Shapr version 1.0.0

.Rprofile

@@ -1,3 +1,7 @@
+if (requireNamespace("testthat", quietly = TRUE)) {
+  testthat::set_max_fails(Inf)
+}
+
 #' Helper function for package development
 #'
 #' This is a manual extension of [testthat::snapshot_review()] which works for the \code{.rds} files used in
@@ -7,17 +11,19 @@
 #' @param ... Additional arguments passed to [waldo::compare()]
 #' Gives the relative path to the test files to review
 #'
-snapshot_review_man <- function(path, tolerance = NULL, ...) {
-  changed <- testthat:::snapshot_meta(path)
-  these_rds <- (tools::file_ext(changed$name) == "rds")
-  if (any(these_rds)) {
-    for (i in which(these_rds)) {
-      old <- readRDS(changed[i, "cur"])
-      new <- readRDS(changed[i, "new"])
+snapshot_review_man <- function(path, tolerance = 10^(-5), max_diffs = 200, ...) {
+  if (requireNamespace("testthat", quietly = TRUE) && requireNamespace("waldo", quietly = TRUE)) {
+    changed <- testthat:::snapshot_meta(path)
+    these_rds <- (tools::file_ext(changed$name) == "rds")
+    if (any(these_rds)) {
+      for (i in which(these_rds)) {
+        old <- readRDS(changed[i, "cur"])
+        new <- readRDS(changed[i, "new"])
 
-      cat(paste0("Difference for check ", changed[i, "name"], " in test ", changed[i, "test"], "\n"))
-      print(waldo::compare(old, new, max_diffs = 50, tolerance = tolerance, ...))
-      browser()
+        cat(paste0("Difference for check ", changed[i, "name"], " in test ", changed[i, "test"], "\n"))
+        print(waldo::compare(old, new, max_diffs = max_diffs, tolerance = tolerance, ...))
+        browser()
+      }
     }
   }
 }

DESCRIPTION

@@ -27,7 +27,7 @@ Encoding: UTF-8
 LazyData: true
 ByteCompile: true
 Language: en-US
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Depends: R (>= 3.5.0)
 Imports: 
     stats,
@@ -40,7 +40,7 @@ Suggests:
     ranger,
     xgboost,
     mgcv,
-    testthat (>= 3.0.0),
+    testthat,
     knitr,
     rmarkdown,
     roxygen2,
@@ -66,7 +66,8 @@ Suggests:
     yardstick,
     hardhat,
     rsample,
-    rlang
+    rlang,
+    cli
 LinkingTo: 
     RcppArmadillo,
     Rcpp

NAMESPACE

@@ -52,15 +52,22 @@ S3method(setup_approach,regression_separate)
 S3method(setup_approach,regression_surrogate)
 S3method(setup_approach,timeseries)
 S3method(setup_approach,vaeac)
+export(additional_regression_setup)
 export(aicc_full_single_cpp)
+export(check_convergence)
+export(coalition_matrix_cpp)
+export(compute_estimates)
 export(compute_shapley_new)
+export(compute_time)
 export(compute_vS)
+export(compute_vS_forecast)
 export(correction_matrix_cpp)
+export(create_coalition_table)
 export(explain)
 export(explain_forecast)
-export(feature_combinations)
-export(feature_matrix_cpp)
 export(finalize_explanation)
+export(finalize_explanation_forecast)
+export(get_adaptive_arguments_default)
 export(get_cov_mat)
 export(get_data_specs)
 export(get_model_specs)
@@ -75,17 +82,23 @@ export(predict_model)
 export(prepare_data)
 export(prepare_data_copula_cpp)
 export(prepare_data_gaussian_cpp)
+export(prepare_next_iteration)
+export(print_iter)
 export(regression.train_model)
 export(rss_cpp)
+export(save_results)
 export(setup)
 export(setup_approach)
 export(setup_computation)
+export(shapley_setup)
+export(testing_cleanup)
 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)
 export(weight_matrix_cpp)
 importFrom(Rcpp,sourceCpp)
 importFrom(data.table,":=")
@@ -110,6 +123,7 @@ importFrom(stats,as.formula)
 importFrom(stats,contrasts)
 importFrom(stats,embed)
 importFrom(stats,formula)
+importFrom(stats,median)
 importFrom(stats,model.frame)
 importFrom(stats,model.matrix)
 importFrom(stats,predict)
@@ -118,6 +132,7 @@ importFrom(stats,qt)
 importFrom(stats,rnorm)
 importFrom(stats,sd)
 importFrom(stats,setNames)
+importFrom(utils,capture.output)
 importFrom(utils,head)
 importFrom(utils,methods)
 importFrom(utils,modifyList)

