Merge branch 'main' into strengejacke/issue1051

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: parameters
 Title: Processing of Model Parameters
-Version: 0.24.0
+Version: 0.24.0.2
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
@@ -167,7 +167,7 @@ Suggests:
     metafor,
     mfx,
     mgcv,
-    mice,
+    mice (>= 3.17.0),
     mmrm,
     multcomp,
     MuMIn,
@@ -224,3 +224,4 @@ Config/testthat/edition: 3
 Config/testthat/parallel: true
 Config/Needs/website: easystats/easystatstemplate
 Config/rcmdcheck/ignore-inconsequential-notes: true
+Remotes: easystats/datawizard

R/dominance_analysis.R

@@ -529,58 +529,54 @@ dominance_analysis <- function(model, sets = NULL, all = NULL,
     datawizard::data_relocate(da_df_res, "subset", after = "ranks")
 
   if (conditional) {
-    da_df_cdl <-
-      .data_frame(Subset = names(domir_res$General_Dominance))
-
-    da_df_cdl <-
-      datawizard::data_merge(
-        da_df_cdl,
-        .data_frame(
-          Subset = names(domir_res$General_Dominance),
-          domir_res$Conditional_Dominance
-        )
-      )
+    da_df_cdl <- .data_frame(Subset = names(domir_res$General_Dominance))
 
-    da_df_cdl <-
-      datawizard::data_rename(
-        da_df_cdl,
-        names(da_df_cdl)[2:length(da_df_cdl)],
-        colnames(domir_res$Conditional_Dominance)
+    da_df_cdl <- datawizard::data_merge(
+      da_df_cdl,
+      .data_frame(
+        Subset = names(domir_res$General_Dominance),
+        domir_res$Conditional_Dominance
       )
+    )
+
+    cols_to_select <- colnames(da_df_cdl)[2:length(da_df_cdl)]
+    da_df_cdl <- datawizard::data_rename(
+      da_df_cdl,
+      select = cols_to_select,
+      replacement = colnames(domir_res$Conditional_Dominance)
+    )
   } else {
     da_df_cdl <- NULL
   }
 
   if (complete) {
-    da_df_cpt <-
-      .data_frame(Subset = names(domir_res$General_Dominance))
-
-    da_df_cpt <-
-      datawizard::data_merge(
-        da_df_cpt,
-        .data_frame(
-          Subset = names(domir_res$General_Dominance),
-          domir_res$Complete_Dominance
-        )
-      )
+    da_df_cpt <- .data_frame(Subset = names(domir_res$General_Dominance))
 
-    da_df_cpt <-
-      datawizard::data_rename(
-        da_df_cpt,
-        names(da_df_cpt)[2:length(da_df_cpt)],
-        colnames(domir_res$Complete_Dominance)
+    da_df_cpt <- datawizard::data_merge(
+      da_df_cpt,
+      .data_frame(
+        Subset = names(domir_res$General_Dominance),
+        domir_res$Complete_Dominance
       )
+    )
+
+    cols_to_select <- colnames(da_df_cpt)[2:length(da_df_cpt)]
+    da_df_cpt <- datawizard::data_rename(
+      da_df_cpt,
+      select = cols_to_select,
+      replacement = colnames(domir_res$Complete_Dominance)
+    )
   } else {
     da_df_cpt <- NULL
   }
 
-  da_df_res <-
-    datawizard::data_rename(da_df_res,
-      replacement = c(
-        "Parameter", "General_Dominance",
-        "Percent", "Ranks", "Subset"
-      )
+  da_df_res <- datawizard::data_rename(
+  da_df_res,
+    replacement = c(
+      "Parameter", "General_Dominance",
+      "Percent", "Ranks", "Subset"
     )
+  )
 
   da_list <- list(
     General = da_df_res,
@@ -615,7 +611,7 @@ print.parameters_da <- function(x, digits = 3, ...) {
   printed_x <- x
 
   printed_x$General <- datawizard::data_rename(x$General,
-    pattern = "General_Dominance",
+    select = "General_Dominance",
     replacement = "General Dominance"
   )
 
