Update docs

R/analyze_variables.R

@@ -186,7 +186,7 @@ s_summary.numeric <- function(x,
   # Convert negative values to NA for log calculation.
   x_no_negative_vals <- x
   x_no_negative_vals[x_no_negative_vals <= 0] <- NA
-  y$geom_mean <- if (all(x == 0) && length(x) > 0) {
+  y$geom_mean <- if (all(!is.na(x)) && all(x == 0) && length(x) > 0) {
     c("geom_mean" = 0)
   } else {
     c("geom_mean" = exp(mean(log(x_no_negative_vals), na.rm = FALSE)))

R/analyze_vars_in_cols.R

@@ -232,7 +232,7 @@ analyze_vars_in_cols <- function(lyt,
           } else {
             res_imp <- imputation_rule(
               .df_row, x_stats, stat,
-              imp = imp_rule, post = as.numeric(tail(.spl_context$value, 1)) > 0
+              imp_rule = imp_rule, post = as.numeric(tail(.spl_context$value, 1)) > 0
             )
             res <- res_imp[["val"]]
             na_level <- res_imp[["na_level"]]
@@ -294,7 +294,7 @@ analyze_vars_in_cols <- function(lyt,
           } else {
             res_imp <- imputation_rule(
               .df_row, x_stats, stat,
-              imp = imp_rule, post = as.numeric(tail(.spl_context$value, 1)) > 0
+              imp_rule = imp_rule, post = as.numeric(tail(.spl_context$value, 1)) > 0
             )
             res <- res_imp[["val"]]
             na_level <- res_imp[["na_level"]]

R/formatting_functions.R

@@ -214,8 +214,6 @@ format_xx <- function(str) {
 #' Format numeric values to print with a specified number of significant figures.
 #'
 #' @param sigfig (`integer`)\cr number of significant figures to display.
-#' @param x (`numeric`)\cr value.
-#' @param ... required for `rtables` interface.
 #'
 #' @return An `rtables` formatting function.
 #'

R/imputation_rule.R

@@ -3,6 +3,9 @@
 #' @description `r lifecycle::badge("stable")`
 #'
 #' @inheritParams argument_convention
+#' @param x_stats (`named list`)\cr a named list of statistics, typically the results of [s_summary()].
+#' @param stat (`character`)\cr statistic to return the value/NA level of according to the imputation
+#'   rule applied.
 #' @param imp_rule (`character`)\cr imputation rule setting. Set to `"1/3"` to implement 1/3 imputation
 #'   rule or `"1/2"` to implement 1/2 imputation rule.
 #' @param post (`flag`)\cr whether the data corresponds to a post-dose time-point (defaults to `FALSE`).