1324 feature request varying decimal precision in a summary

DESCRIPTION

@@ -179,3 +179,4 @@ Collate:
     'utils_grid.R'
     'utils_rtables.R'
     'utils_split_funs.R'
+    'xutils_custom_stats_formats_varying_dp.R'

R/analyze_variables.R

@@ -463,7 +463,53 @@ s_summary.logical <- function(x,
 #'
 #' a_summary(rnorm(10), .N_col = 10, .N_row = 20, .var = "bla")
 #' a_summary(rnorm(10, 5, 1), .ref_group = rnorm(20, -5, 1), .var = "bla", compare = TRUE)
+#' a_summary(
+#'   rnorm(10, 5, 1),
+#'   .ref_group = rnorm(20, -5, 1), .var = "bla", compare = TRUE,
+#'   .stats = "mean",
+#'   fmts_df_var = "variant1",
+#'   d = 2
+#' )
 #'
+#' x1 <- rnorm(10, 5, 1)
+#' xref <- rnorm(20, -5, 1)
+#'
+#' a_summary(
+#'   x1,
+#'   .ref_group = xref, .var = "bla", compare = TRUE,
+#'   .stats = c("mean", "sd"),
+#'   .formats = c("mean" = format_xx("xx.xxx"), "sd" = format_xx("xx.x"))
+#' )
+#' a_summary(
+#'   x1,
+#'   .ref_group = xref, .var = "bla", compare = TRUE,
+#'   .stats = "mean_sd",
+#'   fmt_specs = list(
+#'     fmts_df_var = "variant2",
+#'     d = 1,
+#'     formatting_function = "format_xx"
+#'   )
+#' )
+#' a_summary(
+#'   x1,
+#'   .ref_group = xref, .var = "bla", compare = TRUE,
+#'   .stats = c("mean", "mean_sd", "mean_pval")
+#' )
+#'
+#' our_fmt_specs_variant <- list(
+#'   fmts_df = tern_formats_custom_df(),
+#'   fmts_df_var = "default",
+#'   formatting_function = "format_xx_fixed_dp",
+#'   d = 0
+#' )
+
+#' a_summary(
+#'   x1, .ref_group = xref, .var = "bla", compare = TRUE,
+#'   .stats = c("mean", "mean_sd", "mean_pval"),
+#'   .formats = c("mean_sd" = "xx.d (xx.dxxxx)"),
+#'   fmt_specs = our_fmt_specs_variant
+#' )
+
 #' @export
 a_summary <- function(x,
                       .N_col, # nolint
@@ -479,6 +525,7 @@ a_summary <- function(x,
                       .indent_mods = NULL,
                       na.rm = TRUE, # nolint
                       na_str = default_na_str(),
+                      fmt_specs = default_fmt_specs,
                       ...) {
   extra_args <- list(...)
   if (is.numeric(x)) {
@@ -507,7 +554,28 @@ a_summary <- function(x,
   # Fill in with formatting defaults if needed
   met_grp <- paste0(c("analyze_vars", type), collapse = "_")
   .stats <- get_stats(met_grp, stats_in = .stats, add_pval = compare)
-  .formats <- get_formats_from_stats(.stats, .formats)
+
+  if (is.null(fmt_specs$fmts_df)) {
+    .formats <- get_formats_from_stats(.stats, .formats)
+  } else {
+    d_actual <- derive_d_from_fmt_specs(fmt_specs, .df_row)
+
+    # update the spec with the actual derived d
+    fmt_specs$d <- d_actual
+
+    # core function that does the conversion of the xx.d based formats to the actual format
+    # note that is it most safe to apply formatting functions, as many of the final formats will not belong to
+    # list_valid_format_labels()
+    .formats_all <- get_formats_from_stats_custom(
+      .stats,
+      formats_in = .formats,
+      ### variant specific arguments
+      fmts_specs = fmt_specs
+    )
+    .formats <- .formats_all$fmt
+    .formats_char <- .formats_all$fmt_char
+  }
+
   .indent_mods <- get_indents_from_stats(.stats, .indent_mods)
 
