_1.5-4.1 data.table_1.14.8 checkmate_2.2.0 +## [17] desc_1.4.2 lifecycle_1.0.3 farver_2.1.1 compiler_4.3.1 +## [21] stringr_1.5.0 textshaping_0.3.6 progress_1.2.2 nprobust_0.4.0 +## [25] munsell_0.5.0 codetools_0.2-19 htmltools_0.5.6 sass_0.4.7 +## [29] yaml_2.3.7 glmnet_4.1-7 pillar_1.9.0 pkgdown_2.0.7 +## [33] crayon_1.5.2 jquerylib_0.1.4 MASS_7.3-60 cachem_1.0.8 +## [37] iterators_1.0.14 boot_1.3-28.1 foreach_1.5.2 tidyselect_1.2.0 +## [41] digest_0.6.33 stringi_1.7.12 purrr_1.0.2 labeling_0.4.2 +## [45] splines_4.3.1 distances_0.1.9 rprojroot_2.0.3 fastmap_1.1.1 +## [49] grid_4.3.1 colorspace_2.1-0 cli_3.6.1 magrittr_2.0.3 +## [53] survival_3.5-5 utf8_1.2.3 withr_2.5.0 prettyunits_1.1.1 +## [57] scales_1.2.1 backports_1.4.1 vimp_2.3.1 rmarkdown_2.23 +## [61] ragg_1.2.5 hms_1.1.3 gam_1.22-2 memoise_2.0.1 +## [65] evaluate_0.21 knitr_1.43 rlang_1.1.1 Rcpp_1.0.11 +## [69] glue_1.6.2 quickblock_0.2.0 jsonlite_1.8.7 R6_2.5.1 +## [73] systemfonts_1.0.4 fs_1.6.3

diff --git a/articles/index.html b/articles/index.html index 9a12664..b8a559f 100644 --- a/articles/index.html +++ b/articles/index.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/articles/methodological_details.html b/articles/methodological_details.html index 2a44fbf..3c634ee 100644 --- a/articles/methodological_details.html +++ b/articles/methodological_details.html @@ -40,7 +40,7 @@ tidyhte - 1.0.1 + 1.0.2 @@ -97,7 +97,7 @@

Drew Dimmery

Edward Kennedy (edward@stat.cmu.edu)

-

August 09, 2023

+

August 14, 2023

Source: vignettes/methodological_details.Rmd @@ -441,7 +441,7 @@

Quantities of interestThe resulting tibble provides looks like the following:

 results
-
## # A tibble: 337 × 6
+
## # A tibble: 333 × 6
 ##    estimand term    value level     estimate std_error
 ##    <chr>    <chr>   <dbl> <chr>        <dbl>     <dbl>
 ##  1 MCATE    species    NA Adelie     -97.9        3.06
@@ -454,7 +454,7 @@ 
Quantities of interest##  8 MCATE    sex        NA female      -9.85       7.27
 ##  9 MCATE    year     2007 NA         -13.1        9.36
 ## 10 MCATE    year     2008 NA           0.809      9.41
-## # ℹ 327 more rows

+## # ℹ 323 more rows

The estimand column denotes the class of Quantities of Interest to be estimated, and include such values as “MCATE” and “VIMP”. The term column denotes the covariate being referred to (if diff --git a/articles/observational_analysis.html b/articles/observational_analysis.html index f8d2f75..bd3ef7d 100644 --- a/articles/observational_analysis.html +++ b/articles/observational_analysis.html @@ -39,7 +39,7 @@ tidyhte - 1.0.1 + 1.0.2 @@ -94,7 +94,7 @@

HTE Analysis on Observational Data

Drew Dimmery (ddimmery@univie.ac.at)