NEWS.md

@@ -1,6 +1,8 @@
-# shapr (development version) 
+# shapr 1.0.0
 
-* Release a Python wrapper (`shaprpyr`, [#325](https://github.com/NorskRegnesentral/shapr/pull/325)) for explaining predictions from Python models (from Python) utilizing almost all functionality of `shapr`. The wrapper moves back and forth back and forth between Python and R, doing the prediction in Python, and almost everything else in R. This simplifies maintenance of `shaprpy` significantly. The wrapper is available [here](https://github.com/NorskRegnesentral/shapr/tree/master/python).
+* (Just some notes so far)
+* Adaptive estimatio/convergence detection
+* Verbosity
 * Complete restructuring motivated by introducing the Python wrapper. The restructuring splits the explanation tasks into smaller pieces, which was necessary to allow the Python wrapper to move back and forth between R and Python.
 * As part of the restructuring, we also did a number of design changes, resulting in a series of breaking changes described below.
 
@@ -13,6 +15,8 @@
 
 ### New features
 
+* Adatpive sampling of Shapley value subsets
+* Release a Python wrapper (`shaprpyr`, [#325](https://github.com/NorskRegnesentral/shapr/pull/325)) for explaining predictions from Python models (from Python) utilizing almost all functionality of `shapr`. The wrapper moves back and forth back and forth between Python and R, doing the prediction in Python, and almost everything else in R. This simplifies maintenance of `shaprpy` significantly. The wrapper is available [here](https://github.com/NorskRegnesentral/shapr/tree/master/python).
 * Introduce batch computation of conditional expectations ([#244](https://github.com/NorskRegnesentral/shapr/issues/244)). 
 This essentially compute $v(S)$ for a portion of the $S$-subsets at a time, to reduce the amount of data needed to be held in memory. 
 The user can control the number of batches herself, but we set a reasonable value by default ([#327](https://github.com/NorskRegnesentral/shapr/pull/327)). 

R/RcppExports.R

@@ -110,15 +110,15 @@ inv_gaussian_transform_cpp <- function(z, x) {
 
 #' Generate (Gaussian) Copula MC samples
 #'
-#' @param MC_samples_mat arma::mat. Matrix of dimension (`n_samples`, `n_features`) containing samples from the
+#' @param MC_samples_mat arma::mat. Matrix of dimension (`n_MC_samples`, `n_features`) containing samples from the
 #' univariate standard normal.
 #' @param x_explain_mat arma::mat. Matrix of dimension (`n_explain`, `n_features`) containing the observations
 #' to explain on the original scale.
 #' @param x_explain_gaussian_mat arma::mat. Matrix of dimension (`n_explain`, `n_features`) containing the
 #' observations to explain after being transformed using the Gaussian transform, i.e., the samples have been
 #' transformed to a standardized normal distribution.
 #' @param x_train_mat arma::mat. Matrix of dimension (`n_train`, `n_features`) containing the training observations.
-#' @param S arma::mat. Matrix of dimension (`n_combinations`, `n_features`) containing binary representations of
+#' @param S arma::mat. Matrix of dimension (`n_coalitions`, `n_features`) containing binary representations of
 #' the used coalitions. S cannot contain the empty or grand coalition, i.e., a row containing only zeros or ones.
 #' This is not a problem internally in shapr as the empty and grand coalitions treated differently.
 #' @param mu arma::vec. Vector of length `n_features` containing the mean of each feature after being transformed
@@ -127,8 +127,8 @@ inv_gaussian_transform_cpp <- function(z, x) {
 #' between all pairs of features after being transformed using the Gaussian transform, i.e., the samples have been
 #' transformed to a standardized normal distribution.
 #'
-#' @return An arma::cube/3D array of dimension (`n_samples`, `n_explain` * `n_coalitions`, `n_features`), where
-#' the columns (_,j,_) are matrices of dimension (`n_samples`, `n_features`) containing the conditional Gaussian
+#' @return An arma::cube/3D array of dimension (`n_MC_samples`, `n_explain` * `n_coalitions`, `n_features`), where
+#' the columns (_,j,_) are matrices of dimension (`n_MC_samples`, `n_features`) containing the conditional Gaussian
 #' copula MC samples for each explicand and coalition on the original scale.
 #'
 #' @export
@@ -140,19 +140,19 @@ prepare_data_copula_cpp <- function(MC_samples_mat, x_explain_mat, x_explain_gau
 
