Merge branch 'main' into 2142_derive_summary_records_get_summary_reco…

…rds_mods

NEWS.md

@@ -30,6 +30,8 @@
 
 ## Documentation
 
+- A way to standardize roxygen labels and descriptions for function arguments was implemented and tested (#2034)
+
 ## Various
 
 # admiral 0.12.2

R/call_derivation.R

@@ -3,7 +3,7 @@
 #' Call a single derivation multiple times with some parameters/arguments being fixed across
 #' iterations and others varying.
 #'
-#' @param dataset The input dataset
+#' @param dataset  `r roxygen_param_dataset()`
 #' @param derivation The derivation function to call
 #'
 #'   A function that performs a specific derivation is expected. A derivation

R/create_single_dose_dataset.R

@@ -185,10 +185,8 @@ dose_freq_lookup <- tribble(
 #' necessary when e.g. calculating last dose before an adverse event in `ADAE`
 #' or deriving a total dose parameter in `ADEX` when `EXDOSFRQ != ONCE`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The columns specified by `dose_freq`, `start_date` and the `end_date`
-#'   parameters are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("dose_freq", "start_date", "end_date"))`
 #'
 #' @param dose_freq The dose frequency
 #'

R/derive_adeg_params.R

@@ -6,10 +6,9 @@
 #'
 #' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` and the `unit_var` parameter,
-#'   `PARAMCD`, and `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars", "get_unit_expr"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`
@@ -257,10 +256,9 @@ compute_qtc <- function(qt, rr, method) {
 #' The analysis value of the new parameter is derived as
 #' \deqn{\frac{60000}{HR}}{60000 / HR}
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and `AVAL`
-#'   are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`

R/derive_advs_params.R

@@ -5,10 +5,9 @@
 #'
 #' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and
-#'   `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`
@@ -226,10 +225,9 @@ compute_map <- function(diabp, sysbp, hr = NULL) {
 #'
 #' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and
-#'   `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`
@@ -549,10 +547,9 @@ compute_bsa <- function(height = height,
 #'
 #' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and
-#'   `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`

R/derive_basetype_records.R

@@ -12,9 +12,8 @@
 #' Adds the `BASETYPE` variable to a dataset and duplicates records based upon
 #' the provided conditions.
 #'
-#' @param dataset Input dataset
-#'
-#'   The columns specified in the expressions inside `basetypes` are required.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("basetypes"))`
 #'
 #' @param basetypes A *named* list of expressions created using the
 #' `rlang::exprs()` function

R/derive_date_vars.R

@@ -1252,9 +1252,8 @@ compute_tmf <- function(dtc,
 #' impute, we only enable to impute up to a highest level, i.e. you couldn't
 #' choose to say impute months, but not days.
 #'
-#' @param dataset Input dataset.
-#'
-#'   The date character vector (`dtc`) must be present.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("dtc"))`
 #'
 #' @param new_vars_prefix Prefix used for the output variable(s).
 #'
@@ -1461,9 +1460,8 @@ derive_vars_dt <- function(dataset, # nolint: cyclocomp_linter
 #' impute, we only enable to impute up to a highest level, i.e. you couldn't
 #' choose to say impute months, but not days.
 #'
-#' @param dataset Input dataset
-#'
-#'   The date character vector (`dtc`) must be present.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("dtc"))`
 #'
 #' @param new_vars_prefix Prefix used for the output variable(s).
 #'

R/derive_expected_records.R

@@ -3,10 +3,8 @@
 #' Add expected records as new observations for each 'by group' when the dataset
 #' contains missing observations.
 #'
-#' @param dataset Input dataset
-#'
-#'   A data frame, the columns from `dataset_ref` and specified by the
-#'   `by_vars` parameter are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("dataset_ref", "by_vars"))`
 #'
 #' @param dataset_expected_obs *Deprecated*, please use `dataset_ref` instead.
 #'