-

09 August, 2023

+

14 August, 2023

Source: vignettes/observational_analysis.Rmd @@ -449,24 +449,24 @@

Session Info## ## other attached packages: ## [1] nnls_1.4 SuperLearner_2.0-28.1 dplyr_1.1.2 -## [4] ggplot2_3.4.2 tidyhte_1.0.1 +## [4] ggplot2_3.4.2 tidyhte_1.0.2 ## ## loaded via a namespace (and not attached): -## [1] shape_1.4.6 gtable_0.3.3 xfun_0.39 -## [4] bslib_0.5.0 lattice_0.21-8 quadprog_1.5-8 +## [1] shape_1.4.6 gtable_0.3.3 xfun_0.40 +## [4] bslib_0.5.1 lattice_0.21-8 quadprog_1.5-8 ## [7] vctrs_0.6.3 tools_4.3.1 generics_0.1.3 ## [10] tibble_3.2.1 fansi_1.0.4 highr_0.10 ## [13] pkgconfig_2.0.3 Matrix_1.5-4.1 data.table_1.14.8 ## [16] checkmate_2.2.0 desc_1.4.2 lifecycle_1.0.3 ## [19] farver_2.1.1 compiler_4.3.1 stringr_1.5.0 ## [22] textshaping_0.3.6 progress_1.2.2 nprobust_0.4.0 -## [25] munsell_0.5.0 codetools_0.2-19 htmltools_0.5.5 +## [25] munsell_0.5.0 codetools_0.2-19 htmltools_0.5.6 ## [28] sass_0.4.7 yaml_2.3.7 glmnet_4.1-7 ## [31] pillar_1.9.0 pkgdown_2.0.7 crayon_1.5.2 ## [34] jquerylib_0.1.4 MASS_7.3-60 cachem_1.0.8 ## [37] iterators_1.0.14 boot_1.3-28.1 foreach_1.5.2 ## [40] tidyselect_1.2.0 digest_0.6.33 stringi_1.7.12 -## [43] purrr_1.0.1 labeling_0.4.2 splines_4.3.1 +## [43] purrr_1.0.2 labeling_0.4.2 splines_4.3.1 ## [46] distances_0.1.9 rprojroot_2.0.3 fastmap_1.1.1 ## [49] grid_4.3.1 colorspace_2.1-0 cli_3.6.1 ## [52] magrittr_2.0.3 survival_3.5-5 utf8_1.2.3 diff --git a/authors.html b/authors.html index 0266acb..b3cd477 100644 --- a/authors.html +++ b/authors.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/index.html b/index.html index 741f3a6..072b681 100644 --- a/index.html +++ b/index.html @@ -45,7 +45,7 @@ tidyhte - 1.0.1 + 1.0.2 @@ -199,6 +199,11 @@

DiscordSupport for the package will also be provided in the Experimentation Community Discord:

You are welcome to come in and get support for your usage in the tidyhte channel. Keep in mind that everyone is volunteering their time to help, so try to come prepared with the debugging steps you’ve already taken.

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+

Code of Conduct +

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Please note that the tidyhte project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

