Create layer settings — layer

Configuration object for all layer options. Unused parameters default to NULL and are ignored during build. Type-specific validation happens at build time.

Usage

layer_settings(
  format_strings = NULL,
  stat_columns = NULL,
  denoms_by = NULL,
  shift_denom = "total",
  denom_row = FALSE,
  denom_row_label = "n",
  denom_row_format = NULL,
  denom_where = NULL,
  denom_ignore = NULL,
  distinct_by = NULL,
  total_row = FALSE,
  total_row_label = "Total",
  total_row_count_missings = TRUE,
  missing_count = NULL,
  missing_subjects = FALSE,
  missing_subjects_label = "Missing",
  keep_levels = NULL,
  limit_data_by = NULL,
  custom_summaries = NULL,
  stats_as_columns = FALSE,
  precision_by = NULL,
  precision_on = NULL,
  precision_data = NULL,
  precision_cap = NULL,
  order_count_method = NULL,
  ordering_cols = NULL,
  result_order_var = NULL,
  outer_sort_position = NULL,
  risk_diff = NULL,
  ci_method = c("clopper_pearson", "wilson", "wald", "agresti_coull", "jeffreys"),
  ci_level = 0.95,
  assoc_test = NULL,
  pct_lt = NULL,
  pct_gt = NULL,
  zero_count_display = "full",
  name = NULL
)

Arguments

format_strings: Named list of f_str objects
stat_columns: Named list of f_str objects for count layers. Each entry produces its own result column per column group (e.g. one "n (\ name used as the column sub-label. Column label attributes follow the pattern "<column group> (N=n) | <stat name>". When set, it takes precedence over format_strings. Names may not contain " | " or "(N=", which are reserved by the label grammar.
denoms_by: Character vector of variable names for denominator grouping. This replaces (does not augment) the default denominator grouping, which is the column (cols) variable(s). To get per-column denominators that also break down by a by variable, you must list the cols variable(s) explicitly alongside the by variable(s) — e.g. denoms_by = c("TRT", "SEX"), not denoms_by = "SEX". Passing only the by variable collapses the denominator across the columns.
shift_denom: Denominator basis for shift layers. "total" (default) computes percentages out of the column (cols) total — i.e. the treatment arm. "column" computes them column-wise, out of each shift column group (the "from"/baseline group) within the arm, which is the standard "% within the from group" shift display; the header (N=) labels then reflect the per-column-group denominators. Ignored when denoms_by is set (which specifies the grouping explicitly).
denom_row: Logical, shift layers only. When TRUE, emit the per-column-group denominator (the same total used for the percentages) as an integer row above the shift-to rows — the "n" row of a threshold/normal-range shift table. Pairs naturally with shift_denom = "column". Defaults to FALSE.
denom_row_label: Character string, the row label for the denom_row row. Defaults to "n".
denom_row_format: An f_str object formatting the denom_row cells, shift layers only. Lets the denominator row carry its own width independent of the n_counts format (e.g. f_str("xx", "n") for a plain narrow integer). The f_str must reference a single variable (the denominator count is passed positionally). NULL (default) keeps the legacy behavior of padding the integer to the width of the shift cells. An absent baseline group renders as 0 either way.
denom_where: Expression for separate denominator filter
denom_ignore: Character vector of values to exclude from denominators
distinct_by: Character string naming the variable for distinct counting
total_row: Logical, whether to add a total row
total_row_label: Character string for total row label
total_row_count_missings: Logical, include missing in total
missing_count: List with missing count configuration
missing_subjects: Logical, add missing subjects row
missing_subjects_label: Character string for missing subjects label
keep_levels: Character vector of levels to keep
limit_data_by: Character vector for data limiting
custom_summaries: Named list of expressions for custom summaries
stats_as_columns: Logical, transpose stats to columns
precision_by: Character vector for precision grouping
precision_on: Character string for precision variable
precision_data: Data frame with external precision values
precision_cap: Named numeric vector c(int=, dec=)
order_count_method: Character, ordering method
ordering_cols: Character, which column drives ordering
result_order_var: Character, which result variable for ordering
outer_sort_position: Character, outer sort direction
risk_diff: List with risk difference configuration
ci_method: Method for the single-proportion confidence interval exposed through the ci_lower/ci_upper (and distinct_ci_lower/distinct_ci_upper) count-layer format keywords. One of "clopper_pearson" (default, exact / SAS PROC FREQ EXACT parity), "wilson" (score, matching stats::prop.test(correct = FALSE)), "wald", "agresti_coull", or "jeffreys". See proportion_ci.
ci_level: Numeric coverage probability for the single-proportion confidence interval keywords. Defaults to 0.95.
assoc_test: A assoc_test object attaching an association-test p-value column. Omnibus mode works on count, shift, and desc layers (a desc layer's continuous comparison, e.g. ANOVA/Kruskal); pairwise/per-level mode is count layers only.
pct_lt: Numeric less-than threshold for count-layer percents. A cell with a nonzero count whose percent would display below this value renders the percent as "<" followed by the threshold (e.g. pct_lt = 1 shows 1 ( <1%) instead of 1 ( 0%)). NULL disables.
pct_gt: Numeric greater-than threshold for count-layer percents. A cell whose percent is below 100 but would display above this value renders the percent as ">" followed by the threshold (e.g. pct_gt = 99 shows >99 for 99.6%). NULL disables.
zero_count_display: How to display count-layer cells whose count is zero: "full" (default) keeps the usual "0 ( 0%)"; "count_only" shows only the count field (e.g. " 0"); "blank" shows an empty string.
name: Character string, layer name for identification

Value

A tplyr_layer_settings object

Settings by Layer Type

Not all settings apply to every layer type. The table below shows which settings are applicable for each of the four layer types:

Setting	Count	Desc	Shift	Analyze
`format_strings`	X	X	X	X
`stat_columns`	X
`denoms_by`	X	X	X
`shift_denom`			X
`denom_row`			X
`denom_row_label`			X
`denom_row_format`			X
`denom_where`	X	X	X
`denom_ignore`	X		X
`distinct_by`	X		X
`total_row`	X
`total_row_label`	X
`total_row_count_missings`	X
`missing_count`	X
`missing_subjects`	X
`missing_subjects_label`	X
`keep_levels`	X
`limit_data_by`	X
`custom_summaries`		X
`stats_as_columns`		X
`precision_by`		X
`precision_on`		X
`precision_data`		X
`precision_cap`		X
`order_count_method`	X
`ordering_cols`	X
`result_order_var`	X
`outer_sort_position`	X
`risk_diff`	X
`ci_method`	X
`ci_level`	X
`assoc_test`	X	X	X
`pct_lt`	X
`pct_gt`	X
`zero_count_display`	X
`name`	X	X	X	X

Settings provided for an inapplicable layer type are silently ignored.