   lbls <- get_labels_from_stats(.stats, .labels)
@@ -615,6 +683,59 @@ a_summary <- function(x,
 #'   ) %>%
 #'   build_table(dt)
 #'
+#' # custom format
+#' our_fmt_specs_variant <- list(
+#'   fmts_df = tern_formats_custom_df(),
+#'   fmts_df_var = "variant2",
+#'   formatting_function = "format_xx_fixed_dp",
+#'   d = 0
+#' )
+#'
+#' dt <- data.frame("VAR" = c(0.001, 0.2, 0.0011000, 3, 4))
+#' basic_table() %>%
+#'   analyze_vars(
+#'     vars = "VAR",
+#'     .stats = c("n", "mean", "mean_sd", "range"),
+#'     .formats = c("mean" = "xx.dxx"),
+#'     fmt_specs = our_fmt_specs_variant,
+#'   ) %>%
+#'   build_table(dt)
+#'
+#' # custom format
+#' our_fmt_specs_variant2 <- list(
+#'   fmts_df = tern_formats_custom_df(),
+#'   fmts_df_var = "variant2",
+#'   formatting_function = "format_xx_fixed_dp",
+#'   d = "decimal"
+#' )
+#' dt <- data.frame("VAR" = c(0.001, 0.2, 0.0011000, 3, 4), decimal = 2)
+#' basic_table() %>%
+#'   analyze_vars(
+#'     vars = "VAR",
+#'     .stats = c("n", "mean", "mean_sd", "range"),
+#'     .formats = c("mean" = "xx.dxxxxxx"),
+#'     fmt_specs = our_fmt_specs_variant2,
+#'   ) %>%
+#'   build_table(dt)
+#'
+#' # custom format
+#' dt2 <- data.frame("VAR" = c(0.001, 0.2, 0.0011000, 3, 4, 0.002, 0.004, 0.006), decimal = c(rep(2, 4), rep(1, 4)), by = c(rep("by1", 4), rep("by2", 4)))
+#' our_fmt_specs_variant2 <- list(
+#'   fmts_df = tern_formats_custom_df(),
+#'   fmts_df_var = "variant2",
+#'   formatting_function = "format_xx_fixed_dp",
+#'   d = "decimal",
+#'   d_cap = 3
+#' )
+#' basic_table() %>%
+#'   split_rows_by("by") %>%
+#'   analyze_vars(
+#'     vars = "VAR",
+#'     .stats = c("n", "mean", "mean_sd", "range"),
+#'     fmt_specs = our_fmt_specs_variant2
+#'   ) %>%
+#'   build_table(dt2)
+#'
 #' @export
 #' @order 2
 analyze_vars <- function(lyt,
@@ -630,8 +751,15 @@ analyze_vars <- function(lyt,
                          .stats = c("n", "mean_sd", "median", "range", "count_fraction"),
                          .formats = NULL,
                          .labels = NULL,
-                         .indent_mods = NULL) {
-  extra_args <- list(.stats = .stats, na.rm = na.rm, na_str = na_str, ...)
+                         .indent_mods = NULL,
+                         # varying precision arguments
+                         fmt_specs = default_fmt_specs) {
+  extra_args <- list(
+    .stats = .stats, na.rm = na.rm, na_str = na_str,
+    fmt_specs = fmt_specs,
+    ...
+  )
+
   if (!is.null(.formats)) extra_args[[".formats"]] <- .formats
   if (!is.null(.labels)) extra_args[[".labels"]] <- .labels
   if (!is.null(.indent_mods)) extra_args[[".indent_mods"]] <- .indent_mods

R/formatting_functions.R

@@ -242,6 +242,90 @@ format_xx <- function(str) {
   return(rtable_format)
 }
 
+#' Alternative format XX function :a formatting function with fixed decimal precision
+#'
+#' Translate a string where x and dots are interpreted as number place
+#' holders, and others as formatting elements.
+#'
+#' @param str (`string`)\cr template.
+#'
+#' @return An `rtables` formatting function.
+#'
+#' @examples
+#' test <- list(c(1.658, 0.5761), c(1e1, 785.6))
+#'
+#' z <- format_xx_fixed_dp("xx (xx.x)")
+#' sapply(test, z)
+#'
+#' z <- format_xx_fixed_dp("xx.x - xx.x")
+#' sapply(test, z)
+#'
+#' z <- format_xx_fixed_dp("xx.x, incl. xx.x% NE")
+#' sapply(test, z)
+#' @seealso [format_xx]
+#' @export
+format_xx_fixed_dp <- function(str, na_str) {
+  # Find position in the string.
+  if (grepl(pattern = "xxx.", x = str, fixed = TRUE)) {
+    stop("Error: format_xx_fixed_dp do not use xxx. in input str, replace by xx. instead")
+  }
+  if (!grepl(pattern = "xx", x = str, fixed = TRUE)) {
+    stop("Error: format_xx_fixed_dp: input str should contain xx")
+  }
+  positions <- gregexpr(
+    pattern = "xx\\.?x*", text = str,
+    perl = TRUE
+  )
+  x_positions <- regmatches(x = str, m = positions)[[1]]
+  ### str is splitted into pieces as xx. xx xx.xxx
+  ### xx is no rounding
+  ### xx. rounding to integer (is treated same as rounding to 0 decimal)
+  ### xx.x rounding to 1 decimal, etc
+
+  no_round <- function(x) {
+    if (is.na(x)) {
+      return(na_str)
+    } else {
+      return(x)
+    }
+  }
+  roundfunc <- round
+
+  # Roundings depends on the number of x behind [.].
+  roundings <- lapply(
+    X = x_positions,
+    function(x) {
+      if (x == "xx") {
+        rounding <- no_round
+      } else {
+        y <- strsplit(split = "\\.", x = x)[[1]]
+        digits <- ifelse(length(y) > 1, nchar(y[2]), 0)
+
+        rounding <- function(x) {
+          if (is.na(x)) {
+            return(na_str)
+          } else {
+            format(roundfunc(x, digits = digits),
+              nsmall = digits
+            )
+          }
+        }
+      }
+
+      return(rounding)
+    }
+  )
+
+  rtable_format <- function(x, output) {
+    values <- Map(y = x, fun = roundings, function(y, fun) fun(y))
+    regmatches(x = str, m = positions)[[1]] <- values
+    return(str)
+  }
+
+  return(rtable_format)
+}
+
+
 #' Format numeric values by significant figures
 #'
 #' Format numeric values to print with a specified number of significant figures.