@@ -628,7 +624,7 @@ print.parameters_da <- function(x, digits = 3, ...) {
 
     printed_x$Conditional <-
       datawizard::data_rename(x$Conditional,
-        pattern = cdl_names,
+        select = cdl_names,
         replacement = cdl_names_rep
       )
   }
@@ -644,7 +640,7 @@ print.parameters_da <- function(x, digits = 3, ...) {
 
     printed_x$Complete <-
       datawizard::data_rename(x$Complete,
-        pattern = cpt_names,
+        select = cpt_names,
         replacement = cpt_names_rep
       )
   }

R/extract_random_variances.R

@@ -206,7 +206,7 @@
   # rename columns
   out <- datawizard::data_rename(
     out,
-    pattern = c("grp", "sdcor"),
+    select = c("grp", "sdcor"),
     replacement = c("Group", "Coefficient")
   )
 

R/methods_glmmTMB.R

@@ -426,7 +426,7 @@ ci.glmmTMB <- function(x,
   method <- tolower(method)
   method <- insight::validate_argument(
     method,
-    c("wald", "normal", "ml1", "betwithin", "profile", "uniroot", "robust")
+    c("wald", "normal", "ml1", "betwithin", "profile", "uniroot", "robust", "residual")
   )
   component <- insight::validate_argument(
     component,

R/methods_mice.R

@@ -21,8 +21,8 @@ p_value.mipo <- function(model, ...) {
     p = as.vector(s$p.value)
   )
   # check for ordinal-alike models
-  if ("y.level" %in% colnames(s)) {
-    out$Response <- as.vector(s$y.level)
+  if (!is.null(model$pooled) && "y.level" %in% colnames(model$pooled)) {
+    out$Response <- as.vector(model$pooled$y.level)
   }
   out
 }
@@ -45,8 +45,8 @@ standard_error.mipo <- function(model, ...) {
     SE = as.vector(s$std.error)
   )
   # check for ordinal-alike models
-  if ("y.level" %in% colnames(s)) {
-    out$Response <- as.vector(s$y.level)
+  if (!is.null(model$pooled) && "y.level" %in% colnames(model$pooled)) {
+    out$Response <- as.vector(model$pooled$y.level)
   }
   out
 }
@@ -85,8 +85,7 @@ model_parameters.mipo <- function(model,
   )
 
   # check if we have ordinal/categorical response
-  s <- summary(model)
-  if ("y.level" %in% colnames(s)) {
+  if (!is.null(model$pooled) && "y.level" %in% colnames(model$pooled)) {
     merge_by <- c("Parameter", "Response")
   } else {
     merge_by <- "Parameter"

R/p_function.R

@@ -379,7 +379,7 @@ format.parameters_p_function <- function(x,
     ci <- as.character(i$CI)[1]
     out <- datawizard::data_rename(
       i,
-      pattern = c("CI_low", "CI_high"),
+      select = c("CI_low", "CI_high"),
       replacement = c(sprintf("CI_low_%s", ci), sprintf("CI_high_%s", ci))
     )
     out$CI <- NULL

tests/testthat/test-dominance_analysis.R

@@ -1,5 +1,6 @@
 skip_if_not_installed("performance")
 skip_if_not_installed("domir")
+skip_if_not_installed("datawizard")
 
 DA_test_model <- lm(mpg ~ vs + cyl + carb, data = mtcars)
 

tests/testthat/test-pool_parameters.R

@@ -74,7 +74,7 @@ test_that("pooled parameters, glmmTMB, components", {
   )
   expect_equal(out$Coefficient, c(187.280225, -87.838969), tolerance = 1e-3)
 
-  out <- pool_parameters(models, component = "all", effects = "all")
+  out <- suppressMessages(pool_parameters(models, component = "all", effects = "all"))
   expect_named(
     out,
     c(
@@ -123,7 +123,7 @@ test_that("pooled parameters, glmmTMB, zero-inflated", {
     )
   })
 
-  out <- pool_parameters(models)
+  out <- pool_parameters(models, ci_method = "residual")
   expect_named(
     out,
     c(