progress (#1595)

DESCRIPTION

@@ -46,7 +46,7 @@ Depends:
     R (>= 4.1)
 Imports: 
     broom.helpers,
-    cards (>= 0.0.0.9010),
+    cards (>= 0.0.0.9024),
     cli (>= 3.6.1),
     dplyr (>= 1.1.3),
     glue (>= 1.6.2),
@@ -70,4 +70,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

R/assign_summary_digits.R

@@ -30,7 +30,7 @@ assign_summary_digits <- function(data, statistic, type, digits = NULL) {
         # if the passed value fully specifies the formatting for each 'statistic',
         # then return it. Otherwise, the remaining stat will be filled below
         if (setequal(statistic[[variable]], names(digits[[variable]]))) {
-          return(digits[[variable]])
+          return(lst_all_fmt_fns |> utils::modifyList(digits[[variable]]))
         }
       }
 

R/assign_summary_type.R

@@ -3,11 +3,18 @@
 #' Function inspects data and assigns a summary type when not specified
 #' in the `type` argument.
 #'
-#' @param data a data frame
-#' @param variables character vector of column names in `data`
-#' @param value named list of values to show for dichotomous variables, where
-#' the names are the variables
-#' @param type named list of summary types, where names are the variables
+#' @param data (`data.frame`)\cr
+#'   a data frame
+#' @param variables (`character`)\cr
+#'   character vector of column names in `data`
+#' @param value (`named list`)\cr
+#'   named list of values to show for dichotomous variables, where
+#'   the names are the variables
+#' @param type (`named list`)\cr
+#'   named list of summary types, where names are the variables
+#' @param cat_threshold (`integer`)\cr
+#'   for base R numeric classes with fewer levels than
+#'   this threshold will default to a categorical summary. Default is `10L`
 #'
 #' @return named list
 #' @export
@@ -18,7 +25,7 @@
 #'   variables = c("age", "grade", "response"),
 #'   value = NULL
 #' )
-assign_summary_type <- function(data, variables, value, type = NULL) {
+assign_summary_type <- function(data, variables, value, type = NULL, cat_threshold = 10L) {
   # base classes that can be summarized as continuous
   base_numeric_classes <- c("numeric", "integer", "difftime", "Date", "POSIXt", "double")
 
@@ -32,18 +39,29 @@ assign_summary_type <- function(data, variables, value, type = NULL) {
           return(type[[variable]])
         }
 
+        # if user supplied a dichotomous value, make it dichotomous
         if (!is.null(.get_default_dichotomous_value(data[[variable]]))) {
           return("dichotomous")
         }
 
-        # factors and characters are categorical
-        if (inherits(data[[variable]], c("factor", "character"))) {
+        # factors are categorical
+        if (inherits(data[[variable]], "factor")) {
           return("categorical")
         }
 
-        # numeric variables with fewer than 10 levels will be categorical
+        # if all missing, the continuous
+        if (all(is.na(data[[variable]]))) {
+          return("continuous")
+        }
+
+        # characters are categorical
+        if (inherits(data[[variable]], "character")) {
+          return("categorical")
+        }
+
+        # numeric variables with fewer than 'cat_threshold' levels will be categorical
         if (inherits(data[[variable]], base_numeric_classes) &&
-            length(unique(stats::na.omit(data[[variable]]))) < 10) {
+            length(unique(stats::na.omit(data[[variable]]))) < cat_threshold) {
           return("categorical")
         }
 

R/modify_fmt_fun.R

@@ -35,16 +35,14 @@ modify_fmt_fun <- function(x, update, rows = NULL) {
   # converting update arg to a tidyselect list ---------------------------------
   cards::process_formula_selectors(
     data = x$table_body,
-    udpate = update
+    update = update
   )
   cards::check_list_elements(
-    check = function(x) is_function(x),
-    error_msg = list(
-      check = "The value passed in {.arg {arg_name}} for variable {.val {variable}} must be a function."
-    )
+    x = update,
+    predicate = function(x) is_function(x),
+    error_msg = "The value passed in {.arg {arg_name}} for variable {.val {variable}} must be a function."
   )
 
-
   # updating formatting functions ----------------------------------------------
   x <-
     modify_table_styling(

R/modify_header.R

@@ -18,9 +18,11 @@ modify_header <- function(x, ..., text_interpret = c("md", "html"),
 
   cards::process_formula_selectors(data = x$table_body, dots = dots)
   cards::check_list_elements(
-    dots = function(x) is_string(x),
-    error_msg = list(dots = c("All values passed in {.arg ...} must be strings.",
-                              "i" = "For example, {.code label = '**Variable**'}"))
+    x = dots,
+    predicate = function(x) is_string(x),
+    error_msg =
+      c("All values passed in {.arg ...} must be strings.",
+        "i" = "For example, {.code label = '**Variable**'}")
   )
 
