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Custom split functions

Source: R/custom_split_funs.R
custom_split_funs.Rd

Split functions provide the work-horse for rtables's generalized partitioning. These functions accept a (sub)set of incoming data and a split object, and return "splits" of that data.

Custom Splitting Function Details

User-defined custom split functions can perform any type of computation on the incoming data provided that they meet the requirements for generating "splits" of the incoming data based on the split object.

Split functions are functions that accept:

df

a data.frame of incoming data to be split.

spl

a Split object. This is largely an internal detail custom functions will not need to worry about, but obj_name(spl), for example, will give the name of the split as it will appear in paths in the resulting table.

vals

any pre-calculated values. If given non-NULL values, the values returned should match these. Should be NULL in most cases and can usually be ignored.

labels

any pre-calculated value labels. Same as above for values.

trim

if TRUE, resulting splits that are empty are removed.

(optional) .spl_context

a data.frame describing previously performed splits which collectively arrived at df.

The function must then output a named list with the following elements:

values

the vector of all values corresponding to the splits of df.

datasplit

a list of data.frames representing the groupings of the actual observations from df.

labels

a character vector giving a string label for each value listed in the values element above.

(optional) extras

if present, extra arguments are to be passed to summary and analysis functions whenever they are executed on the corresponding element of datasplit or a subset thereof.

One way to generate custom splitting functions is to wrap existing split functions and modify either the incoming data before they are called or their outputs.

See also

make_split_fun() for the API for creating custom split functions, and split_funcs for a variety of pre-defined split functions.

Examples 

# Example of a picky split function. The number of values in the column variable
# var decrees if we are going to print also the column with all observation
# or not.

picky_splitter <- function(var) {
  # Main layout function
  function(df, spl, vals, labels, trim) {
    orig_vals <- vals

    # Check for number of levels if all are selected
    if (is.null(vals)) {
      vec <- df[[var]]
      vals <- unique(vec)
    }

    # Do a split with or without All obs
    if (length(vals) == 1) {
      do_base_split(spl = spl, df = df, vals = vals, labels = labels, trim = trim)
    } else {
      fnc_tmp <- add_overall_level("Overall", label = "All Obs", first = FALSE)
      fnc_tmp(df = df, spl = spl, vals = orig_vals, trim = trim)
    }
  }
}

# Data sub-set
d1 <- subset(ex_adsl, ARM == "A: Drug X" | (ARM == "B: Placebo" & SEX == "F"))
d1 <- subset(d1, SEX %in% c("M", "F"))
d1$SEX <- factor(d1$SEX)

# This table uses the number of values in the SEX column to add the overall col or not
lyt <- basic_table() %>%
  split_cols_by("ARM", split_fun = drop_split_levels) %>%
  split_cols_by("SEX", split_fun = picky_splitter("SEX")) %>%
  analyze("AGE", show_labels = "visible")
tbl <- build_table(lyt, d1)
tbl
#>                 A: Drug X          B: Placebo
#>            F       M     All Obs       F     
#> —————————————————————————————————————————————
#> AGE                                          
#>   Mean   32.76   35.57    33.86      34.12