Fix #978

easystats · Jun 9, 2024 · e7d3ead · e7d3ead
1 parent 22c1d85
commit e7d3ead
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Showing 14 changed files with 116 additions and 75 deletions.
diff --git a/R/methods_BayesFactor.R b/R/methods_BayesFactor.R
@@ -33,7 +33,7 @@
 #' # Bayesian t-test
 #' model <- BayesFactor::ttestBF(x = rnorm(100, 1, 1))
 #' model_parameters(model)
-#' model_parameters(model, effectsize_type = "cohens_d", ci = 0.9)
+#' model_parameters(model, es_type = "cohens_d", ci = 0.9)
 #'
 #' # Bayesian contingency table analysis
 #' data(raceDolls)
@@ -46,7 +46,7 @@
 #'   centrality = "mean",
 #'   dispersion = TRUE,
 #'   verbose = FALSE,
-#'   effectsize_type = "cramers_v"
+#'   es_type = "cramers_v"
 #' )
 #' }
 #' @return A data frame of indices related to the model's parameters.
@@ -60,9 +60,10 @@ model_parameters.BFBayesFactor <- function(model,
                                            rope_range = "default",
                                            rope_ci = 0.95,
                                            priors = TRUE,
-                                           effectsize_type = NULL,
+                                           es_type = NULL,
                                            include_proportions = FALSE,
                                            verbose = TRUE,
+                                           effectsize_type = NULL,
                                            ...) {
   insight::check_if_installed("BayesFactor")
 
@@ -83,6 +84,12 @@ model_parameters.BFBayesFactor <- function(model,
     return(NULL)
   }
 
+  ## TODO: remove deprecation warning later
+  if (!is.null(effectsize_type)) {
+    insight::format_warning("Argument `effectsize_type` is deprecated. Use `es_type` instead.")
+    es_type <- effectsize_type
+  }
+
   out <- bayestestR::describe_posterior(
     model,
     centrality = centrality,
@@ -132,7 +139,7 @@ model_parameters.BFBayesFactor <- function(model,
   }
 
   # Effect size?
-  if (!is.null(effectsize_type)) {
+  if (!is.null(es_type)) {
     # needs {effectsize} to be installed
     insight::check_if_installed("effectsize")
 
@@ -144,7 +151,7 @@ model_parameters.BFBayesFactor <- function(model,
           dispersion = dispersion,
           ci_method = ci_method,
           rope_ci = rope_ci,
-          type = effectsize_type,
+          type = es_type,
           ...
         )
 

diff --git a/R/methods_aov.R b/R/methods_aov.R
@@ -7,7 +7,7 @@
 #' @param model Object of class [aov()], [anova()],
 #'   `aovlist`, `Gam`, [manova()], `Anova.mlm`,
 #'   `afex_aov` or `maov`.
-#' @param effectsize_type The effect size of interest. Not that possibly not all
+#' @param es_type The effect size of interest. Not that possibly not all
 #'   effect sizes are applicable to the model object. See 'Details'. For Anova
 #'   models, can also be a character vector with multiple effect size names.
 #' @param df_error Denominator degrees of freedom (or degrees of freedom of the
@@ -18,7 +18,7 @@
 #'   ANOVA-tables using `car::Anova()` will be returned. (Ignored for
 #'   `afex_aov`.)
 #' @param ci Confidence Interval (CI) level for effect sizes specified in
-#'   `effectsize_type`. The default, `NULL`, will compute no confidence
+#'   `es_type`. The default, `NULL`, will compute no confidence
 #'   intervals. `ci` should be a scalar between 0 and 1.
 #' @param test String, indicating the type of test for `Anova.mlm` to be
 #'   returned. If `"multivariate"` (or `NULL`), returns the summary of
@@ -35,6 +35,7 @@
 #'   (e.g., `"g"`, `"l"`, `"two"`...). See section *One-Sided CIs* in
 #'   the [effectsize_CIs vignette](https://easystats.github.io/effectsize/).
 #' @inheritParams model_parameters.default
+#' @param effectsize_type Deprecated. Use `es_type` instead.
 #' @param ... Arguments passed to [`effectsize::effectsize()`]. For example,
 #'   to calculate _partial_ effect sizes types, use `partial = TRUE`. For objects
 #'   of class `htest` or `BFBayesFactor`, `adjust = TRUE` can be used to return
@@ -65,13 +66,13 @@
 #' model <- aov(Sepal.Length ~ Sepal.Big, data = df)
 #' model_parameters(model)
 #'
-#' model_parameters(model, effectsize_type = c("omega", "eta"), ci = 0.9)
+#' model_parameters(model, es_type = c("omega", "eta"), ci = 0.9)
 #'
 #' model <- anova(lm(Sepal.Length ~ Sepal.Big, data = df))
 #' model_parameters(model)
 #' model_parameters(
 #'   model,
-#'   effectsize_type = c("omega", "eta", "epsilon"),
+#'   es_type = c("omega", "eta", "epsilon"),
 #'   alternative = "greater"
 #' )
 #'
@@ -91,7 +92,7 @@
 #' # parameters table including effect sizes
 #' model_parameters(
 #'   model,
-#'   effectsize_type = "eta",
+#'   es_type = "eta",
 #'   ci = 0.9,
 #'   df_error = dof_satterthwaite(mm)[2:3]
 #' )
@@ -104,16 +105,23 @@ model_parameters.aov <- function(model,
                                  alternative = NULL,
                                  test = NULL,
                                  power = FALSE,
-                                 effectsize_type = NULL,
+                                 es_type = NULL,
                                  keep = NULL,
                                  drop = NULL,
                                  table_wide = FALSE,
                                  verbose = TRUE,
+                                 effectsize_type = NULL,
                                  ...) {
   # save model object, for later checks
   original_model <- model
   object_name <- insight::safe_deparse_symbol(substitute(model))
 
