varcuts: Split on static or dynamic cuts of the data

In rtables: Reporting Tables

Split on static or dynamic cuts of the data

Description

Create columns (or row splits) based on values (such as quartiles) of var.

Usage

split_cols_by_cuts(
  lyt,
  var,
  cuts,
  cutlabels = NULL,
  split_label = var,
  nested = TRUE,
  cumulative = FALSE
)

split_rows_by_cuts(
  lyt,
  var,
  cuts,
  cutlabels = NULL,
  split_label = var,
  format = NULL,
  na_str = NA_character_,
  nested = TRUE,
  cumulative = FALSE,
  label_pos = "hidden",
  section_div = NA_character_
)

split_cols_by_cutfun(
  lyt,
  var,
  cutfun = qtile_cuts,
  cutlabelfun = function(x) NULL,
  split_label = var,
  nested = TRUE,
  extra_args = list(),
  cumulative = FALSE
)

split_cols_by_quartiles(
  lyt,
  var,
  split_label = var,
  nested = TRUE,
  extra_args = list(),
  cumulative = FALSE
)

split_rows_by_quartiles(
  lyt,
  var,
  split_label = var,
  format = NULL,
  na_str = NA_character_,
  nested = TRUE,
  child_labels = c("default", "visible", "hidden"),
  extra_args = list(),
  cumulative = FALSE,
  indent_mod = 0L,
  label_pos = "hidden",
  section_div = NA_character_
)

split_rows_by_cutfun(
  lyt,
  var,
  cutfun = qtile_cuts,
  cutlabelfun = function(x) NULL,
  split_label = var,
  format = NULL,
  na_str = NA_character_,
  nested = TRUE,
  child_labels = c("default", "visible", "hidden"),
  extra_args = list(),
  cumulative = FALSE,
  indent_mod = 0L,
  label_pos = "hidden",
  section_div = NA_character_
)

Arguments

lyt	layout object pre-data used for tabulation
var	string, variable name
cuts	numeric. Cuts to use
cutlabels	character (or NULL). Labels for the cuts
split_label	string. Label string to be associated with the table generated by the split. Not to be confused with labels assigned to each child (which are based on the data and type of split during tabulation).
nested	boolean. Should this layout instruction be applied within the existing layout structure if possible (TRUE, the default) or as a new top-level element ('FALSE). Ignored if it would nest a split underneath analyses, which is not allowed.
cumulative	logical. Should the cuts be treated as cumulative. Defaults to FALSE
format	FormatSpec. Format associated with this split. Formats can be declared via strings ("xx.x") or function. In cases such as analyze calls, they can character vectors or lists of functions.
na_str	character(1). String that should be displayed when the value of x is missing. Defaults to "NA".
label_pos	character(1). Location the variable label should be displayed, Accepts "hidden" (default for non-analyze row splits), "visible", "topleft", and - for analyze splits only - "default". For analyze calls, "default" indicates that the variable should be visible if and only if multiple variables are analyzed at the same level of nesting.
section_div	character(1). String which should be repeated as a section divider after each group defined by this split instruction, or NA_character_ (the default) for no section divider.
cutfun	function. Function which accepts the full vector of var values and returns cut points to be passed to cut.
cutlabelfun	function. Function which returns either labels for the cuts or NULL when passed the return value of cutfun
extra_args	list. Extra arguments to be passed to the tabulation function. Element position in the list corresponds to the children of this split. Named elements in the child-specific lists are ignored if they do not match a formal argument of the tabulation function.
child_labels	string. One of "default", "visible", "hidden". What should the display behavior be for the labels (i.e. label rows) of the children of this split. Defaults to "default" which flags the label row as visible only if the child has 0 content rows.
indent_mod	numeric. Modifier for the default indent position for the structure created by this function(subtable, content table, or row) and all of that structure's children. Defaults to 0, which corresponds to the unmodified default behavior.

Details

For dynamic cuts, the cut is transformed into a static cut by build_table based on the full dataset, before proceeding. Thus even when nested within another split in column/row space, the resulting split will reflect the overall values (e.g., quartiles) in the dataset, NOT the values for subset it is nested under.

Value

A PreDataTableLayouts object suitable for passing to further layouting functions, and to build_table.

Author(s)

Gabriel Becker

Examples

library(dplyr)

# split_cols_by_cuts
lyt <- basic_table() %>%
    split_cols_by("ARM") %>%
    split_cols_by_cuts("AGE", split_label = "Age",
                       cuts = c(0, 25, 35, 1000),
                       cutlabels = c("young", "medium", "old")) %>%
    analyze(c("BMRKR2", "STRATA2")) %>%
    append_topleft("counts")

tbl <- build_table(lyt, ex_adsl)
tbl

# split_rows_by_cuts
lyt2 <- basic_table() %>%
    split_cols_by("ARM") %>%
    split_rows_by_cuts("AGE", split_label = "Age",
                  cuts = c(0, 25, 35, 1000),
                  cutlabels = c("young", "medium", "old")) %>%
    analyze(c("BMRKR2", "STRATA2")) %>%
    append_topleft("counts")


tbl2 <- build_table(lyt2, ex_adsl)
tbl2

# split_cols_by_quartiles

lyt3 <- basic_table() %>%
    split_cols_by("ARM") %>%
    split_cols_by_quartiles("AGE", split_label = "Age") %>%
    analyze(c("BMRKR2", "STRATA2")) %>%
    append_topleft("counts")

tbl3 <- build_table(lyt3, ex_adsl)
tbl3

# split_rows_by_quartiles
lyt4 <- basic_table(show_colcounts = TRUE) %>%
    split_cols_by("ARM") %>%
    split_rows_by_quartiles("AGE", split_label = "Age") %>%
    analyze("BMRKR2") %>%
    append_topleft(c("Age Quartiles", " Counts BMRKR2"))

tbl4 <- build_table(lyt4, ex_adsl)
tbl4

# split_cols_by_cutfun
cutfun <- function(x) {
  cutpoints <- c(
    min(x),
    mean(x),
    max(x)
  )

  names(cutpoints) <- c("", "Younger", "Older")
  cutpoints
}

lyt5 <- basic_table() %>%
  split_cols_by_cutfun("AGE", cutfun = cutfun) %>%
  analyze("SEX")

tbl5 <- build_table(lyt5, ex_adsl)
tbl5

# split_rows_by_cutfun
lyt6 <- basic_table() %>%
  split_cols_by("SEX") %>%
  split_rows_by_cutfun("AGE", cutfun = cutfun) %>%
  analyze("BMRKR2")

tbl6 <- build_table(lyt6, ex_adsl)
tbl6

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