Merge branch '37_update_authors' of github.com:pharmaverse/admiralmet…

…abolic into 37_update_authors

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: admiralmetabolic
 Title: Metabolism Extension Package for ADaM in 'R' Asset Library
-Version: 0.0.0
+Version: 0.1.0
 Authors@R: c(
     person("Anders", "Askeland", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-2996-129X")),
     person("Andrii", "Yurovskyi", , "[email protected]", role = "aut", comment = c(ORCID = "0009-0006-8606-0929")),
@@ -31,11 +31,13 @@ Depends:
 Imports:
     admiral (>= 1.1.1),
     admiraldev (>= 1.0.0),
+    cli (>= 3.6.2),
     dplyr (>= 0.8.4),
     stringr (>= 1.4.0),
     lifecycle (>= 0.1.0),
     lubridate (>= 1.7.4),
     magrittr (>= 1.5),
+    purrr (>= 0.3.3),
     rlang (>= 0.4.4),
     tidyselect (>= 1.0.0)
 Suggests:

NAMESPACE

@@ -1,6 +1,22 @@
 # Generated by roxygen2: do not edit by hand
 
-export(hello_admiral)
+export(derive_param_waisthgt)
+export(derive_param_waisthip)
+importFrom(admiral,derive_param_computed)
+importFrom(admiraldev,assert_character_scalar)
+importFrom(admiraldev,assert_character_vector)
+importFrom(admiraldev,assert_data_frame)
+importFrom(admiraldev,assert_expr)
+importFrom(admiraldev,assert_filter_cond)
+importFrom(admiraldev,assert_logical_scalar)
+importFrom(admiraldev,assert_numeric_vector)
+importFrom(admiraldev,assert_param_does_not_exist)
+importFrom(admiraldev,assert_unit)
+importFrom(admiraldev,assert_vars)
+importFrom(admiraldev,assert_varval_list)
+importFrom(admiraldev,expect_dfs_equal)
+importFrom(cli,cli_abort)
+importFrom(cli,cli_alert_info)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
@@ -30,6 +46,7 @@ importFrom(dplyr,summarise)
 importFrom(dplyr,summarise_at)
 importFrom(dplyr,tibble)
 importFrom(dplyr,transmute)
+importFrom(dplyr,tribble)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,union)
 importFrom(dplyr,vars)
@@ -53,6 +70,7 @@ importFrom(lubridate,years)
 importFrom(lubridate,ymd)
 importFrom(lubridate,ymd_hms)
 importFrom(magrittr,"%>%")
+importFrom(purrr,discard_at)
 importFrom(rlang,":=")
 importFrom(rlang,.data)
 importFrom(rlang,abort)
@@ -64,12 +82,14 @@ importFrom(rlang,call_name)
 importFrom(rlang,caller_env)
 importFrom(rlang,current_env)
 importFrom(rlang,enexpr)
+importFrom(rlang,enexprs)
 importFrom(rlang,enquo)
 importFrom(rlang,eval_bare)
 importFrom(rlang,eval_tidy)
 importFrom(rlang,expr)
 importFrom(rlang,expr_interp)
 importFrom(rlang,expr_label)
+importFrom(rlang,exprs)
 importFrom(rlang,f_lhs)
 importFrom(rlang,f_rhs)
 importFrom(rlang,inform)
@@ -105,6 +125,7 @@ importFrom(stringr,str_c)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_extract)
 importFrom(stringr,str_glue)
+importFrom(stringr,str_glue_data)
 importFrom(stringr,str_remove)
 importFrom(stringr,str_remove_all)
 importFrom(stringr,str_replace)

NEWS.md

@@ -1,8 +1,14 @@
 # admiralmetabolic 0.1.0
 
-- Initial package release focused on `<<ADD INITIAL SCOPE>>`
+- Initial package release mainly focused on obesity therapeutic area.
 
-Note that after first release you should then start maintaining this `NEWS.md` file for every user-facing update.
-You should categorize the updates under title sections for New Features, Updates of Existing Functions,
-Breaking Changes, Documentation, Various.
-Each update should also reference the original issue by adding at the end: (#ISSUE-NUMBER)
+## Functions
+
+- The function `derive_param_waisthip()` for deriving Waist to Hip Ratio. (#33 &  #52)
+- The function `derive_param_waisthgt()` for deriving Waist to Height Ratio. (#33 & #52)
+
+## Documentation
+
+- Vignette "Creating a Metabolic ADVS ADaM". (#28) 
+- Vignette "Creating a Control of Eating Questionnaire ADaM". (#53)
+- ADVS template scripts `ad_advs.R` which creates a Vital Sign Analysis Dataset with metabolic specific derivations. (#35)

R/admiralmetabolic-package.R

@@ -1,21 +1,28 @@
 #' @keywords internal
 #' @family internal
+#' @importFrom admiraldev assert_numeric_vector assert_character_scalar assert_logical_scalar
+#'             assert_data_frame assert_vars assert_varval_list assert_filter_cond
+#'             assert_param_does_not_exist assert_expr expect_dfs_equal assert_character_vector
+#'             assert_unit
+#' @importFrom admiral derive_param_computed
+#' @importFrom cli cli_abort cli_alert_info
 #' @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
-#'             summarise_at summarise coalesce bind_cols na_if tibble
+#'             summarise_at summarise coalesce bind_cols na_if tibble tribble
 #' @importFrom magrittr %>%
+#' @importFrom purrr discard_at
 #' @importFrom rlang := abort arg_match as_function as_string call2 caller_env
-#'             call_name current_env .data enexpr enquo eval_bare eval_tidy expr
-#'             expr_interp expr_label f_lhs f_rhs inform
+#'             call_name current_env .data enexpr enexprs enquo eval_bare eval_tidy expr
+#'             exprs expr_interp expr_label f_lhs f_rhs inform
 #'             is_bare_formula is_call is_character is_formula is_integerish
 #'             is_logical is_quosure is_quosures is_symbol new_formula
 #'             parse_expr parse_exprs quo quo_get_expr quo_is_call
 #'             quo_is_missing quo_is_null quo_is_symbol quos quo_squash quo_text
 #'             set_names sym syms type_of warn quo_set_env quo_get_env
 #' @importFrom utils capture.output str
 #' @importFrom stringr str_c str_detect str_extract str_remove str_remove_all
-#'             str_replace str_trim str_to_lower str_to_title str_to_upper str_glue
+#'             str_replace str_trim str_to_lower str_to_title str_to_upper str_glue str_glue_data
 #' @importFrom lubridate as_datetime ceiling_date date days duration floor_date is.Date is.instant
 #'             time_length %--% ymd ymd_hms weeks years hours minutes
 #' @importFrom tidyselect all_of contains vars_select

R/data.R

@@ -11,3 +11,14 @@
 #'
 #' @source Constructed using `vs` from the `{pharmaversesdtm}` package and `dm_metabolic` from `{admiralmetabolic}` package
 "vs_metabolic"
+
+#' Example questionnaire dataset
+#'
+#' An example questionnaire SDTM dataset (containing Control of Eating Questionnaire, CoEQ, test data) for metabolic studies.
+#' Note that University of Leeds are the copyright holders of the CoEQ and the test data included within `{admiralmetabolic}`
+#' is for not-for-profit use only within `{admiralmetabolic}` and `pharmaverse`-related examples/documentation. Any persons
+#' or companies wanting to use the CoEQ should request a license to do so from the following
+#' [link](https://licensing.leeds.ac.uk/product/control-of-eating-questionnaire-coeq).
+#'
+#' @source Constructed using `dm_metabolic` from `{admiralmetabolic}` package
+"qs_metabolic"