Fix python version after recent updates (#412)

NAMESPACE

@@ -55,6 +55,9 @@ S3method(setup_approach,vaeac)
 export(additional_regression_setup)
 export(aicc_full_single_cpp)
 export(check_convergence)
+export(cli_compute_vS)
+export(cli_iter)
+export(cli_startup)
 export(coalition_matrix_cpp)
 export(compute_estimates)
 export(compute_shapley_new)

R/cli.R

@@ -1,4 +1,13 @@
-cli_startup <- function(internal, model, verbose) {
+#' Printing startup messages with cli
+#'
+#' @param model_class String.
+#' Class of the model as a string
+#' @inheritParams default_doc_explain
+#' @inheritParams explain
+#'
+#' @export
+#' @keywords internal
+cli_startup <- function(internal, model_class, verbose) {
   init_time <- internal$timing_list$init_time
 
   is_groupwise <- internal$parameters$is_groupwise
@@ -20,7 +29,7 @@ cli_startup <- function(internal, model, verbose) {
   confounding <- internal$parameters$confounding
 
 
-  line_vec <- "Model class: {.cls {class(model)}}"
+  line_vec <- "Model class: {.cls {model_class}}"
   line_vec <- c(line_vec, "Approach: {.emph {approach}}")
   line_vec <- c(line_vec, "Iterative estimation: {.emph {iterative}}")
   line_vec <- c(line_vec, "Number of {.emph {feat_group_txt}} Shapley values: {n_shapley_values}")
@@ -63,7 +72,38 @@ cli_startup <- function(internal, model, verbose) {
   }
 }
 
+#' Printing messages in compute_vS with cli
+#'
+#' @inheritParams default_doc_explain
+#' @inheritParams explain
+#'
+#' @export
+#' @keywords internal
+cli_compute_vS <- function(internal) {
 
+  verbose <- internal$parameters$verbose
+  approach <- internal$parameters$approach
+
+  if ("progress" %in% verbose) {
+    cli::cli_progress_step("Computing vS")
+  }
+  if ("vS_details" %in% verbose) {
+    if ("regression_separate" %in% approach) {
+      tuning <- internal$parameters$regression.tune
+      if (isTRUE(tuning)) {
+        cli::cli_h2("Extra info about the tuning of the regression model")
+      }
+    }
+  }
+}
+
+#' Printing messages in iterative procedure with cli
+#'
+#' @inheritParams default_doc_explain
+#' @inheritParams explain
+#'
+#' @export
+#' @keywords internal
 cli_iter <- function(verbose, internal, iter) {
   iterative <- internal$parameters$iterative
   asymmetric <- internal$parameters$asymmetric

R/compute_vS.R

@@ -14,22 +14,8 @@ compute_vS <- function(internal, model, predict_model, method = "future") {
 
   S_batch <- internal$iter_list[[iter]]$S_batch
 
-  verbose <- internal$parameters$verbose
-  approach <- internal$parameters$approach
-
   # verbose
-  if ("progress" %in% verbose) {
-    cli::cli_progress_step("Computing vS")
-  }
-  if ("vS_details" %in% verbose) {
-    if ("regression_separate" %in% approach) {
-      tuning <- internal$parameters$regression.tune
-      if (isTRUE(tuning)) {
-        cli::cli_h2("Extra info about the tuning of the regression model")
-      }
-    }
-  }
-
+  cli_compute_vS(internal)
 
   if (method == "future") {
     vS_list <- future_compute_vS_batch(
@@ -53,36 +39,7 @@ compute_vS <- function(internal, model, predict_model, method = "future") {
   }
 
