Merge branch 'devel' into 1300_refactor_imputation

bundfussr · Aug 9, 2022 · 96749e0 · 96749e0
2 parents d55ac12 + ea5311e
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diff --git a/NEWS.md b/NEWS.md
@@ -97,6 +97,9 @@ have been removed:
 
 ## Various
 
+- Restructured Reference page and updated **all** functions to use `family` tag 
+in roxygen headers for finding similar functions.  (#1105)
+
 # admiral 0.7.1
 
 - `derive_vars_last_dose()` no longer fails when a variable renamed in `new_vars` is supplied

diff --git a/R/admiral-package.R b/R/admiral-package.R
@@ -1,4 +1,5 @@
 #' @keywords internal
+#' @family internal
 #' @importFrom dplyr arrange bind_rows case_when desc ends_with filter full_join group_by
 #'             if_else mutate mutate_at mutate_if n pull rename rename_at row_number select slice
 #'             starts_with transmute ungroup vars n_distinct union distinct

diff --git a/R/assertions.R b/R/assertions.R
@@ -18,7 +18,8 @@
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' library(admiral.test)
@@ -101,7 +102,8 @@ assert_data_frame <- function(arg,
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' example_fun <- function(msg_type) {
@@ -191,7 +193,8 @@ assert_character_scalar <- function(arg,
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' example_fun <- function(chr) {
@@ -251,7 +254,8 @@ assert_character_vector <- function(arg, values = NULL, optional = FALSE) {
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' example_fun <- function(flag) {
@@ -298,7 +302,8 @@ assert_logical_scalar <- function(arg, optional = FALSE) {
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' library(admiral.test)
@@ -376,7 +381,8 @@ assert_expr <- function(arg, optional = FALSE) {
 #' Otherwise throws an informative error.
 #'
 #' @export
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #' @author Ondrej Slama
 #'
 #' @examples
@@ -434,7 +440,8 @@ assert_filter_cond <- function(arg, optional = FALSE) {
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' example_fun <- function(by_vars) {
@@ -498,7 +505,8 @@ assert_vars <- function(arg, optional = FALSE) {
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' example_fun <- function(by_vars) {
@@ -556,7 +564,8 @@ assert_order_vars <- function(arg, optional = FALSE) {
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' example_fun <- function(num1, num2) {
@@ -614,7 +623,8 @@ assert_integer_scalar <- function(arg, subset = "none", optional = FALSE) {
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' example_fun <- function(num) {
@@ -745,7 +755,8 @@ assert_date_var <- function(dataset, var, dataset_name = NULL, var_name = NULL)
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' example_fun <- function(obj) {
@@ -796,7 +807,8 @@ assert_s3_class <- function(arg, class, optional = TRUE) {
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' example_fun <- function(list) {
@@ -892,7 +904,8 @@ assert_list_of_formulas <- function(arg, optional = FALSE) {
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' library(admiral.test)
@@ -943,7 +956,8 @@ assert_has_variables <- function(dataset, required_vars) {
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' example_fun <- function(fun) {
@@ -1032,7 +1046,8 @@ assert_function_param <- function(arg, params) {
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' library(tibble)
@@ -1102,7 +1117,8 @@ assert_unit <- function(dataset, param, required_unit, get_unit_expr) {
 #'
 #' @export
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @examples
 #' library(tibble)
@@ -1150,7 +1166,8 @@ assert_param_does_not_exist <- function(dataset, param) {
 #' The function throws an error if `arg` is not a list of variable-value expressions.
 #' Otherwise, the input it returned invisibly.
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @export
 #'
@@ -1300,7 +1317,8 @@ assert_varval_list <- function(arg, # nolint
 #' @return
 #' An error if the condition is not meet. The input otherwise.
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @export
 #'
@@ -1393,7 +1411,8 @@ assert_list_element <- function(list, element, condition, message_text, ...) {
 #' @return
 #' An error if the condition is not meet. The input otherwise.
 #'
-#' @keywords assertion
+#' @family move_adm_dev
+#' @keywords move_adm_dev
 #'
 #' @export
 #'

diff --git a/R/call_derivation.R b/R/call_derivation.R
@@ -17,7 +17,8 @@
 #' The input dataset with additional records/variables added depending on
 #' which `derivation` has been used.
 #'
-#' @keywords user_utility high_order_function
+#' @family high_order_function
+#' @keywords high_order_function
 #'
 #' @export
 #'
@@ -102,6 +103,7 @@ call_derivation <- function(dataset = NULL, derivation, variable_params, ...) {
 #'
 #' @return An object of class `params`
 #'
+#' @family source_specifications
 #' @keywords source_specifications
 #'
 #' @export

