List options in .stats argument descriptions

R/abnormal.R

@@ -23,8 +23,9 @@
 #'   for example, `abnormal = list(Low = c("LOW", "LOW LOW"), High = c("HIGH", "HIGH HIGH"))`.
 #' @param exclude_base_abn (`flag`)\cr whether to exclude subjects with baseline abnormality
 #'   from numerator and denominator.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("abnormal")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("abnormal"))``
 #'
 #' @note
 #' * `count_abnormal()` only considers a single variable that contains multiple abnormal levels.

R/abnormal_by_baseline.R

@@ -29,8 +29,9 @@
 #'
 #' @inheritParams argument_convention
 #' @param abnormal (`character`)\cr values identifying the abnormal range level(s) in `.var`.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("abnormal_by_baseline")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("abnormal_by_baseline"))``
 #'
 #' @note
 #' * `df` should be filtered to include only post-baseline records.

R/abnormal_by_marked.R

@@ -28,8 +28,9 @@
 #' @inheritParams argument_convention
 #' @param category (`list`)\cr a list with different marked category names for single
 #'   and last or replicated.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("abnormal_by_marked")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("abnormal_by_marked"))``
 #'
 #' @note `Single, not last` and `Last or replicated` levels are mutually exclusive. If a patient has
 #'   abnormalities that meet both the `Single, not last` and `Last or replicated` criteria, then the

R/abnormal_by_worst_grade.R

@@ -27,8 +27,9 @@
 #' splits, one on variable `param` and one on variable `grade_dir`.
 #'
 #' @inheritParams argument_convention
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("abnormal_by_worst_grade")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("abnormal_by_worst_grade"))``
 #'
 #' @seealso [h_adlb_abnormal_by_worst_grade()] which pre-processes ADLB data frames to be used in
 #'   [count_abnormal_by_worst_grade()].

R/abnormal_by_worst_grade_worsen.R

@@ -28,8 +28,9 @@
 #'   * `id` (`string`)\cr subject variable name.
 #'   * `baseline_var` (`string`)\cr name of the data column containing baseline toxicity variable.
 #'   * `direction_var` (`string`)\cr see `direction_var` for more details.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("abnormal_by_worst_grade_worsen")`
-#'   to see all available statistics.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("abnormal_by_worst_grade_worsen"))``
 #'
 #' @seealso Relevant helper functions [h_adlb_worsen()] and [h_worsen_counter()] which are used within
 #' [s_count_abnormal_lab_worsen_by_baseline()] to process input data.

R/analyze_variables.R

@@ -45,9 +45,11 @@ control_analyze_vars <- function(conf_level = 0.95,
 #' columns) will be considered (`.df_row[[.var]]`, see [`rtables::additional_fun_params`]) and not the whole dataset.
 #'
 #' @inheritParams argument_convention
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("analyze_vars_numeric")` to see
-#'   statistics available for numeric variables, and `get_stats("analyze_vars_counts")` for statistics available
-#'   for non-numeric variables.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options for numeric variables are: ``r shQuote(get_stats("analyze_vars_numeric"))``
+#'
+#'   Options for non-numeric variables are: ``r shQuote(get_stats("analyze_vars_counts"))``
 #'
 #' @name analyze_variables
 #' @order 1

R/compare_variables.R

@@ -14,9 +14,11 @@
 #' statistic.
 #'
 #' @inheritParams argument_convention
-#' @param .stats (`character`)\cr statistics to select for the table. Run
-#'   `get_stats("analyze_vars_numeric", add_pval = TRUE)` to see statistics available for numeric variables, and
-#'   `get_stats("analyze_vars_counts", add_pval = TRUE)` for statistics available for non-numeric variables.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options for numeric variables are: ``r shQuote(get_stats("analyze_vars_numeric", add_pval = TRUE))``
+#'
+#'   Options for non-numeric variables are: ``r shQuote(get_stats("analyze_vars_counts", add_pval = TRUE))``
 #'
 #' @note
 #' * For factor variables, `denom` for factor proportions can only be `n` since the purpose is to compare proportions

