Remove deprecated arguments

R/export_table.R

@@ -48,7 +48,6 @@
 #'   if `table_width` is numeric and table rows are larger than `table_width`,
 #'   the table is split into two parts.
 #' @param ... Currently not used.
-#' @param group_by Deprecated, please use `by` instead.
 #' @inheritParams format_value
 #' @inheritParams get_data
 #'
@@ -102,7 +101,7 @@
 #' export_table(d, width = c(x = 5, z = 10))
 #' export_table(d, width = c(x = 5, y = 5, z = 10), align = "lcr")
 #' @export
 export_table <- function(x,
                          sep = " | ",
                          header = "-",
                          cross = NULL,
@@ -118,7 +117,6 @@
                          footer = NULL,
                          align = NULL,
                          by = NULL,
-                         group_by = NULL,
                          zap_small = FALSE,
                          table_width = NULL,
                          verbose = TRUE,
@@ -133,12 +131,6 @@
     format <- "markdown"
   }
 
-  ## TODO: deprecate later
-  if (!is.null(group_by)) {
-    format_warning("Argument `group_by` is deprecated and will be removed in a future release. Please use `by` instead.") # nolint
-    by <- group_by
-  }
-
   # validation check
   if (is.null(x) || (is.data.frame(x) && nrow(x) == 0) || is_empty_object(x)) {
     if (isTRUE(verbose)) {
@@ -474,7 +466,7 @@
 # plain text formatting ------------------------
 
 
 .format_basic_table <- function(final,
                                 header,
                                 sep,
                                 cross = NULL,
@@ -577,14 +569,14 @@
 
     # width of first table row of complete table. Currently, "final" is still
     # a matrix, so we need to paste the columns of the first row into a string
     row_width <- nchar(paste0(final[1, ], collapse = sep), type = "width")
 
     # possibly first split - all table columns longer than "line_width"
     # (i.e. first table row) go into a second string
     if (row_width > line_width) {
       i <- 1
       # determine how many columns fit into the first line
       while (nchar(paste0(final[1, 1:i], collapse = sep), type = "width") < line_width) {
         i <- i + 1
       }
       # copy first column, and all columns that did not fit into the first line
@@ -596,14 +588,14 @@
     }
 
     # width of first table row of remaing second table part
     row_width <- nchar(paste0(final2[1, ], collapse = sep), type = "width")
 
     # possibly second split - all table columns longer than "line_width"
     # (i.e. first table row) go into a third string - we repeat the same
     # procedure as above
     if (row_width > line_width) {
       i <- 1
       while (nchar(paste0(final2[1, 1:i], collapse = sep), type = "width") < line_width) {
         i <- i + 1
       }
       if (i > 2 && i < ncol(final2)) {
@@ -674,7 +666,7 @@
   for (row in seq_len(nrow(final))) {
     # create a string for each row, where cells from original matrix are
     # separated by the separator char
     final_row <- paste0(final[row, ], collapse = sep)
     # check if we have an empty row, and if so, fill with an
     # "empty line separator", if requested by user
     if (!is.null(empty_line) && !any(nzchar(trim_ws(final[row, ])))) {
@@ -685,7 +677,7 @@
         # the empty line, which is just empty cells with separator char,
         # will now be replaced by the "empty line char", so we have a
         # clean separator line
         paste0(rep_len(empty_line, nchar(final_row, type = "width")), collapse = ""),
         cross, sep, final_row,
         is_last_row = row == nrow(final)
       )
@@ -699,7 +691,7 @@
       # check whether user wants to have a "cross" char where vertical and
       # horizontal lines (from header line) cross.
       header_line <- .insert_cross(
         paste0(rep_len(header, nchar(final_row, type = "width")), collapse = ""),
         cross, sep, final_row,
         is_last_row = row == nrow(final)
       )
@@ -817,7 +809,7 @@
 
 # markdown formatting -------------------
 
 .format_markdown_table <- function(final,
                                    x,
                                    caption = NULL,
                                    subtitle = NULL,

R/get_datagrid.R

@@ -112,7 +112,6 @@
 #' @param verbose Toggle warnings.
 #' @param ... Arguments passed to or from other methods (for instance, `length`
 #'   or `range` to control the spread of numeric variables.).
-#' @param at Deprecated. Use `by` instead.
 #'
 #' @return Reference grid data frame.
 #'
@@ -197,14 +196,7 @@ get_datagrid.data.frame <- function(x,
                                     reference = x,
                                     length = 10,
                                     range = "range",
-                                    at,
                                     ...) {
-  ## TODO: deprecate later
-  if (!missing(at)) {
-    format_warning("Argument `at` is deprecated and will be removed in a future release. Please use `by` instead.") # nolint
-    by <- at
-  }
-
   # find numerics that were coerced to factor in-formula
   numeric_factors <- colnames(x)[vapply(x, function(i) isTRUE(attributes(i)$factor), logical(1))]
 
@@ -494,14 +486,7 @@ get_datagrid.default <- function(x,
                                  include_response = FALSE,
                                  data = NULL,
                                  verbose = TRUE,
-                                 at,
                                  ...) {
-  ## TODO: deprecate later
-  if (!missing(at)) {
-    format_warning("Argument `at` is deprecated and will be removed in a future release. Please use `by` instead.") # nolint
-    by <- at
-  }
-
   # validation check
   if (!is_model(x)) {
     format_error("`x` must be a statistical model.")

