Analysis function count and percentage in column design controlled by combosdf

Usage

a_freq_combos_j(
  df,
  labelstr = NULL,
  .var = NA,
  val = NULL,
  combosdf = NULL,
  do_not_filter = NULL,
  filter_var = NULL,
  flag_var = NULL,
  .df_row,
  .spl_context,
  .N_col,
  id = "USUBJID",
  denom = c("N_col", "n_df", "n_altdf", "n_rowdf", "n_parentdf"),
  label = NULL,
  label_fstr = NULL,
  label_map = NULL,
  .alt_df_full = NULL,
  denom_by = NULL,
  .stats = "count_unique_denom_fraction",
  .formats = NULL,
  .labels_n = NULL,
  .indent_mods = NULL,
  na_str = rep(NA, 3)
)

Arguments

df

(`data.frame`)
data set containing all analysis variables.

labelstr

(`character`)
label of the level of the parent split currently being summarized (must be present as second argument in Content Row Functions). See [rtables::summarize_row_groups()] for more information.

.var

(`string`)
single variable name that is passed by `rtables` when requested by a statistics function.

val

(`character` or NULL)
When NULL, all levels of the incoming variable (variable used in the `analyze` call) will be considered.
When a single `string`, only that current level/value of the incoming variable will be considered.
When multiple levels, only those levels/values of the incoming variable will be considered.
When no values are observed (eg zero row input df), a row with row-label `No data reported` will be included in the table.

combosdf

The df which provides the mapping of facets to produce cumulative counts for .N_col.

do_not_filter

A vector of facets (i.e., column headers), identifying headers for which no filtering of records should occur. That is, the numerator should contain cumulative counts. Generally, this will be used for a "Total" column, or something similar.

filter_var

The variable which identifies the records to count in the numerator for any given column. Generally, this will contain text matching the column header for the column associated with a given record.

flag_var

Variable which identifies the occurrence (or first occurrence) of an event. The flag variable is expected to have a value of "Y" identifying that the event should be counted, or NA otherwise.

.df_row

(`data.frame`)
data frame across all of the columns for the given row split.

.spl_context

(`data.frame`)
gives information about ancestor split states that is passed by `rtables`.

.N_col

(`integer`)
column-wise N (column count) for the full column being analyzed that is typically passed by `rtables`.

id

(`string`)
subject variable name.

denom

(`string`)
One of

N_col Column count,
n_df Number of patients (based upon the main input dataframe `df`),
n_altdf Number of patients from the secondary dataframe (`.alt_df_full`),
Note that argument `denom_by` will perform a row-split on the `.alt_df_full` dataframe.
It is a requirement that variables specified in `denom_by` are part of the row split specifications.
n_rowdf Number of patients from the current row-level dataframe (`.row_df` from the rtables splitting machinery).
n_parentdf Number of patients from a higher row-level split than the current split.
This higher row-level split is specified in the argument `denom_by`.

label

(`string`)
When `val`is a single `string`, the row label to be shown on the output can be specified using this argument.
When `val` is a `character vector`, the `label_map` argument can be specified to control the row-labels.

label_fstr

(`string`)
a sprintf style format string. It can contain up to one "%s" which takes the current split value and generates the row/column label.
It will be combined with the `labelstr` argument, when utilizing this function as a `cfun` in a `summarize_row_groups` call.
It is recommended not to utilize this argument for other purposes. The label argument could be used instead (if `val` is a single string)

label_map

(`tibble`)
A mapping tibble to translate levels from the incoming variable into a different row label to be presented on the table.

.alt_df_full

(`dataframe`)
Denominator dataset for fraction and relative risk calculations.
.alt_df_full is a crucial parameter for the relative risk calculations if this parameter is not set to utilize `alt_counts_df`, then the values in the relative risk columns might not be correct.
Once the rtables PR is integrated, this argument gets populated by the rtables split machinery (see [rtables::additional_fun_params]).

denom_by

(`character`)
Variables from row-split to be used in the denominator derivation.
This controls both `denom = "n_parentdf"` and `denom = "n_altdf"`.
When `denom = "n_altdf"`, the denominator is derived from `.alt_df_full` in combination with `denom_by` argument

.stats

(`character`)
statistics to select for the table.

.formats

(named 'character' or 'list')
formats for the statistics.

.labels_n

(named `character`)
String to control row labels for the 'n'-statistics.
Only useful when more than one 'n'-statistic is requested (rare situations only).

.indent_mods

(named `integer`)
indent modifiers for the labels. Defaults to 0, which corresponds to the unmodified default behavior. Can be negative.

na_str

(`string`)
string used to replace all `NA` or empty values in the output.

Value

list of requested statistics with formatted `rtables::CellValue()`.

Note

: These extra records must then be removed from the numerator via the filter_var parameter to avoid double counting of events.