R/count_cumulative.R

@@ -14,8 +14,9 @@
 #' @inheritParams h_count_cumulative
 #' @inheritParams argument_convention
 #' @param thresholds (`numeric`)\cr vector of cutoff values for the counts.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("count_cumulative")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("count_cumulative"))``
 #'
 #' @seealso Relevant helper function [h_count_cumulative()], and descriptive function [d_count_cumulative()].
 #'

R/count_missed_doses.R

@@ -12,8 +12,9 @@
 #' @inheritParams s_count_cumulative
 #' @inheritParams argument_convention
 #' @param thresholds (`numeric`)\cr minimum number of missed doses the patients had.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("count_missed_doses")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("count_missed_doses"))``
 #'
 #' @seealso
 #' * Relevant description function [d_count_missed_doses()] which generates labels for [count_missed_doses()].

R/count_occurrences.R

@@ -17,8 +17,9 @@
 #' @inheritParams argument_convention
 #' @param drop (`flag`)\cr whether non-appearing occurrence levels should be dropped from the resulting table.
 #'   Note that in that case the remaining occurrence levels in the table are sorted alphabetically.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("count_occurrences")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("count_occurrences"))``
 #'
 #' @note By default, occurrences which don't appear in a given row split are dropped from the table and
 #'   the occurrences in the table are sorted alphabetically per row split. Therefore, the corresponding layout

R/count_occurrences_by_grade.R

@@ -24,8 +24,9 @@
 #' @param only_grade_groups (`flag`)\cr whether only the specified grade groups should be
 #'   included, with individual grade rows removed (`TRUE`), or all grades and grade groups
 #'   should be displayed (`FALSE`).
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("count_occurrences_by_grade")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("count_occurrences_by_grade"))``
 #'
 #' @seealso Relevant helper function [h_append_grade_groups()].
 #'

R/count_patients_events_in_cols.R

@@ -19,9 +19,10 @@
 #'   that corresponding table cells will stay blank.
 #' @param custom_label (`string` or `NULL`)\cr if provided and `labelstr` is empty then this will
 #'   be used as label.
-#' @param .stats (`character`)\cr statistics to select for the table. Run
-#'   `get_stats("summarize_patients_events_in_cols")` to see available statistics for this function, in addition
-#'   to any added using `filters_list`.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   In addition to any statistics added using `filters_list`, statistic options are:
+#'   ``r shQuote(get_stats("summarize_patients_events_in_cols"))``
 #'
 #' @name count_patients_events_in_cols
 #' @order 1

R/count_patients_with_event.R

@@ -17,8 +17,9 @@
 #'   Multiple column names and flags are accepted in this format
 #'   `c("column_name1" = "flag1", "column_name2" = "flag2")`.
 #'   Note that only equality is being accepted as condition.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("count_patients_with_event")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("count_patients_with_event"))``
 #'
 #' @seealso [count_patients_with_flags]
 #'

R/count_patients_with_flags.R

@@ -15,8 +15,9 @@
 #' @param flag_variables (`character`)\cr a vector specifying the names of `logical` variables from analysis dataset
 #'   used for counting the number of unique identifiers.
 #' @param flag_labels (`character`)\cr vector of labels to use for flag variables.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("count_patients_with_flags")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("count_patients_with_flags"))``
 #'
 #' @seealso [count_patients_with_event]
 #'

R/count_values.R

@@ -11,8 +11,9 @@
 #'
 #' @inheritParams argument_convention
 #' @param values (`character`)\cr specific values that should be counted.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("count_values")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("count_values"))``
 #'
 #' @note
 #' * For `factor` variables, `s_count_values` checks whether `values` are all included in the levels of `x`