+
@@ -207,6 +212,7 @@

Discord

Links

 @@ -220,6 +226,12 @@

License

+
+

Community

+ +

Citation

diff --git a/news/index.html b/news/index.html index d54945e..aeb9bc1 100644 --- a/news/index.html +++ b/news/index.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2
diff --git a/pkgdown.yml b/pkgdown.yml index 2b33f5b..76b17a7 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -5,5 +5,8 @@ articles: experimental_analysis: experimental_analysis.html methodological_details: methodological_details.html observational_analysis: observational_analysis.html -last_built: 2023-08-09T09:43Z +last_built: 2023-08-14T14:15Z +urls: + reference: https://ddimmery.github.io/tidyhte/reference + article: https://ddimmery.github.io/tidyhte/articles diff --git a/reference/Constant_cfg.html b/reference/Constant_cfg.html index 55bb18b..7ee3529 100644 --- a/reference/Constant_cfg.html +++ b/reference/Constant_cfg.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/Diagnostics_cfg.html b/reference/Diagnostics_cfg.html index 61aed57..4acd224 100644 --- a/reference/Diagnostics_cfg.html +++ b/reference/Diagnostics_cfg.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/FX.Predictor.html b/reference/FX.Predictor.html index bff13c1..68a19a1 100644 --- a/reference/FX.Predictor.html +++ b/reference/FX.Predictor.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/HTEFold.html b/reference/HTEFold.html index a4b62f0..c80183c 100644 --- a/reference/HTEFold.html +++ b/reference/HTEFold.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/HTE_cfg.html b/reference/HTE_cfg.html index 748a1fb..d1d4cc4 100644 --- a/reference/HTE_cfg.html +++ b/reference/HTE_cfg.html @@ -25,7 +25,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/KernelSmooth_cfg.html b/reference/KernelSmooth_cfg.html index 7b0d698..fb5b20d 100644 --- a/reference/KernelSmooth_cfg.html +++ b/reference/KernelSmooth_cfg.html @@ -27,7 +27,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/Known_cfg.html b/reference/Known_cfg.html index 61f9d0d..a2ebd5d 100644 --- a/reference/Known_cfg.html +++ b/reference/Known_cfg.html @@ -26,7 +26,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/MCATE_cfg.html b/reference/MCATE_cfg.html index 5532e81..5bb0357 100644 --- a/reference/MCATE_cfg.html +++ b/reference/MCATE_cfg.html @@ -27,7 +27,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/Model_cfg.html b/reference/Model_cfg.html index 4a93f03..adfc3bd 100644 --- a/reference/Model_cfg.html +++ b/reference/Model_cfg.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/Model_data.html b/reference/Model_data.html index 2a4023a..4556390 100644 --- a/reference/Model_data.html +++ b/reference/Model_data.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/PCATE_cfg.html b/reference/PCATE_cfg.html index 27e7a43..58314ba 100644 --- a/reference/PCATE_cfg.html +++ b/reference/PCATE_cfg.html @@ -30,7 +30,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/QoI_cfg.html b/reference/QoI_cfg.html index 9ab251c..28ea7cc 100644 --- a/reference/QoI_cfg.html +++ b/reference/QoI_cfg.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/SL.glmnet.interaction.html b/reference/SL.glmnet.interaction.html index 5ff5af6..21c561b 100644 --- a/reference/SL.glmnet.interaction.html +++ b/reference/SL.glmnet.interaction.html @@ -27,7 +27,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/SLEnsemble_cfg.html b/reference/SLEnsemble_cfg.html index b30f0f4..4c25e74 100644 --- a/reference/SLEnsemble_cfg.html +++ b/reference/SLEnsemble_cfg.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/SLLearner_cfg.html b/reference/SLLearner_cfg.html index cc9e58f..0e254ce 100644 --- a/reference/SLLearner_cfg.html +++ b/reference/SLLearner_cfg.html @@ -28,7 +28,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/Stratified_cfg.html b/reference/Stratified_cfg.html index 92512dc..59c100f 100644 --- a/reference/Stratified_cfg.html +++ b/reference/Stratified_cfg.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/VIMP_cfg.html b/reference/VIMP_cfg.html index b79b832..7a9e50d 100644 --- a/reference/VIMP_cfg.html +++ b/reference/VIMP_cfg.html @@ -25,7 +25,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/add_effect_diagnostic.html b/reference/add_effect_diagnostic.html index d71077b..d0df6f8 100644 --- a/reference/add_effect_diagnostic.html +++ b/reference/add_effect_diagnostic.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/add_effect_model.html b/reference/add_effect_model.html index 22be244..db02858 100644 --- a/reference/add_effect_model.html +++ b/reference/add_effect_model.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/add_known_propensity_score.html b/reference/add_known_propensity_score.html index 2490782..ee8de7e 100644 --- a/reference/add_known_propensity_score.html +++ b/reference/add_known_propensity_score.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/add_moderator.html b/reference/add_moderator.html index 79d014d..e496889 100644 --- a/reference/add_moderator.html +++ b/reference/add_moderator.html @@ -25,7 +25,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/add_outcome_diagnostic.html b/reference/add_outcome_diagnostic.html index d84d912..493028b 100644 --- a/reference/add_outcome_diagnostic.html +++ b/reference/add_outcome_diagnostic.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/add_outcome_model.html b/reference/add_outcome_model.html index 7bd03a5..3493bf7 100644 --- a/reference/add_outcome_model.html +++ b/reference/add_outcome_model.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/add_propensity_diagnostic.html b/reference/add_propensity_diagnostic.html index 64728f5..9f03cfd 100644 --- a/reference/add_propensity_diagnostic.html +++ b/reference/add_propensity_diagnostic.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/add_propensity_score_model.html b/reference/add_propensity_score_model.html index 293dee1..409b0df 100644 --- a/reference/add_propensity_score_model.html +++ b/reference/add_propensity_score_model.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/add_vimp.html b/reference/add_vimp.html index 597a0e6..3fe5c20 100644 --- a/reference/add_vimp.html +++ b/reference/add_vimp.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/attach_config.html b/reference/attach_config.html index 86568fc..4a2ebf5 100644 --- a/reference/attach_config.html +++ b/reference/attach_config.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 @@ -106,14 +106,53 @@