   #### Adds v_S output above to any vS_list already computed ####
-  ### Need to map the old id_coalitions to the new numbers for this merging to work out
-  if (iter > 1) {
-    prev_coalition_map <- internal$iter_list[[iter - 1]]$coalition_map
-    prev_vS_list <- internal$iter_list[[iter - 1]]$vS_list
-
-    current_coalition_map <- internal$iter_list[[iter]]$coalition_map
-
-
-    # Creates a mapper from the last id_coalition to the new id_coalition numbering
-    id_coalitions_mapper <- merge(prev_coalition_map,
-      current_coalition_map,
-      by = "coalitions_str",
-      suffixes = c("", "_new")
-    )
-    prev_vS_list_new <- list()
-
-    # Applies the mapper to update the prev_vS_list ot the new id_coalition numbering
-    for (k in seq_along(prev_vS_list)) {
-      prev_vS_list_new[[k]] <- merge(prev_vS_list[[k]],
-        id_coalitions_mapper[, .(id_coalition, id_coalition_new)],
-        by = "id_coalition"
-      )
-      prev_vS_list_new[[k]][, id_coalition := id_coalition_new]
-      prev_vS_list_new[[k]][, id_coalition_new := NULL]
-    }
-
-    # Merge the new vS_list with the old vS_list
-    vS_list <- c(prev_vS_list_new, vS_list)
-  }
-
+  vS_list <- append_vS_list(vS_list, internal)
 
 
   return(vS_list)
@@ -264,3 +221,47 @@ compute_MCint <- function(dt, pred_cols = "p_hat") {
 
   return(dt_mat)
 }
+
+#' Appends the new vS_list to the prev vS_list
+#'
+#'
+#' @inheritParams compute_estimates
+#'
+#' @export
+#' @keywords internal
+append_vS_list <- function(vS_list, internal) {
+
+  iter <- length(internal$iter_list)
+
+  # Adds v_S output above to any vS_list already computed
+  if (iter > 1) {
+    prev_coalition_map <- internal$iter_list[[iter - 1]]$coalition_map
+    prev_vS_list <- internal$iter_list[[iter - 1]]$vS_list
+
+    # Need to map the old id_coalitions to the new numbers for this merging to work out
+    current_coalition_map <- internal$iter_list[[iter]]$coalition_map
+
+    # Creates a mapper from the last id_coalition to the new id_coalition numbering
+    id_coalitions_mapper <- merge(prev_coalition_map,
+                                  current_coalition_map,
+                                  by = "coalitions_str",
+                                  suffixes = c("", "_new")
+    )
+    prev_vS_list_new <- list()
+
+    # Applies the mapper to update the prev_vS_list ot the new id_coalition numbering
+    for (k in seq_along(prev_vS_list)) {
+      prev_vS_list_new[[k]] <- merge(prev_vS_list[[k]],
+                                     id_coalitions_mapper[, .(id_coalition, id_coalition_new)],
+                                     by = "id_coalition"
+      )
+      prev_vS_list_new[[k]][, id_coalition := id_coalition_new]
+      prev_vS_list_new[[k]][, id_coalition_new := NULL]
+    }
+
+    # Merge the new vS_list with the old vS_list
+    vS_list <- c(prev_vS_list_new, vS_list)
+  }
+  return(vS_list)
+
+}

R/documentation.R

@@ -31,6 +31,9 @@ default_doc <- function(internal, model, predict_model, output_size, extra, ...)
 
 #' Exported documentation helper function.
 #'
+#' @param iter Integer.
+#' The iteration number. Only used internally.
+#'
 #' @param internal List.
 #' Not used directly, but passed through from [explain()].
 #'

R/explain.R

@@ -482,7 +482,7 @@ explain <- function(model,
     set.seed(seed)
   }
 
-  cli_startup(internal, model, verbose)
+  cli_startup(internal, class(model), verbose)
 
 
   while (converged == FALSE) {

R/explain_forecast.R

@@ -178,7 +178,7 @@ explain_forecast <- function(model,
     set.seed(seed)
   }
 
-  cli_startup(internal, model, verbose)
+  cli_startup(internal, class(model), verbose)
 
   while (converged == FALSE) {
     cli_iter(verbose, internal, iter)

R/plot.R

@@ -241,7 +241,7 @@ plot.shapr <- function(x,
       desc_mat[, i] <- paste0(shap_names[i], " = ", desc_mat[, i])
     }
   } else {
-    desc_mat <- trimws(format(x$shapley_values_est[, -c("explain_id", "none")], digits = digits))
+    desc_mat <- trimws(format(x$shapley_values_est[, -c("none")], digits = digits))
     for (i in seq_len(ncol(desc_mat))) {
       desc_mat[, i] <- paste0(shap_names[i])
     }