 #' Generate Gaussian MC samples
 #'
-#' @param MC_samples_mat arma::mat. Matrix of dimension (`n_samples`, `n_features`) containing samples from the
+#' @param MC_samples_mat arma::mat. Matrix of dimension (`n_MC_samples`, `n_features`) containing samples from the
 #' univariate standard normal.
 #' @param x_explain_mat arma::mat. Matrix of dimension (`n_explain`, `n_features`) containing the observations
 #' to explain.
-#' @param S arma::mat. Matrix of dimension (`n_combinations`, `n_features`) containing binary representations of
+#' @param S arma::mat. Matrix of dimension (`n_coalitions`, `n_features`) containing binary representations of
 #' the used coalitions. S cannot contain the empty or grand coalition, i.e., a row containing only zeros or ones.
 #' This is not a problem internally in shapr as the empty and grand coalitions treated differently.
 #' @param mu arma::vec. Vector of length `n_features` containing the mean of each feature.
 #' @param cov_mat arma::mat. Matrix of dimension (`n_features`, `n_features`) containing the pairwise covariance
 #' between all pairs of features.
 #'
-#' @return An arma::cube/3D array of dimension (`n_samples`, `n_explain` * `n_coalitions`, `n_features`), where
-#' the columns (_,j,_) are matrices of dimension (`n_samples`, `n_features`) containing the conditional Gaussian
+#' @return An arma::cube/3D array of dimension (`n_MC_samples`, `n_explain` * `n_coalitions`, `n_features`), where
+#' the columns (_,j,_) are matrices of dimension (`n_MC_samples`, `n_features`) containing the conditional Gaussian
 #' MC samples for each explicand and coalition.
 #'
 #' @export
@@ -199,7 +199,7 @@ sample_features_cpp <- function(m, n_features) {
 #'
 #' @param xtest Numeric matrix. Represents a single test observation.
 #'
-#' @param S Integer matrix of dimension \code{n_combinations x m}, where \code{n_combinations} equals
+#' @param S Integer matrix of dimension \code{n_coalitions x m}, where \code{n_coalitions} equals
 #' the total number of sampled/non-sampled feature combinations and \code{m} equals
 #' the total number of unique features. Note that \code{m = ncol(xtrain)}. See details
 #' for more information.
@@ -228,34 +228,34 @@ observation_impute_cpp <- function(index_xtrain, index_s, xtrain, xtest, S) {
 
 #' Calculate weight matrix
 #'
-#' @param subsets List. Each of the elements equals an integer
+#' @param coalitions List. Each of the elements equals an integer
 #' vector representing a valid combination of features/feature groups.
 #' @param m Integer. Number of features/feature groups
 #' @param n Integer. Number of combinations
 #' @param w Numeric vector of length \code{n}, i.e. \code{w[i]} equals
 #' the Shapley weight of feature/feature group combination \code{i}, represented by
-#' \code{subsets[[i]]}.
+#' \code{coalitions[[i]]}.
 #'
 #' @export
 #' @keywords internal
 #'
 #' @return Matrix of dimension n x m + 1
-#' @author Nikolai Sellereite
-weight_matrix_cpp <- function(subsets, m, n, w) {
-    .Call(`_shapr_weight_matrix_cpp`, subsets, m, n, w)
+#' @author Nikolai Sellereite, Martin Jullum
+weight_matrix_cpp <- function(coalitions, m, n, w) {
+    .Call(`_shapr_weight_matrix_cpp`, coalitions, m, n, w)
 }
 
