Release {admiral} v0.7.1

.github/workflows/R-CMD-check.yml

@@ -3,10 +3,12 @@ on:
   push:
     branches:
       - main
+      - patch
       - devel
   pull_request:
     branches:
       - main
+      - patch
       - devel
 
 name: R-CMD-check
@@ -65,7 +67,7 @@ jobs:
         run: |
           options(repos = Sys.getenv("R_REPOS"))
           remotes::install_deps(dependencies = TRUE)
-          ref <- if (Sys.getenv("GITHUB_REF_NAME") == "main") "main" else "devel"
+          ref <- if (Sys.getenv("GITHUB_REF_NAME") %in% c("main", "patch")) "main" else "devel"
           remotes::install_github(
             "pharmaverse/admiral.test",
             ref = ref,

.github/workflows/code-coverage.yml

@@ -3,10 +3,12 @@ on:
   push:
     branches:
       - main
+      - patch
       - devel
   pull_request:
     branches:
       - main
+      - patch
       - devel
 
 name: Code Coverage ☂

.github/workflows/lintr.yaml

@@ -3,10 +3,12 @@ on:
   push:
     branches:
       - main
+      - patch
       - devel
   pull_request:
     branches:
       - main
+      - patch
       - devel
 
 name: lint
@@ -50,7 +52,6 @@ jobs:
         run: |
           if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
           renv::restore()
-          renv::install("lintr")
         shell: Rscript {0}
 
       - name: Install package

.github/workflows/man-pages.yml

@@ -6,10 +6,12 @@ on:
   push:
     branches:
       - main
+      - patch
       - devel
   pull_request:
     branches:
       - main
+      - patch
       - devel
   issue_comment:
     types: [created]

.github/workflows/spellcheck.yml

@@ -6,10 +6,12 @@ on:
   push:
     branches:
       - main
+      - patch
       - devel
   pull_request:
     branches:
       - main
+      - patch
       - devel
 
 concurrency:
@@ -60,7 +62,7 @@ jobs:
           do
             eval sudo $cmd
           done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-      
+
       - name: Install spelling 🎓
         run: |
           if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")

.github/workflows/style.yml

@@ -6,10 +6,12 @@ on:
   push:
     branches:
       - main
+      - patch
       - devel
   pull_request:
     branches:
       - main
+      - patch
       - devel
 
 concurrency:

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: admiral
 Type: Package
 Title: ADaM in R Asset Library
-Version: 0.7.0
+Version: 0.7.1
 Authors@R: c(
     person("Thomas", "Neitmann", email = "[email protected]", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut"),

NEWS.md

@@ -1,3 +1,18 @@
+# admiral 0.7.1
+
+- `derive_vars_last_dose()` no longer fails when a variable renamed in `new_vars` is supplied
+to the `dose_date` parameter (#1206)
+
+- `derive_vars_duration()` updated to not display units when there is missing
+duration (#1207)
+
+- `derive_param_first_event()` was updated (#1214) such that
+    - `AVAL` is derived instead of `AVALN` and
+    - all variables from the source dataset are kept.
+
+- `slice_derivation()` was updated such that it no longer fails if a slice is
+empty (#1309)
+
 # admiral 0.7.0
 
 ## New Features

R/derive_param_first_event.R

@@ -73,6 +73,9 @@
 #'   subjects with event `AVALC` is set to `"Y"`, `AVAL` to `1`, and `ADT` to
 #'   the first date where the event condition is fulfilled. For all other
 #'   subjects `AVALC` is set to `"N"`, `AVAL` to `0`, and `ADT` to `NA`.
+#'   For subjects with event all variables from `dataset_source` are kept. For
+#'   subjects without event all variables which are in both `dataset_adsl` and
+#'   `dataset_source` are kept.
 #'   1. The variables specified by the `set_values_to` parameter are added to
 #'   the new observations.
 #'   1. The new observations are added to input dataset.
@@ -169,19 +172,26 @@ derive_param_first_event <- function(dataset,
   assert_param_does_not_exist(dataset, quo_get_expr(set_values_to$PARAMCD))
 
