Adding the VAEAC approach (#369)

.Rbuildignore

@@ -22,3 +22,10 @@ inst/compare_lundberg\.xgb\.obj
 ^CRAN-SUBMISSION$
 ^.Rprofile
 ^python$
+^rebuild-long-running-vignette\.R$
+^vignettes/understanding_shapr_vaeac\.Rmd\.orig$
+^vignettes/understanding_shapr\.Rmd\.orig$
+^vignettes/figure_main/*$
+^vignettes/cache_main/*$
+^vignettes/figure_vaeac/*$
+^vignettes/cache_vaeac/*$

.github/workflows/R-CMD-check.yaml

@@ -49,6 +49,10 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
+      - name: Set the value
+        shell: bash # Default on non-Windows, but needs to be specfied for this to run on Windows
+        run: echo "TORCH_INSTALL=1" >> "$GITHUB_ENV"
+
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-pandoc@v2
@@ -64,6 +68,11 @@ jobs:
           extra-packages: any::rcmdcheck
           needs: check
 
+# Try to do this with the env variable TORCH_INSTALL instead to hopefully get setup-r-dependencies to cache the installation
+#      - name: Install torch dependencies
+#        run: torch::install_torch()
+#        shell: Rscript {0}
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           args: 'c("--no-manual")' # I.e. exclude the as-cran comment here

.lintr

@@ -8,7 +8,7 @@ linters: linters_with_defaults(
     )
 exclusions: list(
         "inst/scripts",
-        "vignettes/understanding_shapr.R",
+        "vignettes",
         "R/RcppExports.R",
         "R/zzz.R"
     )

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: shapr
-Version: 0.2.3.9100
+Version: 0.2.3.9200
 Title: Prediction Explanation with Dependence-Aware Shapley Values
 Description: Complex machine learning models are often hard to interpret. However, in 
   many situations it is crucial to understand and explain why a model made a specific 
@@ -12,6 +12,7 @@ Description: Complex machine learning models are often hard to interpret. Howeve
 Authors@R: c(
     person("Nikolai", "Sellereite", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-4671-0337")),
     person("Martin", "Jullum", email = "[email protected]", role = c("cre", "aut"), comment = c(ORCID = "0000-0003-3908-5155")),
+    person("Lars Henry Berge", "Olsen", email = "[email protected]", role = "aut", comment = c(ORCID = "0009-0006-9360-6993")),
     person("Annabelle", "Redelmeier", email = "[email protected]", role = "aut"),
     person("Jon", "Lachmann", email = "[email protected]", role = "aut"),
     person("Anders", "Løland", email = "[email protected]", role = "ctb"), 
@@ -26,14 +27,15 @@ Encoding: UTF-8
 LazyData: true
 ByteCompile: true
 Language: en-US
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Depends: R (>= 3.5.0)
 Imports: 
     stats,
     data.table,
     Rcpp (>= 0.12.15),
     Matrix,
-    future.apply
+    future.apply,
+    methods
 Suggests: 
     ranger,
     xgboost,
@@ -51,7 +53,11 @@ Suggests:
     future,
     ggbeeswarm,
     vdiffr,
-    forecast
+    forecast,
+    torch,
+    GGally,
+    progress,
+    coro
 LinkingTo: 
     RcppArmadillo,
     Rcpp

NAMESPACE

@@ -34,6 +34,7 @@ S3method(prepare_data,empirical)
 S3method(prepare_data,gaussian)
 S3method(prepare_data,independence)
 S3method(prepare_data,timeseries)
+S3method(prepare_data,vaeac)
 S3method(print,shapr)
 S3method(setup_approach,categorical)
 S3method(setup_approach,combined)
@@ -43,6 +44,7 @@ S3method(setup_approach,empirical)
 S3method(setup_approach,gaussian)
 S3method(setup_approach,independence)
 S3method(setup_approach,timeseries)
+S3method(setup_approach,vaeac)
 export(aicc_full_single_cpp)
 export(compute_shapley_new)
 export(compute_vS)
@@ -61,6 +63,7 @@ export(hat_matrix_cpp)
 export(mahalanobis_distance_cpp)
 export(observation_impute_cpp)
 export(plot_MSEv_eval_crit)
+export(plot_SV_several_approaches)
 export(predict_model)
 export(prepare_data)
 export(prepare_data_copula_cpp)
@@ -69,6 +72,12 @@ export(rss_cpp)
 export(setup)
 export(setup_approach)
 export(setup_computation)
+export(vaeac_get_evaluation_criteria)
+export(vaeac_get_extra_para_default)
+export(vaeac_plot_eval_crit)
+export(vaeac_plot_imputed_ggpairs)
+export(vaeac_train_model)
+export(vaeac_train_model_continue)
 export(weight_matrix_cpp)
 importFrom(Rcpp,sourceCpp)
 importFrom(data.table,":=")
@@ -103,5 +112,6 @@ importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(utils,head)
 importFrom(utils,methods)
+importFrom(utils,modifyList)
 importFrom(utils,tail)
 useDynLib(shapr, .registration = TRUE)

R/approach.R

@@ -82,5 +82,5 @@ insert_defaults <- function(internal, defaults) {
 
 #' @keywords internal
 get_factor_approaches <- function() {
-  c("'independence' (not recommended)", "'ctree'", "'categorical'")
+  c("'independence' (not recommended)", "'ctree'", "'vaeac'", "'categorical'")
 }