See also

Examples

- 
if (FALSE) {
-cfg <- basic_config()
-attach_config(data, cfg) %>%
-make_splits(unitid, .num_splits = 10) %>%
-produce_plugin_estimates(outcome, treatment, covariate1, covariate2) %>%
-construct_pseudo_outcomes(outcome, treatment) %>%
-estimate_QoI(covariate1, covariate2)
+    
library("dplyr")
+if(require("palmerpenguins")) {
+data(package = 'palmerpenguins')
+penguins$unitid = seq_len(nrow(penguins))
+penguins$propensity = rep(0.5, nrow(penguins))
+penguins$treatment = rbinom(nrow(penguins), 1, penguins$propensity)
+cfg <- basic_config() %>% 
+add_known_propensity_score("propensity") %>%
+add_outcome_model("SL.glm.interaction") %>%
+remove_vimp()
+attach_config(penguins, cfg) %>%
+make_splits(unitid, .num_splits = 4) %>%
+produce_plugin_estimates(outcome = body_mass_g, treatment = treatment, species, sex) %>%
+construct_pseudo_outcomes(body_mass_g, treatment) %>%
+estimate_QoI(species, sex)
 }
+#> Loading required package: palmerpenguins
+#> Dropped 11 of 344 rows (3.2%) through listwise deletion.
+#> 

+#> estimating nuisance models [-----------------------------------] splits: 0 / 4
+#> Loading required package: nnls
+#> 

+#> estimating nuisance models [========>--------------------------] splits: 1 / 4
+#> 

+#> estimating nuisance models [=================>-----------------] splits: 2 / 4
+#> 

+#> estimating nuisance models [=========================>---------] splits: 3 / 4
+#> 

+#> estimating nuisance models [===================================] splits: 4 / 4
+#> 
                                                                              
+#> 

+#> Dropped 11 of 344 rows (3.2%) through listwise deletion.
+#> Skipping diagnostic on .pseudo_outcome due to lack of model.
+#> # A tibble: 11 × 5
+#>    estimand       term                   level                estimate std_error
+#>    <chr>          <chr>                  <chr>                   <dbl>     <dbl>
+#>  1 MSE            body_mass_g            Control Response    93313.      9.63e+3
+#>  2 MSE            body_mass_g            Treatment Response 110938.      1.07e+4
+#>  3 SL risk        SL.glm.interaction_All Control Response    96493.      1.83e+3
+#>  4 SL risk        SL.glm_All             Control Response    95552.      1.75e+3
+#>  5 SL risk        SL.glm.interaction_All Treatment Response 111116.      1.79e+3
+#>  6 SL risk        SL.glm_All             Treatment Response 117905.      4.42e+3
+#>  7 SL coefficient SL.glm.interaction_All Control Response        0.396   4.46e-2
+#>  8 SL coefficient SL.glm_All             Control Response        0.604   4.46e-2
+#>  9 SL coefficient SL.glm.interaction_All Treatment Response      0.770   1.02e-1
+#> 10 SL coefficient SL.glm_All             Treatment Response      0.230   1.02e-1
+#> 11 SATE           NA                     NA                     37.3     3.46e+1
diff --git a/reference/basic_config.html b/reference/basic_config.html index b4bf4b3..ca8ca02 100644 --- a/reference/basic_config.html +++ b/reference/basic_config.html @@ -28,7 +28,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/calculate_ate.html b/reference/calculate_ate.html index a439b28..f27d887 100644 --- a/reference/calculate_ate.html +++ b/reference/calculate_ate.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/calculate_diagnostics.html b/reference/calculate_diagnostics.html index c7c2c97..a0404f0 100644 --- a/reference/calculate_diagnostics.html +++ b/reference/calculate_diagnostics.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/calculate_linear_vimp.html b/reference/calculate_linear_vimp.html index 888bae4..b858e67 100644 --- a/reference/calculate_linear_vimp.html +++ b/reference/calculate_linear_vimp.html @@ -26,7 +26,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/calculate_pcate_quantities.html b/reference/calculate_pcate_quantities.html index 650cb2c..c521333 100644 --- a/reference/calculate_pcate_quantities.html +++ b/reference/calculate_pcate_quantities.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/calculate_rroc.html b/reference/calculate_rroc.html index c24f074..e322f84 100644 --- a/reference/calculate_rroc.html +++ b/reference/calculate_rroc.html @@ -32,7 +32,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/calculate_vimp.html b/reference/calculate_vimp.html index cfc558e..e4d513f 100644 --- a/reference/calculate_vimp.html +++ b/reference/calculate_vimp.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/check_data_has_hte_cfg.html b/reference/check_data_has_hte_cfg.html index ac6de63..ba764ac 100644 --- a/reference/check_data_has_hte_cfg.html +++ b/reference/check_data_has_hte_cfg.html @@ -25,7 +25,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/check_identifier.html b/reference/check_identifier.html index 6fa3f12..277545c 100644 --- a/reference/check_identifier.html +++ b/reference/check_identifier.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/check_nuisance_models.html b/reference/check_nuisance_models.html index e403d47..0af3229 100644 --- a/reference/check_nuisance_models.html +++ b/reference/check_nuisance_models.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/check_splits.html b/reference/check_splits.html index a972532..94f1da2 100644 --- a/reference/check_splits.html +++ b/reference/check_splits.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/check_weights.html b/reference/check_weights.html index ffd1cd3..f1e10e8 100644 --- a/reference/check_weights.html +++ b/reference/check_weights.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/construct_pseudo_outcomes.html b/reference/construct_pseudo_outcomes.html index d9c6da1..dc311ff 100644 --- a/reference/construct_pseudo_outcomes.html +++ b/reference/construct_pseudo_outcomes.html @@ -26,7 +26,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/estimate_QoI.html b/reference/estimate_QoI.html index 9110412..560812a 100644 --- a/reference/estimate_QoI.html +++ b/reference/estimate_QoI.html @@ -25,7 +25,7 @@ tidyhte - 1.0.1 + 1.0.2 @@ -107,14 +107,51 @@