R/estimate_multinomial_rsp.R

@@ -7,8 +7,9 @@
 #' `var`, should be a factor variable, the values of which will be used as labels within the output table.
 #'
 #' @inheritParams argument_convention
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("estimate_multinomial_response")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("estimate_multinomial_response"))``
 #'
 #' @seealso Relevant description function [d_onco_rsp_label()].
 #'

R/estimate_proportion.R

@@ -10,12 +10,13 @@
 #'
 #' @inheritParams prop_strat_wilson
 #' @inheritParams argument_convention
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("estimate_proportion")`
-#'   to see available statistics for this function.
 #' @param method (`string`)\cr the method used to construct the confidence interval
 #'   for proportion of successful outcomes; one of `waldcc`, `wald`, `clopper-pearson`,
 #'   `wilson`, `wilsonc`, `strat_wilson`, `strat_wilsonc`, `agresti-coull` or `jeffreys`.
 #' @param long (`flag`)\cr whether a long description is required.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("estimate_proportion"))``
 #'
 #' @seealso [h_proportions]
 #'

R/incidence_rate.R

@@ -19,8 +19,9 @@
 #' @param n_events (`string`)\cr name of integer variable indicating whether an event has been observed (1) or not (0).
 #' @param id_var (`string`)\cr name of variable used as patient identifier if `"n_unique"` is included in `.stats`.
 #'   Defaults to `"USUBJID"`.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("estimate_incidence_rate")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("estimate_incidence_rate"))``
 #' @param summarize (`flag`)\cr whether the function should act as an analyze function (`summarize = FALSE`), or a
 #'   summarize function (`summarize = TRUE`). Defaults to `FALSE`.
 #' @param label_fmt (`string`)\cr how labels should be formatted after a row split occurs if `summarize = TRUE`. The

R/odds_ratio.R

@@ -11,8 +11,9 @@
 #'
 #' @inheritParams split_cols_by_groups
 #' @inheritParams argument_convention
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("estimate_odds_ratio")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("estimate_odds_ratio"))``
 #' @param method (`string`)\cr whether to use the correct (`"exact"`) calculation in the conditional likelihood or one
 #'   of the approximations. See [survival::clogit()] for details.
 #'

R/prop_diff.R

@@ -12,8 +12,9 @@
 #' @inheritParams prop_diff_strat_nc
 #' @inheritParams argument_convention
 #' @param method (`string`)\cr the method used for the confidence interval estimation.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("estimate_proportion_diff")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("estimate_proportion_diff"))``
 #'
 #' @seealso [d_proportion_diff()]
 #'

R/prop_diff_test.R

@@ -10,8 +10,9 @@
 #' @inheritParams argument_convention
 #' @param method (`string`)\cr one of `chisq`, `cmh`, `fisher`, or `schouten`; specifies the test used
 #'   to calculate the p-value.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("test_proportion_diff")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("test_proportion_diff"))``
 #'
 #' @seealso [h_prop_diff_test]
 #'

R/summarize_ancova.R

@@ -17,8 +17,9 @@
 #' @inheritParams argument_convention
 #' @param interaction_y (`string` or `flag`)\cr a selected item inside of the `interaction_item` variable which will be
 #'   used to select the specific ANCOVA results. if the interaction is not needed, the default option is `FALSE`.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("summarize_ancova")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("summarize_ancova"))``
 #'
 #' @name summarize_ancova
 #' @order 1

R/summarize_change.R

@@ -12,8 +12,9 @@
 #' or the change from baseline values (post-baseline) are then summarized.
 #'
 #' @inheritParams argument_convention
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("analyze_vars_numeric)`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("analyze_vars_numeric"))``
 #'
 #' @name summarize_change
 #' @order 1