diff --git a/R/call_user_fun.R b/R/call_user_fun.R
@@ -9,7 +9,8 @@
 #'
 #' @return The return value of the function call
 #'
-#' @keywords dev_utility
+#' @family utils_help
+#' @keywords utils_help
 #'
 #' @export
 #'

diff --git a/R/compute_duration.R b/R/compute_duration.R
@@ -69,7 +69,9 @@
 #'
 #' @return The duration between the two date in the specified unit
 #'
-#' @keywords computation adam timing
+#' @family com_date_time
+#'
+#' @keywords com_date_time
 #'
 #' @export
 #'

diff --git a/R/create_query_data.R b/R/create_query_data.R
@@ -140,7 +140,8 @@
 #' @return A dataset to be used as input dataset to the `dataset_queries`
 #'   argument in `derive_vars_query()`
 #'
-#' @keywords adae adcm user_utility
+#' @family der_occds
+#' @keywords der_occds
 #'
 #' @seealso [derive_vars_query()], [query()], [smq_select()], [sdg_select()], [Queries Dataset
 #' Documentation](../articles/queries_dataset.html)
@@ -381,6 +382,9 @@ create_query_data <- function(queries,
 #'
 #'   *Permitted Values*: `"smq"`, `"sdg"`
 #'
+#' @family der_occds
+#' @keywords der_occds
+#'
 #' @return Output dataset of the access function
 #'
 #' @author Stefan Bundfuss
@@ -452,6 +456,9 @@ get_terms_from_db <- function(version,
 #'
 #' Should be `"SMQ`" or `"SDG"`.
 #'
+#' @keywords move_adm_dev
+#' @family move_adm_dev
+#'
 #' @return An error is issued if `version` or `fun` is null.
 #'
 #' @author Stefan Bundfuss
@@ -562,6 +569,7 @@ assert_db_requirements <- function(version, version_arg_name, fun, fun_arg_name,
 #' @seealso [create_query_data()], [smq_select()], [sdg_select()], [Queries Dataset
 #' Documentation](../articles/queries_dataset.html)
 #'
+#' @family source_specifications
 #' @keywords source_specifications
 #'
 #' @export
@@ -654,6 +662,9 @@ query <- function(prefix,
 #'
 #' @author Stefan Bundfuss
 #'
+#' @keywords move_adm_dev
+#' @family move_adm_dev
+#'
 #' @seealso [query()]
 #'
 #' @export
@@ -795,7 +806,8 @@ validate_query <- function(obj) {
 #'
 #' @seealso [create_query_data()], [query()]
 #'
-#' @keywords assertion
+#' @keywords move_adm_dev
+#' @family move_adm_dev
 #'
 #' @author Stefan Bundfuss
 assert_terms <- function(terms,
@@ -885,6 +897,7 @@ assert_terms <- function(terms,
 #'
 #' @seealso [create_query_data()], [query()]
 #'
+#' @family source_specifications
 #' @keywords source_specifications
 #'
 #' @export
@@ -906,6 +919,9 @@ smq_select <- function(name = NULL,
 #'
 #' @seealso [smq_select()]
 #'
+#' @keywords move_adm_dev
+#' @family move_adm_dev
+#'
 #' @author Stefan Bundfuss
 #'
 #' @export
@@ -951,7 +967,8 @@ validate_smq_select <- function(obj) {
 #'
 #' @seealso [smq_select()]
 #'
-#' @keywords dev_utility
+#' @keywords move_adm_dev
+#' @family move_adm_dev
 #'
 #' @export
 #'
@@ -986,6 +1003,7 @@ format.smq_select <- function(x, ...) {
 #'
 #' @seealso [create_query_data()], [query()]
 #'
+#' @family source_specifications
 #' @keywords source_specifications
 #'
 #' @export
@@ -1007,6 +1025,9 @@ sdg_select <- function(name = NULL,
 #'
 #' @seealso [sdg_select()]
 #'
+#' @keywords move_adm_dev
+#' @family move_adm_dev
+#'
 #' @export
 #'
 #' @return The original object.
@@ -1045,7 +1066,8 @@ validate_sdg_select <- function(obj) {
 #'
 #' @seealso [sdg_select()]
 #'
-#' @keywords dev_utility
+#' @keywords move_adm_dev
+#' @family move_adm_dev
 #'
 #' @export
 #'

diff --git a/R/create_single_dose_dataset.R b/R/create_single_dose_dataset.R
@@ -36,6 +36,7 @@
 #' @export
 #'
 #' @keywords metadata
+#' @family metadata
 #'
 #' @rdname dose_freq_lookup
 
@@ -240,7 +241,8 @@ dose_freq_lookup <- tibble::tribble(
 #'
 #' @author Michael Thorpe, Andrew Smith
 #'
-#' @keywords adae adex user_utility
+#' @family der_occds
+#' @keywords der_occds
 #'
 #' @return The input dataset with a single dose per row.
 #'