See also

Examples

- 
if (FALSE) {
-cfg <- basic_config()
-attach_config(data, cfg) %>%
-make_splits(unitid, .num_splits = 10) %>%
-produce_plugin_estimates(outcome, treatment, covariate1, covariate2) %>%
-construct_pseudo_outcomes(outcome, treatment) %>%
-estimate_QoI(covariate1, covariate2)
+    
library("dplyr")
+if(require("palmerpenguins")) {
+data(package = 'palmerpenguins')
+penguins$unitid = seq_len(nrow(penguins))
+penguins$propensity = rep(0.5, nrow(penguins))
+penguins$treatment = rbinom(nrow(penguins), 1, penguins$propensity)
+cfg <- basic_config() %>% 
+add_known_propensity_score("propensity") %>%
+add_outcome_model("SL.glm.interaction") %>%
+remove_vimp()
+attach_config(penguins, cfg) %>%
+make_splits(unitid, .num_splits = 4) %>%
+produce_plugin_estimates(outcome = body_mass_g, treatment = treatment, species, sex) %>%
+construct_pseudo_outcomes(body_mass_g, treatment) %>%
+estimate_QoI(species, sex)
 }
+#> Dropped 11 of 344 rows (3.2%) through listwise deletion.
+#> 

+#> estimating nuisance models [-----------------------------------] splits: 0 / 4
+#> 

+#> estimating nuisance models [========>--------------------------] splits: 1 / 4
+#> 

+#> estimating nuisance models [=================>-----------------] splits: 2 / 4
+#> 

+#> estimating nuisance models [=========================>---------] splits: 3 / 4
+#> 

+#> estimating nuisance models [===================================] splits: 4 / 4
+#> 
                                                                              
+#> 

+#> Dropped 11 of 344 rows (3.2%) through listwise deletion.
+#> Skipping diagnostic on .pseudo_outcome due to lack of model.
+#> # A tibble: 11 × 5
+#>    estimand       term                   level                estimate std_error
+#>    <chr>          <chr>                  <chr>                   <dbl>     <dbl>
+#>  1 MSE            body_mass_g            Control Response      1.21e+5   1.13e+4
+#>  2 MSE            body_mass_g            Treatment Response    7.15e+4   7.79e+3
+#>  3 SL risk        SL.glm.interaction_All Control Response      1.34e+5   8.04e+3
+#>  4 SL risk        SL.glm_All             Control Response      1.20e+5   5.36e+3
+#>  5 SL risk        SL.glm.interaction_All Treatment Response    7.25e+4   2.65e+3
+#>  6 SL risk        SL.glm_All             Treatment Response    8.05e+4   2.37e+3
+#>  7 SL coefficient SL.glm.interaction_All Control Response      8.30e-2   5.91e-2
+#>  8 SL coefficient SL.glm_All             Control Response      9.17e-1   5.91e-2
+#>  9 SL coefficient SL.glm.interaction_All Treatment Response    8.91e-1   1.55e-2
+#> 10 SL coefficient SL.glm_All             Treatment Response    1.09e-1   1.55e-2
+#> 11 SATE           NA                     NA                    6.18e+0   3.41e+1
diff --git a/reference/estimate_diagnostic.html b/reference/estimate_diagnostic.html index c0e61de..f78bf5c 100644 --- a/reference/estimate_diagnostic.html +++ b/reference/estimate_diagnostic.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 @@ -109,11 +109,11 @@