R/get_varcov_sandwich.R

@@ -7,36 +7,10 @@
                                  ...) {
   dots <- list(...)
 
-  ## TODO: remove deprecated warnings in a future update
-
-  # deprecated
-  if (isTRUE(verbose) && "vcov_type" %in% names(dots)) {
-    format_warning("The `vcov_type` argument is superseded by the `vcov_args` argument.")
-  }
-  if (isTRUE(verbose) && "robust" %in% names(dots)) {
-    format_warning("The `robust` argument is superseded by the `vcov` argument.")
-  }
-
   if (is.null(vcov_args)) {
     vcov_args <- list()
   }
 
-  # deprecated: `vcov_estimation`
-  if (is.null(vcov_fun) && "vcov_estimation" %in% names(dots)) {
-    vcov_fun <- dots[["vcov_estimation"]]
-  }
-
-  # deprecated: `robust`
-  if (isTRUE(dots[["robust"]]) && is.null(vcov_fun)) {
-    dots[["robust"]] <- NULL
-    vcov_fun <- "HC3"
-  }
-
-  # deprecated: `vcov_type`
-  if ("vcov_type" %in% names(dots) && !"type" %in% names(vcov_args)) {
-    vcov_args[["type"]] <- dots[["vcov_type"]]
-  }
-
   # vcov_fun is a matrix
   if (is.matrix(vcov_fun)) {
     return(vcov_fun)

R/print_parameters.R

@@ -43,7 +43,6 @@
 #'   and `subtitles` may be any length from 1 to same length as returned
 #'   list elements. If `titles` and `subtitles` are shorter than
 #'   existing elements, only the first default attributes are overwritten.
-#' @param split_by Deprecated, please use `by` instead.
 #'
 #' @return
 #'
@@ -110,14 +109,7 @@ print_parameters <- function(x,
                              keep_parameter_column = TRUE,
                              remove_empty_column = FALSE,
                              titles = NULL,
-                             subtitles = NULL,
-                             split_by = NULL) {
-  ## TODO: deprecte later
-  if (!is.null(split_by)) {
-    format_warning("Argument `split_by` is deprecated and will be removed in a future release. Please use `by` instead.") # nolint
-    by <- split_by
-  }
-
+                             subtitles = NULL) {
   obj <- list(...)
 
   # save attributes of original object

R/utilities.R

@@ -89,7 +89,7 @@ n_unique <- function(x, ...) {
 
 #' @rdname trim_ws
 #' @export
-n_unique.default <- function(x, remove_na = TRUE, na.rm = remove_na, ...) {
+n_unique.default <- function(x, remove_na = TRUE, na.rm = TRUE, ...) {
   if (is.null(x)) {
     return(0)
   }
@@ -103,23 +103,23 @@ n_unique.default <- function(x, remove_na = TRUE, na.rm = remove_na, ...) {
 }
 
 #' @export
-n_unique.data.frame <- function(x, remove_na = TRUE, na.rm = remove_na, ...) {
+n_unique.data.frame <- function(x, remove_na = TRUE, na.rm = TRUE, ...) {
   ## TODO:: remove deprecation warning later
   if (!missing(na.rm)) {
     format_warning("The `na.rm` argument is deprecated. Use `remove_na` instead.")
     remove_na <- na.rm
   }
-  vapply(x, n_unique, na.rm = remove_na, FUN.VALUE = numeric(1L))
+  vapply(x, n_unique, remove_na = remove_na, FUN.VALUE = numeric(1L))
 }
 
 #' @export
-n_unique.list <- function(x, remove_na = TRUE, na.rm = remove_na, ...) {
+n_unique.list <- function(x, remove_na = TRUE, na.rm = TRUE, ...) {
   ## TODO:: remove deprecation warning later
   if (!missing(na.rm)) {
     format_warning("The `na.rm` argument is deprecated. Use `remove_na` instead.")
     remove_na <- na.rm
   }
-  lapply(x, n_unique, na.rm = remove_na)
+  lapply(x, n_unique, remove_na = remove_na)
 }
 
 
@@ -155,7 +155,7 @@ safe_deparse_symbol <- function(x) {
 
 #' @rdname trim_ws
 #' @export
-has_single_value <- function(x, remove_na = FALSE, na.rm = remove_na, ...) {
+has_single_value <- function(x, remove_na = FALSE, na.rm = TRUE, ...) {
   ## TODO:: remove deprecation warning later
   if (!missing(na.rm)) {
     format_warning("The `na.rm` argument is deprecated. Use `remove_na` instead.")

