analyze: Generate Rows Analyzing Variables Across Columns

In rtables: Reporting Tables

Generate Rows Analyzing Variables Across Columns

Description

Adding analyzed variables to our table layout defines the primary tabulation to be performed. We do this by adding calls to analyze and/or analyze_colvars into our layout pipeline. As with adding further splitting, the tabulation will occur at the current/next level of nesting by default.

Usage

analyze(
  lyt,
  vars,
  afun = simple_analysis,
  var_labels = vars,
  table_names = vars,
  format = NULL,
  na_str = NA_character_,
  nested = TRUE,
  inclNAs = FALSE,
  extra_args = list(),
  show_labels = c("default", "visible", "hidden"),
  indent_mod = 0L,
  section_div = NA_character_
)

Arguments

lyt	layout object pre-data used for tabulation
vars	character vector. Multiple variable names.
afun	function. Analysis function, must take x or df as its first parameter. Can optionally take other parameters which will be populated by the tabulation framework. See Details in analyze.
var_labels	character. Variable labels for 1 or more variables
table_names	character. Names for the tables representing each atomic analysis. Defaults to var.
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".
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.
inclNAs	boolean. Should observations with NA in the var variable(s) be included when performing this analysis. Defaults to FALSE
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.
show_labels	character(1). Should the variable labels for corresponding to the variable(s) in vars be visible in the resulting table.
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.
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.

Details

When non-NULL format is used to specify formats for all generated rows, and can be a character vector, a function, or a list of functions. It will be repped out to the number of rows once this is known during the tabulation process, but will be overridden by formats specified within rcell calls in afun.

The analysis function (afun) should take as its first parameter either x or df. Which of these the function accepts changes the behavior when tabulation is performed.

• If afun's first parameter is x, it will receive the corresponding subset vector of data from the relevant column (from var here) of the raw data being used to build the table.

• If afun's first parameter is df, it will receive the corresponding subset data.frame (i.e. all columns) of the raw data being tabulated

In addition to differentiation on the first argument, the analysis function can optionally accept a number of other parameters which, if and only if present in the formals will be passed to the function by the tabulation machinery. These are listed and described in additional_fun_params.

Value

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

Note

None of the arguments described in the Details section can be overridden via extra_args or when calling make_afun. .N_col and .N_total can be overridden via the col_counts argument to build_table. Alternative values for the others must be calculated within afun based on a combination of extra arguments and the unmodified values provided by the tabulation framework.

Author(s)

Gabriel Becker

Examples

lyt <- basic_table() %>%
    split_cols_by("ARM") %>%
    analyze("AGE", afun = list_wrap_x(summary) , format = "xx.xx")
lyt

tbl <- build_table(lyt, DM)
tbl

lyt2 <- basic_table() %>%
    split_cols_by("Species") %>%
    analyze(head(names(iris), -1), afun = function(x) {
        list(
            "mean / sd" = rcell(c(mean(x), sd(x)), format = "xx.xx (xx.xx)"),
            "range" = rcell(diff(range(x)), format = "xx.xx")
        )
    })
lyt2

tbl2 <- build_table(lyt2, iris)
tbl2

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