Examples

df <- dplyr::tibble(y = rbinom(100, 1, 0.5), p = rep(0.5, 100), w = rexp(100), u = 1:100)
 attr(df, "weights") <- "w"
 attr(df, "identifier") <- "u"
-tidyhte:::estimate_diagnostic(df, "y", "p", "AUC")
+estimate_diagnostic(df, "y", "p", "AUC")
 #> # A tibble: 1 × 4
 #>   estimand term  estimate std_error
 #>   <chr>    <chr>    <dbl>     <dbl>
-#> 1 AUC      y          0.5    0.0721
+#> 1 AUC      y          0.5    0.0785
diff --git a/reference/fit_effect.html b/reference/fit_effect.html index 668e6cb..17e40d0 100644 --- a/reference/fit_effect.html +++ b/reference/fit_effect.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/fit_fx_predictor.html b/reference/fit_fx_predictor.html index e24c1cd..3b0c497 100644 --- a/reference/fit_fx_predictor.html +++ b/reference/fit_fx_predictor.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/fit_plugin.html b/reference/fit_plugin.html index 94981a1..6a6f805 100644 --- a/reference/fit_plugin.html +++ b/reference/fit_plugin.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/fit_plugin_A.html b/reference/fit_plugin_A.html index 6be28ee..903d6fd 100644 --- a/reference/fit_plugin_A.html +++ b/reference/fit_plugin_A.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/fit_plugin_Y.html b/reference/fit_plugin_Y.html index a24bf22..d327252 100644 --- a/reference/fit_plugin_Y.html +++ b/reference/fit_plugin_Y.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/index.html b/reference/index.html index bae9a09..ce7efcd 100644 --- a/reference/index.html +++ b/reference/index.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2 @@ -136,6 +136,10 @@

Recipe API add_vimp()

Adds variable importance information

+ +

remove_vimp()

+ +

Removes variable importance information

Model Configuration

Classes to define the configuration of models to be used in the eventual HTE analysis. These are the classes which define the underlying configurations in the Recipe API. They’re most useful for advanced users who want the most granular control over their analysis, but most users will be best served by the Recipe API.

diff --git a/reference/listwise_deletion.html b/reference/listwise_deletion.html index 50f4cdc..91c21c0 100644 --- a/reference/listwise_deletion.html +++ b/reference/listwise_deletion.html @@ -25,7 +25,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/make_splits.html b/reference/make_splits.html index 91702fd..e5fcd12 100644 --- a/reference/make_splits.html +++ b/reference/make_splits.html @@ -26,7 +26,7 @@ tidyhte - 1.0.1 + 1.0.2 @@ -123,14 +123,51 @@

See also

Examples

- 
if (FALSE) {
-cfg <- basic_config()
-attach_config(data, cfg) %>%
-make_splits(unitid, .num_splits = 10) %>%
-produce_plugin_estimates(outcome, treatment, covariate1, covariate2) %>%
-construct_pseudo_outcomes(outcome, treatment) %>%
-estimate_QoI(covariate1, covariate2)
+    
library("dplyr")
+if(require("palmerpenguins")) {
+data(package = 'palmerpenguins')
+penguins$unitid = seq_len(nrow(penguins))
+penguins$propensity = rep(0.5, nrow(penguins))
+penguins$treatment = rbinom(nrow(penguins), 1, penguins$propensity)
+cfg <- basic_config() %>% 
+add_known_propensity_score("propensity") %>%
+add_outcome_model("SL.glm.interaction") %>%
+remove_vimp()
+attach_config(penguins, cfg) %>%
+make_splits(unitid, .num_splits = 4) %>%
+produce_plugin_estimates(outcome = body_mass_g, treatment = treatment, species, sex) %>%
+construct_pseudo_outcomes(body_mass_g, treatment) %>%
+estimate_QoI(species, sex)
 }
+#> Dropped 11 of 344 rows (3.2%) through listwise deletion.
+#> 