   # Create new observations
-  new_obs <- derive_vars_merged(
-    select(dataset_adsl, !!!subject_keys),
-    dataset_add = dataset_source,
-    filter_add = !!filter_source,
-    by_vars = subject_keys,
-    order = vars(!!date_var),
-    new_vars = vars(ADT = !!date_var),
-    mode = "first",
-    check_type = check_type
-  ) %>%
+  source_vars <- colnames(dataset_source)
+  adsl_vars <- colnames(dataset_adsl)
+
+  events <- dataset_source %>%
+    filter_if(filter_source) %>%
+    filter_extreme(
+      by_vars = subject_keys,
+      order = vars(!!date_var),
+      mode = "first",
+      check_type = check_type
+    )
+  noevents <- anti_join(
+    select(dataset_adsl, intersect(source_vars, adsl_vars)),
+    select(events, !!!subject_keys)
+  )
+  new_obs <- bind_rows(events, noevents) %>%
     mutate(
+      ADT = !!date_var,
       AVALC = if_else(!is.na(ADT), "Y", "N"),
-      AVALN = if_else(!is.na(ADT), 1, 0),
+      AVAL = if_else(!is.na(ADT), 1, 0),
       !!!set_values_to
     )
 

R/derive_var_ontrtfl.R

@@ -92,10 +92,11 @@
 #' @export
 #'
 #' @examples
+#' library(tibble)
 #' library(dplyr)
 #' library(lubridate, warn.conflict = FALSE)
 #'
-#' advs <- tibble::tribble(
+#' advs <- tribble(
 #'   ~USUBJID, ~ADT,              ~TRTSDT,           ~TRTEDT,
 #'   "P01",    ymd("2020-02-24"), ymd("2020-01-01"), ymd("2020-03-01"),
 #'   "P02",    ymd("2020-01-01"), ymd("2020-01-01"), ymd("2020-03-01"),
@@ -108,7 +109,7 @@
 #'   ref_end_date = TRTEDT
 #' )
 #'
-#' advs <- tibble::tribble(
+#' advs <- tribble(
 #'   ~USUBJID, ~ADT,              ~TRTSDT,           ~TRTEDT,
 #'   "P01",    ymd("2020-07-01"), ymd("2020-01-01"), ymd("2020-03-01"),
 #'   "P02",    ymd("2020-04-30"), ymd("2020-01-01"), ymd("2020-03-01"),
@@ -122,11 +123,11 @@
 #'   ref_end_window = 60
 #' )
 #'
-#' advs <- tibble::tribble(
-#'   ~USUBJID, ~ADTM,                   ~TRTSDTM,                   ~TRTEDTM,
-#'   "P01",    ymd("2020-01-02T12:00"), ymd_hm("2020-01-01T12:00"), ymd_hm("2020-03-01T12:00"),
-#'   "P02",    ymd("2020-01-01"),       ymd_hm("2020-01-01T12:00"), ymd_hm("2020-03-01T12:00"),
-#'   "P03",    ymd("2019-12-31"),       ymd_hm("2020-01-01T12:00"), ymd_hm("2020-03-01T12:00"),
+#' advs <- tribble(
+#'   ~USUBJID, ~ADTM,                      ~TRTSDTM,                   ~TRTEDTM,
+#'   "P01",    ymd_hm("2020-01-02T12:00"), ymd_hm("2020-01-01T12:00"), ymd_hm("2020-03-01T12:00"),
+#'   "P02",    ymd("2020-01-01"),          ymd_hm("2020-01-01T12:00"), ymd_hm("2020-03-01T12:00"),
+#'   "P03",    ymd("2019-12-31"),          ymd_hm("2020-01-01T12:00"), ymd_hm("2020-03-01T12:00"),
 #' ) %>%
 #'   mutate(TPT = c(NA, "PRE", NA))
 #' derive_var_ontrtfl(
@@ -137,7 +138,7 @@
 #'   filter_pre_timepoint = TPT == "PRE"
 #' )
 #'
-#' advs <- tibble::tribble(
+#' advs <- tribble(
 #'   ~USUBJID, ~ASTDT,            ~TRTSDT,           ~TRTEDT,           ~AENDT,
 #'   "P01",    ymd("2020-03-15"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-12-01"),
 #'   "P02",    ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-03-15"),
@@ -153,7 +154,7 @@
 #'   span_period = "Y"
 #' )
 #'
-#' advs <- tibble::tribble(
+#' advs <- tribble(
 #'   ~USUBJID, ~ASTDT,            ~AP01SDT,          ~AP01EDT,          ~AENDT,
 #'   "P01",    ymd("2020-03-15"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-12-01"),
 #'   "P02",    ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-03-15"),