   # evaluate the strings with glue

R/select_helpers.R

@@ -38,27 +38,27 @@ NULL
 all_continuous <- function(continuous2 = TRUE) {
   types <- if (continuous2) c("continuous", "continuous2") else "continuous"
 
-  where(function(x) attr(x, "gtsummary.type") %in% types)
+  where(function(x) isTRUE(attr(x, "gtsummary.type") %in% types))
 }
 
 #' @rdname select_helpers
 #' @export
 all_continuous2 <- function() {
-  where(function(x) attr(x, "gtsummary.type") %in% "continuous2")
+  where(function(x) isTRUE(attr(x, "gtsummary.type") %in% "continuous2"))
 }
 
 #' @rdname select_helpers
 #' @export
 all_categorical <- function(dichotomous = TRUE) {
   types <- if (dichotomous) c("categorical", "dichotomous") else "categorical"
 
-  where(function(x) attr(x, "gtsummary.type") %in% types)
+  where(function(x) isTRUE(attr(x, "gtsummary.type") %in% types))
 }
 
 #' @rdname select_helpers
 #' @export
 all_dichotomous <- function() {
-  where(function(x) attr(x, "gtsummary.type") %in% "dichotomous")
+  where(function(x) isTRUE(attr(x, "gtsummary.type") %in% "dichotomous"))
 }
 
 # #' @rdname select_helpers

R/standalone-checks.R

@@ -18,6 +18,7 @@
 #' @param x object whose class will be checked
 #' @param class character vector or string indicating accepted classes.
 #' Passed to `inherits(what=class)`
+#' @param length if not `NULL`, the `x` object must be length specified
 #' @param allow_empty logical indicating whether empty arguments are allowed.
 #' Empty is defined by `rlang::is_empty()`, where empty elements include
 #' `NULL`, `list()`, `character()`, etc. Default is `FALSE`
@@ -30,8 +31,15 @@
 NULL
 
 #' @rdname check_class
-check_class <- function(x, class, allow_empty = FALSE,
+check_class <- function(x, class, length = NULL, allow_empty = FALSE,
                         arg_name = rlang::caller_arg(x), call = rlang::caller_env()) {
+  if (isTRUE(allow_empty) && rlang::is_empty(x)) {
+    return(invisible())
+  }
+  if (!is.null(length)) {
+    check_length(x = x, length = length, arg_name = arg_name, call = call)
+  }
+
   if (!inherits(x, class)) {
     cli::cli_abort(
       c("Argument {.arg {arg_name}} must be class {.cls {class}}.",
@@ -43,7 +51,7 @@ check_class <- function(x, class, allow_empty = FALSE,
 }
 
 #' @rdname check_class
-check_class_data_frame <- function(x, arg_name = rlang::caller_arg(x), call = rlang::caller_env()) {
+check_class_data_frame <- function(x, arg_name = rlang::caller_arg(x), call = parent.frame()) {
   check_class(x = x, class = "data.frame", arg_name = arg_name, call = call)
 }
 
@@ -53,9 +61,33 @@ check_class_data_frame <- function(x, arg_name = rlang::caller_arg(x), call = rl
 #' @param arg_name string indicating the name of the argument. Used in the error messaging.
 #' @inheritParams check_class
 #' @keywords internal
-check_not_missing <- function(x, arg_name = rlang::caller_arg(x), call = rlang::caller_env()) {
+check_not_missing <- function(x, arg_name = rlang::caller_arg(x), call = parent.frame()) {
   if (missing(x)) {
     cli::cli_abort("The {.arg {arg_name}} argument cannot be missing.", call = call)
   }
   invisible()
 }
+
+#' Check Length
+#'
+#' @param msg (`string`)\cr
+#'   string passed to `cli::cli_abort(message=)`
+#' @param length (`integer(1)`)\cr
+#'   integer specifying the required length
+#' @inheritParams check_class
+#' @keywords internal
+#' @name check_length
+NULL
+
+#' @rdname check_length
+check_length <- function(x, length, arg_name = caller_arg(x), call = parent.frame()) {
+  if (length(x) != length) {
+    cli::cli_abort("The {.arg {arg_name}} argument must be length {.val {length}}.", call = call)
+  }
+  invisible()
+}
+
+#' @rdname check_length
+check_scalar <- function(x, arg_name = caller_arg(x), call = parent.frame()) {
+  check_length(x = x, length = 1L, arg_name = arg_name, call = call)
+}