+  ## TODO: remove deprecation warning later
+  if (!is.null(effectsize_type)) {
+    insight::format_warning("Argument `effectsize_type` is deprecated. Use `es_type` instead.")
+    es_type <- effectsize_type
+  }
+
   if (inherits(model, "aov") && !is.null(type) && type > 1) {
     if (requireNamespace("car", quietly = TRUE)) {
       model <- car::Anova(model, type = type)
@@ -144,7 +152,7 @@ model_parameters.aov <- function(model,
   params <- .effectsizes_for_aov(
     model,
     params = params,
-    effectsize_type = effectsize_type,
+    es_type = es_type,
     df_error = df_error,
     ci = ci,
     alternative = alternative,
@@ -250,7 +258,7 @@ model_parameters.aovlist <- model_parameters.aov
 #' @rdname model_parameters.aov
 #' @export
 model_parameters.afex_aov <- function(model,
-                                      effectsize_type = NULL,
+                                      es_type = NULL,
                                       df_error = NULL,
                                       type = NULL,
                                       keep = NULL,
@@ -270,7 +278,7 @@ model_parameters.afex_aov <- function(model,
   out <- .effectsizes_for_aov(
     model,
     params = out,
-    effectsize_type = effectsize_type,
+    es_type = es_type,
     df_error = df_error,
     verbose = verbose,
     ...
@@ -432,19 +440,19 @@ model_parameters.maov <- model_parameters.aov
 
 .effectsizes_for_aov <- function(model,
                                  params,
-                                 effectsize_type = NULL,
+                                 es_type = NULL,
                                  df_error = NULL,
                                  ci = NULL,
                                  alternative = NULL,
                                  verbose = TRUE,
                                  ...) {
   # user actually does not want to compute effect sizes
-  if (is.null(effectsize_type)) {
+  if (is.null(es_type)) {
     return(params)
   }
 
   # is valid effect size?
-  if (!all(effectsize_type %in% c("eta", "omega", "epsilon", "f", "f2"))) {
+  if (!all(es_type %in% c("eta", "omega", "epsilon", "f", "f2"))) {
     return(params)
   }
 
@@ -462,7 +470,7 @@ model_parameters.maov <- model_parameters.aov
   }
 
   # multiple effect sizes possible
-  for (es in effectsize_type) {
+  for (es in es_type) {
     fx <- effectsize::effectsize(
       model,
       type = es,

diff --git a/R/methods_htest.R b/R/methods_htest.R
@@ -16,13 +16,13 @@
 #' model_parameters(model)
 #'
 #' model <- t.test(iris$Sepal.Width, iris$Sepal.Length)
-#' model_parameters(model, effectsize_type = "hedges_g")
+#' model_parameters(model, es_type = "hedges_g")
 #'
 #' model <- t.test(mtcars$mpg ~ mtcars$vs)
-#' model_parameters(model, effectsize_type = "hedges_g")
+#' model_parameters(model, es_type = "hedges_g")
 #'
 #' model <- t.test(iris$Sepal.Width, mu = 1)
-#' model_parameters(model, effectsize_type = "cohens_d")
+#' model_parameters(model, es_type = "cohens_d")
 #'
 #' data(airquality)
 #' airquality$Month <- factor(airquality$Month, labels = month.abb[5:9])
@@ -35,7 +35,7 @@
 #' model_parameters(model)
 #'
 #' model <- suppressWarnings(chisq.test(table(mtcars$am, mtcars$cyl)))
-#' model_parameters(model, effectsize_type = "cramers_v")
+#' model_parameters(model, es_type = "cramers_v")
 #'
 #' @return A data frame of indices related to the model's parameters.
 #'
@@ -44,15 +44,22 @@ model_parameters.htest <- function(model,
                                    ci = 0.95,
                                    alternative = NULL,
                                    bootstrap = FALSE,
-                                   effectsize_type = NULL,
+                                   es_type = NULL,
                                    verbose = TRUE,
+                                   effectsize_type = NULL,
                                    ...) {
+  ## TODO: remove deprecation warning later
+  if (!is.null(effectsize_type)) {
+    insight::format_warning("Argument `effectsize_type` is deprecated. Use `es_type` instead.")
+    es_type <- effectsize_type
+  }
+
   if (bootstrap) {
     insight::format_error("Bootstrapped h-tests are not yet implemented.")
   } else {
     parameters <- .extract_parameters_htest(
       model,
-      effectsize_type = effectsize_type,
+      es_type = es_type,
       ci = ci,
       alternative = alternative,
       verbose = verbose,
@@ -121,7 +128,7 @@ model_parameters.svytable <- function(model, verbose = TRUE, ...) {
 
