Major revision

DESCRIPTION

@@ -17,17 +17,23 @@ RoxygenNote: 7.3.3
 Imports: 
     apollo,
     dplyr,
+    fs,
+    ggpattern,
     ggplot2,
     ggsignif,
     gt,
     katex,
     magrittr,
+    patchwork,
     pkgdown,
     readxl,
     rlang,
+    stats,
     stringr,
     svglite,
-    tidyr
+    tibble,
+    tidyr,
+    utils
 Suggests: 
     testthat (>= 3.0.0)
 Config/testthat/edition: 3

NAMESPACE

@@ -1,18 +1,26 @@
 # Generated by roxygen2: do not edit by hand
 
-export(coefficient_to_variable)
 export(compare_models)
 export(create_criteria_table)
-export(create_group_comparison_table)
+export(create_group_comparison_tables)
 export(create_model_weights_tables)
+export(create_pooled_group_comparison_tables)
+export(feature_importance)
+export(feature_importance_all)
 export(fit_bait_binary)
 export(fit_bait_multinomial)
+export(fit_pooled_interaction_binary)
+export(fit_pooled_interaction_multinomial)
+export(fit_pooled_models)
 export(load_responses)
 export(maximum_utility_contribution)
 export(plot_group_comparison)
+export(plot_pooled_group_comparison)
 export(plot_relative_importance)
 export(predict)
+export(run_linearity_tests)
 export(standardized_coefficients)
+export(wald_interaction)
 importFrom(magrittr,"%>%")
 importFrom(rlang,.data)
 importFrom(stats,filter)

R/bait_binary.R

@@ -11,7 +11,7 @@
 #' @export
 #'
 #' @examples
-#' fit_bait_binary()
+#' baitlist::fit_bait_binary(elimination_threshold = 1)
 fit_bait_binary <- function(elimination_threshold = 0.20) {
 
   groups <- c(
@@ -163,7 +163,7 @@ fit_bait_binary <- function(elimination_threshold = 0.20) {
       coef <- model$estimate
       se <- model$robse
       wald_stat <- coef^2/se^2
-      p_value <- 1 - pchisq(wald_stat, df=1)
+      p_value <- 1 - stats::pchisq(wald_stat, df=1)
 
       # determine coefficients that are above threshold
       nonsig <- p_value[(p_value > elimination_threshold)]
@@ -196,7 +196,7 @@ fit_bait_binary <- function(elimination_threshold = 0.20) {
                                wald = wald_stat,
                                p_value = p_value
     )
-    write.csv(tbl_wald,
+    utils::write.csv(tbl_wald,
               fs::path_package("extdata/apollo/binary/", paste0(apollo_control$modelName, "_weights_wald.csv"),
                                package = "baitlist"),
       row.names = FALSE

R/bait_multinomial.R

@@ -11,7 +11,7 @@
 #' @export
 #'
 #' @examples
-#' fit_bait_multinomial()
+#' baitlist::fit_bait_multinomial(elimination_threshold = 1)
 fit_bait_multinomial <- function(elimination_threshold = 0.20) {
 
   groups <- c(
@@ -201,7 +201,7 @@ fit_bait_multinomial <- function(elimination_threshold = 0.20) {
       coef <- model$estimate
       se <- model$robse
       wald_stat <- coef^2/se^2
-      p_value <- 1 - pchisq(wald_stat, df=1)
+      p_value <- 1 - stats::pchisq(wald_stat, df=1)
 
       # determine coefficients that are above threshold
       nonsig <- p_value[(p_value > elimination_threshold)]
@@ -234,7 +234,7 @@ fit_bait_multinomial <- function(elimination_threshold = 0.20) {
                                wald = wald_stat,
                                p_value = p_value
     )
-    write.csv(tbl_wald,
+    utils::write.csv(tbl_wald,
               fs::path_package("extdata/apollo/multinomial/", paste0(apollo_control$modelName, "_weights_wald.csv"),
                                package = "baitlist"),
       row.names = FALSE