tests/testthat/test-get_datagrid.R

@@ -246,7 +246,7 @@ test_that("get_datagrid - emmeans", {
   # emm_list
   em1 <- emmeans::emmeans(mod1, pairwise ~ cyl | hp, at = list(hp = hp_vals))
   em2 <- emmeans::emmeans(mod1, pairwise ~ cyl | hp, at = list(hp = hp_vals), regrid = TRUE)
-  em3 <- emmeans::emmeans(mod2, pairwise  ~ cyl | hp, at = list(hp = hp_vals))
+  em3 <- emmeans::emmeans(mod2, pairwise ~ cyl | hp, at = list(hp = hp_vals))
 
   res <- get_datagrid(em1)
   expect_identical(res, get_datagrid(em2))
@@ -268,10 +268,14 @@ test_that("get_datagrid - marginaleffects", {
   mod1 <- glm(am ~ hp + factor(cyl), family = binomial("logit"), data = mtcars)
   mod2 <- lm(mpg ~ hp + factor(cyl), data = mtcars)
 
-  mp1 <- marginaleffects::avg_predictions(mod1, variables = list("hp" = c(50, 100)),
-                                          by = c("cyl", "hp"))
-  mp2 <- marginaleffects::avg_predictions(mod2, variables = list("hp" = c(50, 100),
-                                                                 cyl = unique))
+  mp1 <- marginaleffects::avg_predictions(mod1,
+    variables = list(hp = c(50, 100)),
+    by = c("cyl", "hp")
+  )
+  mp2 <- marginaleffects::avg_predictions(mod2, variables = list(
+    hp = c(50, 100),
+    cyl = unique
+  ))
 
   res <- get_datagrid(mp1)
   expect_s3_class(res, "data.frame")
@@ -290,9 +294,10 @@ test_that("get_datagrid - marginaleffects", {
 
   mod <- lm(mpg ~ wt + hp + qsec, data = mtcars)
   myme <- marginaleffects::comparisons(mod,
-                                       variables = c("wt", "hp"),
-                                       cross = TRUE,
-                                       newdata = marginaleffects::datagrid(qsec = range))
+    variables = c("wt", "hp"),
+    cross = TRUE,
+    newdata = marginaleffects::datagrid(qsec = range)
+  )
   res <- get_datagrid(myme)
   expect_true(all(c("wt", "mpg", "hp", "qsec") %in% colnames(res)))
   expect_true(all(c("contrast_hp", "contrast_wt") %in% colnames(res)))
@@ -396,15 +401,3 @@ test_that("get_datagrid - multiple weight variables", {
     tolerance = 1e-3
   )
 })
-
-
-test_that("get_datagrid - deprecated arg doesn't cause memory allocation issues", {
-  data(iris)
-  expect_warning(
-    {
-      out <- get_datagrid(iris, at = NULL)
-    },
-    regex = "Argument `at` is deprecated"
-  )
-  expect_identical(nrow(out), 1L)
-})

tests/testthat/test-get_predicted.R

@@ -158,8 +158,8 @@ test_that("robust vcov", {
   skip_if_not_installed("sandwich")
   mod <- lm(mpg ~ hp, data = mtcars)
   se0 <- get_predicted_se(mod)
-  se1 <- suppressWarnings(get_predicted_se(mod, vcov_estimation = "HC"))
-  se2 <- suppressWarnings(get_predicted_se(mod, vcov_estimation = "HC", vcov_type = "HC3"))
+  se1 <- suppressWarnings(get_predicted_se(mod, vcov = "HC"))
+  se2 <- suppressWarnings(get_predicted_se(mod, vcov = "HC3"))
   se3 <- get_predicted_se(mod, vcov = "HC", vcov_args = list(type = "HC3"))
   expect_true(all(se0 != se1))
   expect_true(all(se1 == se2))
@@ -173,13 +173,11 @@ test_that("robust vcov", {
   ignore_attr = TRUE
   )
   # various user inputs
-  se1 <- suppressWarnings(get_predicted_se(mod, vcov_estimation = "HC", vcov_type = "HC2"))
-  se2 <- get_predicted_se(mod, vcov = "HC2")
-  se3 <- get_predicted_se(mod, vcov = "vcovHC", vcov_args = list(type = "HC2"))
-  se4 <- get_predicted_se(mod, vcov = sandwich::vcovHC, vcov_args = list(type = "HC2"))
+  se1 <- get_predicted_se(mod, vcov = "HC2")
+  se2 <- get_predicted_se(mod, vcov = "vcovHC", vcov_args = list(type = "HC2"))
+  se3 <- get_predicted_se(mod, vcov = sandwich::vcovHC, vcov_args = list(type = "HC2"))
   expect_true(all(se1 == se2))
   expect_true(all(se1 == se3))
-  expect_true(all(se1 == se4))
   se1 <- get_predicted_se(mod, vcov = "HC1")
   se2 <- get_predicted_se(mod, vcov = sandwich::vcovHC, vcov_args = list(type = "HC1"))
   expect_true(all(se1 == se2))