 #' @keywords internal
 .extract_parameters_htest <- function(model,
-                                      effectsize_type = NULL,
+                                      es_type = NULL,
                                       ci = 0.95,
                                       alternative = NULL,
                                       verbose = TRUE,
@@ -164,7 +171,7 @@ model_parameters.svytable <- function(model, verbose = TRUE, ...) {
 
   out <- .add_effectsize_htest(model,
     out,
-    effectsize_type = effectsize_type,
+    es_type = es_type,
     ci = ci,
     alternative = alternative,
     verbose = verbose,
@@ -568,20 +575,20 @@ model_parameters.svytable <- function(model, verbose = TRUE, ...) {
 
 .add_effectsize_htest <- function(model,
                                   out,
-                                  effectsize_type = NULL,
+                                  es_type = NULL,
                                   ci = 0.95,
                                   alternative = NULL,
                                   verbose = TRUE,
                                   ...) {
   # check if effect sizes are requested
-  if (!requireNamespace("effectsize", quietly = TRUE) || is.null(effectsize_type)) {
+  if (!requireNamespace("effectsize", quietly = TRUE) || is.null(es_type)) {
     return(out)
   }
 
   # return on invalid options. We may have partial matching with argument
-  # `effects` for `effectsize_type`, and thus all "effects" options should be
+  # `effects` for `es_type`, and thus all "effects" options should be
   # ignored.
-  if (effectsize_type %in% c("fixed", "random", "all")) {
+  if (es_type %in% c("fixed", "random", "all")) {
     return(out)
   }
 
@@ -590,7 +597,7 @@ model_parameters.svytable <- function(model, verbose = TRUE, ...) {
     {
       effectsize::effectsize(
         model,
-        type = effectsize_type,
+        type = es_type,
         ci = ci,
         alternative = alternative,
         verbose = verbose,
@@ -600,7 +607,7 @@ model_parameters.svytable <- function(model, verbose = TRUE, ...) {
     error = function(e) {
       if (verbose) {
         msg <- c(
-          paste0("Could not compute effectsize ", effectsize::get_effectsize_label(effectsize_type), "."),
+          paste0("Could not compute effectsize ", effectsize::get_effectsize_label(es_type), "."),
           paste0("Possible reason: ", e$message)
         )
         insight::format_alert(msg)
@@ -616,7 +623,7 @@ model_parameters.svytable <- function(model, verbose = TRUE, ...) {
   ## TODO: check if effectsize prefixes are correct @mattansb
 
   # Find prefix for CI-columns
-  prefix <- switch(effectsize_type,
+  prefix <- switch(es_type,
     cohens_g = "Cohens_",
     cramers_v = "Cramers_",
     phi = "phi_",

diff --git a/R/methods_other.R b/R/methods_other.R
@@ -36,15 +36,22 @@ degrees_of_freedom.complmrob <- function(model, method = "wald", ...) {
 #' @inheritParams model_parameters.aov
 #' @export
 model_parameters.Gam <- function(model,
-                                 effectsize_type = NULL,
+                                 es_type = NULL,
                                  df_error = NULL,
                                  type = NULL,
                                  table_wide = FALSE,
                                  verbose = TRUE,
+                                 effectsize_type = NULL,
                                  ...) {
+  ## TODO: remove deprecation warning later
+  if (!is.null(effectsize_type)) {
+    insight::format_warning("Argument `effectsize_type` is deprecated. Use `es_type` instead.")
+    es_type <- effectsize_type
+  }
+
   model_parameters(
     summary(model)$parametric.anova,
-    effectsize_type = effectsize_type,
+    es_type = es_type,
     df_error = df_error,
     type = type,
     table_wide = table_wide,

diff --git a/man/model_parameters.BFBayesFactor.Rd b/man/model_parameters.BFBayesFactor.Rd