-#' Get feature matrix
+#' Get coalition matrix
 #'
-#' @param features List
-#' @param m Positive integer. Total number of features
+#' @param coalitions List
+#' @param m Positive integer. Total number of coalitions
 #'
 #' @export
 #' @keywords internal
 #'
 #' @return Matrix
-#' @author Nikolai Sellereite
-feature_matrix_cpp <- function(features, m) {
-    .Call(`_shapr_feature_matrix_cpp`, features, m)
+#' @author Nikolai Sellereite, Martin Jullum
+coalition_matrix_cpp <- function(coalitions, m) {
+    .Call(`_shapr_coalition_matrix_cpp`, coalitions, m)
 }
 

R/approach.R

@@ -9,17 +9,49 @@
 #'
 #' @export
 setup_approach <- function(internal, ...) {
+  verbose <- internal$parameters$verbose
+
   approach <- internal$parameters$approach
 
-  this_class <- ""
+  iter <- length(internal$iter_list)
+  X <- internal$iter_list[[iter]]$X
 
-  if (length(approach) > 1) {
-    class(this_class) <- "combined"
+
+
+  needs_X <- c("regression_surrogate", "vaeac")
+
+  run_now <- (isFALSE(any(needs_X %in% approach)) && isTRUE(is.null(X))) ||
+    (isTRUE(any(needs_X %in% approach)) && isFALSE(is.null(X)))
+
+  if (isFALSE(run_now)) { # Do nothing
+    return(internal)
   } else {
-    class(this_class) <- approach
-  }
+    if ("progress" %in% verbose) {
+      cli::cli_progress_step("Setting up approach(es)")
+    }
+    if ("vS_details" %in% verbose) {
+      if ("vaeac" %in% approach) {
+        pretrained_provided <- internal$parameters$vaeac.extra_parameters$vaeac.pretrained_vaeac_model_provided
+        if (isFALSE(pretrained_provided)) {
+          cli::cli_h2("Extra info about the training/tuning of the vaeac model")
+        } else {
+          cli::cli_h2("Extra info about the pretrained vaeac model")
+        }
+      }
+    }
+
+    this_class <- ""
+
+    if (length(approach) > 1) {
+      class(this_class) <- "combined"
+    } else {
+      class(this_class) <- approach
+    }
+
+    UseMethod("setup_approach", this_class)
 
-  UseMethod("setup_approach", this_class)
+    internal$timing_list$setup_approach <- Sys.time()
+  }
 }
 
 #' @inheritParams default_doc
@@ -49,6 +81,10 @@ setup_approach.combined <- function(internal, ...) {
 #' @export
 #' @keywords internal
 prepare_data <- function(internal, index_features = NULL, ...) {
+  iter <- length(internal$iter_list)
+
+  X <- internal$iter_list[[iter]]$X
+
   # Extract the used approach(es)
   approach <- internal$parameters$approach
 
@@ -57,9 +93,9 @@ prepare_data <- function(internal, index_features = NULL, ...) {
 
   # Check if the user provided one or several approaches.
   if (length(approach) > 1) {
-    # Picks the relevant approach from the internal$objects$X table which list the unique approach of the batch
+    # Picks the relevant approach from the X table which list the unique approach of the batch
     # matches by index_features
-    class(this_class) <- internal$objects$X[id_combination == index_features[1], approach]
+    class(this_class) <- X[id_coalition == index_features[1], approach]
   } else {
     # Only one approach for all coalitions sizes
     class(this_class) <- approach