+#> estimating nuisance models [-----------------------------------] splits: 0 / 4
+#> 

+#> estimating nuisance models [========>--------------------------] splits: 1 / 4
+#> 

+#> estimating nuisance models [=================>-----------------] splits: 2 / 4
+#> 

+#> estimating nuisance models [=========================>---------] splits: 3 / 4
+#> 

+#> estimating nuisance models [===================================] splits: 4 / 4
+#> 
                                                                              
+#> 

+#> Dropped 11 of 344 rows (3.2%) through listwise deletion.
+#> Skipping diagnostic on .pseudo_outcome due to lack of model.
+#> # A tibble: 11 × 5
+#>    estimand       term                   level                estimate std_error
+#>    <chr>          <chr>                  <chr>                   <dbl>     <dbl>
+#>  1 MSE            body_mass_g            Control Response   101019.    10670.   
+#>  2 MSE            body_mass_g            Treatment Response  97656.     9718.   
+#>  3 SL risk        SL.glm.interaction_All Control Response   101139.     4266.   
+#>  4 SL risk        SL.glm_All             Control Response   103637.     5534.   
+#>  5 SL risk        SL.glm.interaction_All Treatment Response  98217.     5473.   
+#>  6 SL risk        SL.glm_All             Treatment Response 100650.     3581.   
+#>  7 SL coefficient SL.glm.interaction_All Control Response        0.655     0.131
+#>  8 SL coefficient SL.glm_All             Control Response        0.345     0.131
+#>  9 SL coefficient SL.glm.interaction_All Treatment Response      0.664     0.134
+#> 10 SL coefficient SL.glm_All             Treatment Response      0.336     0.134
+#> 11 SATE           NA                     NA                    -31.6      33.9
diff --git a/reference/predict.SL.glmnet.interaction.html b/reference/predict.SL.glmnet.interaction.html index 2051ba5..d163b04 100644 --- a/reference/predict.SL.glmnet.interaction.html +++ b/reference/predict.SL.glmnet.interaction.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/produce_plugin_estimates.html b/reference/produce_plugin_estimates.html index 3c2ce9e..77edba3 100644 --- a/reference/produce_plugin_estimates.html +++ b/reference/produce_plugin_estimates.html @@ -27,7 +27,7 @@ tidyhte - 1.0.1 + 1.0.2 @@ -122,14 +122,51 @@

See also

Examples

- 
if (FALSE) {
-cfg <- basic_config()
-attach_config(data, cfg) %>%
-make_splits(unitid, .num_splits = 10) %>%
-produce_plugin_estimates(outcome, treatment, covariate1, covariate2) %>%
-construct_pseudo_outcomes(outcome, treatment) %>%
-estimate_QoI(covariate1, covariate2)
+    
library("dplyr")
+if(require("palmerpenguins")) {
+data(package = 'palmerpenguins')
+penguins$unitid = seq_len(nrow(penguins))
+penguins$propensity = rep(0.5, nrow(penguins))
+penguins$treatment = rbinom(nrow(penguins), 1, penguins$propensity)
+cfg <- basic_config() %>% 
+add_known_propensity_score("propensity") %>%
+add_outcome_model("SL.glm.interaction") %>%
+remove_vimp()
+attach_config(penguins, cfg) %>%
+make_splits(unitid, .num_splits = 4) %>%
+produce_plugin_estimates(outcome = body_mass_g, treatment = treatment, species, sex) %>%
+construct_pseudo_outcomes(body_mass_g, treatment) %>%
+estimate_QoI(species, sex)
 }
+#> Dropped 11 of 344 rows (3.2%) through listwise deletion.
+#> 

+#> estimating nuisance models [-----------------------------------] splits: 0 / 4
+#> 

+#> estimating nuisance models [========>--------------------------] splits: 1 / 4
+#> 

+#> estimating nuisance models [=================>-----------------] splits: 2 / 4
+#> 

+#> estimating nuisance models [=========================>---------] splits: 3 / 4
+#> 

+#> estimating nuisance models [===================================] splits: 4 / 4
+#> 
                                                                              
