argument_convention: Standard arguments

In tern: Create Common TLGs Used in Clinical Trials

Standard arguments

Description

The documentation to this function lists all the arguments in tern that are used repeatedly to express an analysis.

Arguments

...	additional arguments for the lower level functions.
.aligns	(character or NULL) alignment for table contents (not including labels). When NULL, "center" is applied. See formatters::list_valid_aligns() for a list of all currently supported alignments.
.all_col_counts	(integer) vector where each value represents a global count for a column. Values are taken from alt_counts_df if specified (see rtables::build_table()).
.df_row	(data.frame) data frame across all of the columns for the given row split.
.formats	(named character or list) formats for the statistics. See Details in analyze_vars for more information on the "auto" setting.
.in_ref_col	(flag) TRUE when working with the reference level, FALSE otherwise.
.indent_mods	(named integer) indent modifiers for the labels. Defaults to 0, which corresponds to the unmodified default behavior. Can be negative.
.labels	(named character) labels for the statistics (without indent).
.N_col	(integer(1)) column-wise N (column count) for the full column being analyzed that is typically passed by rtables.
.N_row	(integer(1)) row-wise N (row group count) for the group of observations being analyzed (i.e. with no column-based subsetting) that is typically passed by rtables.
.ref_group	(data.frame or vector) the data corresponding to the reference group.
.spl_context	(data.frame) gives information about ancestor split states that is passed by rtables.
.stats	(character) statistics to select for the table.
.var	(string) single variable name that is passed by rtables when requested by a statistics function.
add_total_level	(flag) adds a "total" level after the others which includes all the levels that constitute the split. A custom label can be set for this level via the custom_label argument.
col_by	(factor) defining column groups.
conf_level	(proportion) confidence level of the interval.
data	(data.frame) the dataset containing the variables to summarize.
df	(data.frame) data set containing all analysis variables.
groups_lists	(named list of list) optionally contains for each subgroups variable a list, which specifies the new group levels via the names and the levels that belong to it in the character vectors that are elements of the list.
id	(string) subject variable name.
is_event	(flag) TRUE if event, FALSE if time to event is censored.
label_all	(string) label for the total population analysis.
labelstr	(string) 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.
lyt	(PreDataTableLayouts) layout that analyses will be added to.
method	(string or NULL) specifies the test used to calculate the p-value for the difference between two proportions. For options, see test_proportion_diff(). Default is NULL so no test is performed.
na.rm	(flag) whether NA values should be removed from x prior to analysis.
na_str	(string) string used to replace all NA or empty values in the output.
nested	(flag) whether this layout instruction should 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.
prune_zero_rows	(flag) whether to prune all zero rows.
riskdiff	(flag) whether a risk difference column is present. When set to TRUE, add_riskdiff() must be used as split_fun in the prior column split of the table layout, specifying which columns should be compared. See stat_propdiff_ci() for details on risk difference calculation.
rsp	(logical) vector indicating whether each subject is a responder or not.
show_labels	(string) label visibility: one of "default", "visible" and "hidden".
section_div	(string) 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.
table_names	(character) this can be customized in the case that the same vars are analyzed multiple times, to avoid warnings from rtables.
tte	(numeric) vector of time-to-event duration values.
var_labels	(character) variable labels.
variables	(named list of string) list of additional analysis variables.
vars	(character) variable names for the primary analysis variable to be iterated over.
var	(string) single variable name for the primary analysis variable.
x	(numeric) vector of numbers we want to analyze.
xlim	(numeric(2)) vector containing lower and upper limits for the x-axis, respectively. If NULL (default), the default scale range is used.
ylim	(numeric(2)) vector containing lower and upper limits for the y-axis, respectively. If NULL (default), the default scale range is used.

Details

Although this function just returns NULL it has two uses, for the tern users it provides a documentation of arguments that are commonly and consistently used in the framework. For the developer it adds a single reference point to import the roxygen argument description with: ⁠@inheritParams argument_convention⁠

tern documentation built on Sept. 24, 2024, 9:06 a.m.