R/derive_extreme_records.R

@@ -7,7 +7,7 @@
 #' distinguishes `derive_extreme_records()` from `derive_summary_records()`,
 #' where only the by variables are populated for the new records.
 #'
-#' @param dataset Input dataset
+#' @param dataset `r roxygen_param_dataset()`
 #'
 #'   If `dataset_add` is not specified, the new records are selected from the
 #'   input dataset. In this case the variables specified by `by_vars` and
@@ -92,6 +92,14 @@
 #'   automatically.
 #'
 #'
+#' @param keep_source_vars Variables to be kept in the new records
+#'
+#'   A named list or tidyselect expressions created by `exprs()` defining the
+#'   variables to be kept for the new records. The variables specified for
+#'   `by_vars` and `set_values_to` need not be specified here as they are kept
+#'   automatically.
+#'
+#'
 #' @inheritParams filter_extreme
 #' @inheritParams derive_summary_records
 #'

R/derive_joined.R

@@ -6,9 +6,8 @@
 #' variables from both datasets. For example, add the lowest value (nadir)
 #' before the current observation.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by `by_vars` are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("by_vars"))`
 #'
 #' @param dataset_add Additional dataset
 #'

R/derive_locf_records.R

@@ -3,10 +3,8 @@
 #' Adds LOCF records as new observations for each 'by group' when the dataset
 #' does not contain observations for missed visits/time points.
 #'
-#' @param dataset Input dataset
-#'
-#'   The columns specified by the `by_vars`, `analysis_var`, `order`,
-#'   `keep_vars` parameters are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("by_vars", "analysis_var", "order", "keep_vars"))`
 #'
 #' @param dataset_expected_obs *Deprecated*, please use `dataset_ref` instead.
 #'

R/derive_merged.R

@@ -6,9 +6,8 @@
 #' (`filter_add` argument) and/or selecting the first or last observation for
 #' each by group (`order` and `mode` argument).
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` argument are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("by_vars"))`
 #'
 #' @param dataset_add Additional dataset
 #'
@@ -710,9 +709,8 @@ get_not_mapped <- function() {
 #'
 #' **Note:** This is a wrapper function for the more generic `derive_vars_merged`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` argument are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("by_vars"))`
 #'
 #' @param dataset_add Additional dataset
 #'

R/derive_param_computed.R

@@ -7,9 +7,9 @@
 #' blood pressure (DIABP) with the formula
 #' \deqn{MAP = \frac{SYSBP + 2 DIABP}{3}}{MAP = (SYSBP + 2 DIABP) / 3}
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'  `PARAMCD` is expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`
@@ -428,7 +428,8 @@ assert_parameters_argument <- function(parameters, optional = TRUE) {
 #' The function creates temporary parameters and variables of the form
 #' `<variable>.<parameter>`, e.g., `AVAL.WEIGHT`.
 #'
-#' @param dataset Input dataset
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("by_vars"))`
 #'
 #' @param by_vars By variables
 #'

R/derive_param_doseint.R

@@ -8,10 +8,9 @@
 #' The analysis value of the new parameter is derived as
 #' Total Dose / Planned Dose * 100
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and
-#'   `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`

R/derive_param_exist_flag.R

@@ -5,10 +5,9 @@
 #' function can derive a parameter indicating if there is measurable disease at
 #' baseline.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified for `by_vars` and the `PARAMCD` variable are
-#'   expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD` is expected as well.
 #'
 #' @param dataset_ref Reference dataset, e.g., ADSL
 #'

R/derive_param_exposure.R

@@ -3,10 +3,9 @@
 #' Add a record computed from the aggregated analysis value of another parameter and compute the
 #' start (`ASTDT(M)`)and end date (`AENDT(M)`) as the minimum and maximum date by `by_vars`.
 #'
-#' @param dataset Input dataset
-#'
-#'   + The variables specified by the `by_vars`,`analysis_var` parameters and `PARAMCD` are
-#'   expected,
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars", "analysis_var"))`
+#'   `PARAMCD` is expected as well,
 #'   + Either `ASTDTM` and `AENDTM` or `ASTDT` and `AENDT` are also expected.
 #'
 #' @param filter Filter condition