+#> 

+#> Dropped 11 of 344 rows (3.2%) through listwise deletion.
+#> Skipping diagnostic on .pseudo_outcome due to lack of model.
+#> # A tibble: 11 × 5
+#>    estimand       term                   level                estimate std_error
+#>    <chr>          <chr>                  <chr>                   <dbl>     <dbl>
+#>  1 MSE            body_mass_g            Control Response      1.08e+5   1.02e+4
+#>  2 MSE            body_mass_g            Treatment Response    9.41e+4   1.11e+4
+#>  3 SL risk        SL.glm.interaction_All Control Response      1.11e+5   1.98e+3
+#>  4 SL risk        SL.glm_All             Control Response      1.21e+5   3.56e+3
+#>  5 SL risk        SL.glm.interaction_All Treatment Response    9.72e+4   4.66e+3
+#>  6 SL risk        SL.glm_All             Treatment Response    9.21e+4   1.69e+3
+#>  7 SL coefficient SL.glm.interaction_All Control Response      9.54e-1   3.90e-2
+#>  8 SL coefficient SL.glm_All             Control Response      4.61e-2   3.90e-2
+#>  9 SL coefficient SL.glm.interaction_All Treatment Response    2.04e-1   2.04e-1
+#> 10 SL coefficient SL.glm_All             Treatment Response    7.96e-1   2.04e-1
+#> 11 SATE           NA                     NA                    2.55e+1   3.42e+1
diff --git a/reference/remove_vimp.html b/reference/remove_vimp.html new file mode 100644 index 0000000..7131461 --- /dev/null +++ b/reference/remove_vimp.html @@ -0,0 +1,126 @@ + +Removes variable importance information — remove_vimp • tidyhte + + +
+
+ + + +
+
+
+

Removes variable importance information

+ Source: R/recipe-api.R + +
+ +
+

This removes the variable importance quantity of interest +from an HTE_cfg.

+
+ +
+ 
remove_vimp(hte_cfg)
+
+ +
+

Arguments

+
hte_cfg
+

HTE_cfg object to update.

+ +
+
+

Value

+ + +

Updated HTE_cfg object

+
+ +
+

Examples

+ 
library("dplyr")
+basic_config() %>%
+   remove_vimp() -> hte_cfg
+
+
+
+ +
+ + +
+

Developed by Drew Dimmery.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + + diff --git a/reference/split_data.html b/reference/split_data.html index 19fe907..67891e0 100644 --- a/reference/split_data.html +++ b/reference/split_data.html @@ -24,7 +24,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/reference/tidyhte-package.html b/reference/tidyhte-package.html index e1114c4..6e53b13 100644 --- a/reference/tidyhte-package.html +++ b/reference/tidyhte-package.html @@ -23,7 +23,7 @@ tidyhte - 1.0.1 + 1.0.2 diff --git a/sitemap.xml b/sitemap.xml index 350c54b..14bc003 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1,195 +1,201 @@ - /404.html + https://ddimmery.github.io/tidyhte/404.html - /LICENSE-text.html + https://ddimmery.github.io/tidyhte/CODE_OF_CONDUCT.html - /LICENSE.html + https://ddimmery.github.io/tidyhte/LICENSE-text.html - /articles/experimental_analysis.html + https://ddimmery.github.io/tidyhte/LICENSE.html - /articles/index.html + https://ddimmery.github.io/tidyhte/articles/experimental_analysis.html - /articles/methodological_details.html + https://ddimmery.github.io/tidyhte/articles/index.html - 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/reference/Model_cfg.html + https://ddimmery.github.io/tidyhte/reference/MCATE_cfg.html - /reference/Model_data.html + https://ddimmery.github.io/tidyhte/reference/Model_cfg.html - /reference/PCATE_cfg.html + https://ddimmery.github.io/tidyhte/reference/Model_data.html - /reference/QoI_cfg.html + https://ddimmery.github.io/tidyhte/reference/PCATE_cfg.html - /reference/SL.glmnet.interaction.html + https://ddimmery.github.io/tidyhte/reference/QoI_cfg.html - /reference/SLEnsemble_cfg.html + https://ddimmery.github.io/tidyhte/reference/SL.glmnet.interaction.html - /reference/SLLearner_cfg.html + https://ddimmery.github.io/tidyhte/reference/SLEnsemble_cfg.html - /reference/Stratified_cfg.html + https://ddimmery.github.io/tidyhte/reference/SLLearner_cfg.html - /reference/VIMP_cfg.html + https://ddimmery.github.io/tidyhte/reference/Stratified_cfg.html - /reference/add_effect_diagnostic.html + https://ddimmery.github.io/tidyhte/reference/VIMP_cfg.html - /reference/add_effect_model.html + https://ddimmery.github.io/tidyhte/reference/add_effect_diagnostic.html - 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