R/summarize_coxreg.R

@@ -5,8 +5,9 @@
 #' Fits a Cox regression model and estimates hazard ratio to describe the effect size in a survival analysis.
 #'
 #' @inheritParams argument_convention
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("summarize_coxreg")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("summarize_coxreg"))``
 #'
 #' @details Cox models are the most commonly used methods to estimate the magnitude of
 #'   the effect in survival analysis. It assumes proportional hazards: the ratio

R/summarize_glm_count.R

@@ -14,8 +14,9 @@
 #' @param rate_mean_method (`character(1)`)\cr method used to estimate the mean odds ratio. Defaults to `emmeans`.
 #'   see details for more information.
 #' @param scale (`numeric(1)`)\cr linear scaling factor for rate and confidence intervals. Defaults to `1`.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("summarize_glm_count")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("summarize_glm_count"))``
 #'
 #' @details
 #' `summarize_glm_count()` uses `s_glm_count()` to calculate the statistics for the table. This

R/summarize_num_patients.R

@@ -19,8 +19,9 @@
 #'   `nonunique` records.
 #' @param unique_count_suffix (`flag`)\cr whether the `"(n)"` suffix should be added to `unique_count` labels.
 #'   Defaults to `TRUE`.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("summarize_num_patients")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("summarize_num_patients"))``
 #'
 #' @name summarize_num_patients
 #' @order 1

R/summarize_patients_exposure_in_cols.R

@@ -21,8 +21,9 @@
 #' @inheritParams argument_convention
 #' @param ex_var (`string`)\cr name of the variable in `df` containing exposure values.
 #' @param custom_label (`string` or `NULL`)\cr if provided and `labelstr` is empty, this will be used as label.
-#' @param .stats (`character`)\cr statistics to select for the table. Run
-#'   `get_stats("analyze_patients_exposure_in_cols")` to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("analyze_patients_exposure_in_cols"))``
 #'
 #' @name summarize_patients_exposure_in_cols
 #' @order 1

R/survival_coxph_pairwise.R

@@ -20,8 +20,9 @@
 #'   * `ties` (`string`)\cr specifying the method for tie handling. Default is `"efron"`,
 #'     can also be set to `"breslow"` or `"exact"`. See more in [survival::coxph()].
 #'   * `conf_level` (`proportion`)\cr confidence level of the interval for HR.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("coxph_pairwise")`
-#'   to see available statistics for this function.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("coxph_pairwise"))``
 #'
 #' @name survival_coxph_pairwise
 #' @order 1

R/survival_time.R

@@ -16,11 +16,12 @@
 #'   * `quantiles` (`numeric`)\cr vector of length two to specify the quantiles of survival time.
 #' @param ref_fn_censor (`flag`)\cr whether referential footnotes indicating censored observations should be printed
 #'   when the `range` statistic is included.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("surv_time")`
-#'   to see available statistics for this function.
 #' @param .indent_mods (named `integer`)\cr indent modifiers for the labels. Each element of the vector
 #'   should be a name-value pair with name corresponding to a statistic specified in `.stats` and value the indentation
 #'   for that statistic's row label.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("surv_time"))``
 #'
 #' @examples
 #' library(dplyr)

R/survival_timepoint.R

@@ -21,11 +21,12 @@
 #'   control), or `"both"`.
 #' @param table_names_suffix (`string`)\cr optional suffix for the `table_names` used for the `rtables` to
 #'   avoid warnings from duplicate table names.
-#' @param .stats (`character`)\cr statistics to select for the table. Run `get_stats("surv_timepoint")`
-#'   to see available statistics for this function.
 #' @param .indent_mods (named `integer`)\cr indent modifiers for the labels. Each element of the vector
 #'   should be a name-value pair with name corresponding to a statistic specified in `.stats` and value the indentation
 #'   for that statistic's row label.
+#' @param .stats (`character`)\cr statistics to select for the table.
+#'
+#'   Options are: ``r shQuote(get_stats("surv_timepoint"))``
 #'
 #' @name survival_timepoint
 #' @order 1