R/derive_param_extreme_record.R

@@ -4,7 +4,7 @@
 #' source datasets, based on user-defined filter, order and by group criteria.
 #' All variables of the selected observation are kept.
 #'
-#' @param dataset Input dataset
+#' @param dataset `r roxygen_param_dataset()`
 #'
 #' @param sources Sources
 #'

R/derive_param_framingham.R

@@ -4,10 +4,9 @@
 #' Adds a record for framingham score (FCVD101) for each by group
 #' (e.g., subject and visit) where the source parameters are available.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and
-#'   `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`

R/derive_param_tte.R

@@ -2,9 +2,8 @@
 #'
 #' Add a time-to-event parameter to the input dataset.
 #'
-#' @param dataset Input dataset
-#'
-#'   The `PARAMCD` variable is expected.
+#' @param dataset `r roxygen_param_dataset()`
+#'   `PARAMCD` is expected.
 #'
 #' @param dataset_adsl ADSL input dataset
 #'

R/derive_param_wbc_abs.R

@@ -4,10 +4,9 @@
 #'
 #' Add a parameter by converting lab differentials from fraction or percentage to absolute values
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` argument, `PARAMCD`, and `AVAL`
-#'   are expected to be present.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset, and to the parameters specified by `wbc_code` and `diff_code`.

R/derive_summary_records.R

@@ -11,7 +11,7 @@
 #' retain those common values in the newly derived records. Otherwise new value
 #' will be set to `NA`.
 #'
-#' @param dataset A data frame.
+#' @param dataset  `r roxygen_param_dataset(expected_vars = c("by_vars", "analysis_var"))`
 #'
 #' @param by_vars Variables to consider for generation of groupwise summary
 #'   records. Providing the names of variables in [exprs()] will create a

R/derive_var_analysis_ratio.R

@@ -2,7 +2,8 @@
 #'
 #' Derives a ratio variable for a BDS dataset based on user specified variables.
 #'
-#' @param dataset Input dataset
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("numer_var", "denom_var"))`
 #'
 #' @param numer_var Variable containing numeric values to be used in the numerator of
 #'  the ratio calculation.

R/derive_var_anrind.R

@@ -1,6 +1,10 @@
 #' Derive Reference Range Indicator
 #'
-#' @param dataset The input dataset
+#' @param dataset
+#'   `r roxygen_param_dataset()`
+#'   `ANRLO`, `ANRHI`, and `AVAL` are expected and if `use_a1hia1lo` is set to `TRUE`,
+#'   `A1LO` and `A1H1` are expected as well.
+#'
 #' @param use_a1hia1lo A logical value indicating whether to use `A1H1` and `A1LO` in
 #' the derivation of `ANRIND`.
 #'

R/derive_var_atoxgr.R

@@ -3,9 +3,8 @@
 #' @description
 #' Derives a character lab grade based on severity/toxicity criteria.
 #'
-#' @param dataset Input data set
-#'
-#'   The columns specified by `tox_description_var` parameter is expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("tox_description_var"))`
 #'
 #' @param new_var Name of the character grade variable to create, for example, `ATOXGRH`
 #' or `ATOXGRL`.
@@ -246,10 +245,9 @@ derive_var_atoxgr_dir <- function(dataset,
 #'
 #' Derives character lab grade based on high and low severity/toxicity grade(s).
 #'
-#' @param dataset Input data set
-#'
-#'   The columns `ATOXGRL`, `ATOXGRH` and specified by `lotox_description_var`,
-#'   and `hitox_description_var` parameters are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("lotox_description_var", "hitox_description_var"))`
+#'   `ATOXGRL`, and `ATOXGRH` are expected as well.
 #'
 #' @param lotox_description_var Variable containing the toxicity grade description
 #' for low values, eg. "Anemia"