make_afun: Create custom analysis function wrapping existing function

In rtables: Reporting Tables

Create custom analysis function wrapping existing function

Description

Create custom analysis function wrapping existing function

Usage

make_afun(
  fun,
  .stats = NULL,
  .formats = NULL,
  .labels = NULL,
  .indent_mods = NULL,
  .ungroup_stats = NULL,
  .format_na_strs = NULL,
  ...,
  .null_ref_cells = ".in_ref_col" %in% names(formals(fun))
)

Arguments

fun	function. The function to be wrapped in a new customized analysis fun. Should return named list.
.stats	character. Names of elements to keep from fun's full output.
.formats	ANY. vector/list of formats to override any defaults applied by fun.
.labels	character. Vector of labels to override defaults returned by fun
.indent_mods	integer. Named vector of indent modifiers for the generated rows.
.ungroup_stats	character. Vector of names, which must match elements of .stats
.format_na_strs	ANY. vector/list of na strings to override any defaults applied by fun.
...	dots. Additional arguments to fun which effectively become new defaults. These can still be overridden by extra_args within a split.
.null_ref_cells	logical(1). Should cells for the reference column be NULL-ed by the returned analysis function. Defaults to TRUE if fun accepts .in_ref_col as a formal argument. Note this argument occurs after ... so it must be fully specified by name when set.

Value

A function suitable for use in analyze with element selection, reformatting, and relabeling performed automatically.

Note

setting .ungroup_stats to non-null changes the structure of the value(s) returned by fun, rather than just labeling (.labels), formatting (.formats), and selecting amongst (.stats) them. This means that subsequent make_afun calls to customize the output further both can and must operate on the new structure, NOT the original structure returned by fun. See the final pair of examples below.

See Also

analyze()

Examples

s_summary <- function(x) {
  stopifnot(is.numeric(x))

  list(
    n = sum(!is.na(x)),
    mean_sd = c(mean = mean(x), sd = sd(x)),
    min_max = range(x)
  )
}

s_summary(iris$Sepal.Length)

a_summary <- make_afun(
  fun = s_summary,
  .formats = c(n = "xx", mean_sd = "xx.xx (xx.xx)", min_max = "xx.xx - xx.xx"),
  .labels = c(n = "n", mean_sd = "Mean (sd)", min_max = "min - max")
)

a_summary(x = iris$Sepal.Length)

a_summary2 <- make_afun(a_summary, .stats = c("n", "mean_sd"))

a_summary2(x = iris$Sepal.Length)

a_summary3 <- make_afun(a_summary, .formats = c(mean_sd = "(xx.xxx, xx.xxx)"))



s_foo <- function(df, .N_col, a = 1, b = 2) {
   list(
      nrow_df = nrow(df),
      .N_col = .N_col,
      a = a,
      b = b
   )
}

s_foo(iris, 40)

a_foo <- make_afun(s_foo, b = 4,
 .formats = c(nrow_df = "xx.xx", ".N_col" = "xx.", a = "xx", b = "xx.x"),
 .labels = c(nrow_df = "Nrow df",
             ".N_col" = "n in cols", a = "a value", b = "b value"),
 .indent_mods = c(nrow_df = 2L, a = 1L)
)

a_foo(iris, .N_col = 40)
a_foo2 <- make_afun(a_foo, .labels = c(nrow_df = "Number of Rows"))
a_foo2(iris, .N_col = 40)

#grouping and further customization
s_grp <- function(df, .N_col, a = 1, b = 2) {
   list(
      nrow_df = nrow(df),
      .N_col = .N_col,
      letters = list(a = a,
                     b = b)
   )
}
a_grp <- make_afun(s_grp, b = 3,
                   .labels = c(nrow_df = "row count",
                               .N_col = "count in column"),
                   .formats = c(nrow_df = "xx.", .N_col = "xx."),
                   .indent_mod = c(letters = 1L),
                   .ungroup_stats ="letters")
a_grp(iris, 40)
a_aftergrp <- make_afun(a_grp, .stats = c("nrow_df", "b"),
                        .formats = c(b = "xx."))
a_aftergrp(iris, 40)

s_ref <- function(x, .in_ref_col, .ref_group) {
   list(
         mean_diff = mean(x) - mean(.ref_group)
       )
}

a_ref <- make_afun(s_ref,
                   .labels = c( mean_diff = "Mean Difference from Ref"))
a_ref(iris$Sepal.Length, .in_ref_col = TRUE, 1:10)
a_ref(iris$Sepal.Length, .in_ref_col = FALSE, 1:10)

rtables documentation built on Aug. 30, 2023, 5:07 p.m.