R/derive_vars_duration.R

@@ -86,9 +86,15 @@
 #' @seealso [compute_duration()]
 #'
 #' @examples
-#' data <- tibble::tribble(
+#' library(lubridate)
+#' library(tibble)
+#'
+#' data <- tribble(
 #'   ~BRTHDT, ~RANDDT,
-#'   lubridate::ymd("1984-09-06"), lubridate::ymd("2020-02-24")
+#'   ymd("1984-09-06"), ymd("2020-02-24"),
+#'   ymd("1985-01-01"), NA,
+#'   NA, ymd("2021-03-10"),
+#'   NA, NA
 #' )
 #'
 #' derive_vars_duration(data,
@@ -143,7 +149,8 @@ derive_vars_duration <- function(dataset,
     )
 
   if (!quo_is_null(new_var_unit)) {
-    dataset <- dataset %>% mutate(!!new_var_unit := toupper(out_unit))
+    dataset <- dataset %>%
+      mutate(!!new_var_unit := if_else(is.na(!!new_var), NA_character_, toupper(out_unit)))
   }
 
   dataset

R/derive_vars_last_dose.R

@@ -1,26 +1,36 @@
 #' Derive Last Dose
 #'
 #' Add EX source variables from last dose to the input dataset.
+#'
 #' @param dataset Input dataset.
 #' The variables specified by the `by_vars` and `analysis_date` parameters are expected.
+#'
 #' @param dataset_ex Input EX dataset.
 #' The variables specified by the `by_vars`, `dose_date`, `new_vars` parameters,
 #' and source variables from `traceability_vars` parameter are expected.
+#'
 #' @param filter_ex Filtering condition applied to EX dataset.
 #' For example, it can be used to filter for valid dose.
 #' Defaults to NULL.
+#'
 #' @param by_vars Variables to join by (created by `dplyr::vars`).
+#'
 #' @param dose_id Variables to identify unique dose (created by `dplyr::vars`).
 #' Defaults to empty `vars()`.
+#'
 #' @param new_vars Variables to keep from `dataset_ex`, with the option to rename. Can either
 #' be variables created by `dplyr::vars` (e.g. `vars(VISIT)`), or named list returned by [`vars()`]
 #' (e.g. `vars(LSTEXVIS = VISIT)`). If set to `NULL`, then all variables from `dataset_ex` are
 #' kept without renaming.
 #' Defaults to `NULL`.
+#'
 #' @param dose_date The EX dose date variable. A date or date-time object is expected.
+#'
 #' @param analysis_date The analysis date variable. A date or date-time object is expected.
+#'
 #' @param single_dose_condition The condition for checking if `dataset_ex` is single dose. An error
 #' is issued if the condition is not true. Defaults to `(EXDOSFRQ == "ONCE")`.
+#'
 #' @param traceability_vars A named list returned by [`vars()`] listing the traceability variables,
 #' e.g. `vars(LDOSEDOM = "EX", LDOSESEQ = EXSEQ)`.
 #' The left-hand side (names of the list elements) gives the names of the traceability variables
@@ -29,14 +39,16 @@
 #' in the returned dataset.
 #' These can be either strings or symbols referring to existing variables.
 #'
-#' @details All date (date-time) variables can be characters in standard ISO format or
+#' @details
+#' All date (date-time) variables can be characters in standard ISO format or
 #' of date / date-time class.
 #' For ISO format, see [`impute_dtc`] - parameter `dtc` for further details.
 #' When doing date comparison to identify last dose, date-time imputations are done as follows:
 #' * `dose_date`: no date imputation, time imputation to `00:00:00` if time is missing.
 #' * `analysis_date`: no date imputation, time imputation to `23:59:59` if time is missing.
 #'
 #' The last dose records are identified as follows:
+#'
 #' 1. The `dataset_ex` is filtered using `filter_ex`, if provided.
 #' This is useful for, for example, filtering for valid dose only.
 #' 2. The datasets `dataset` and `dataset_ex` are joined using `by_vars`.
@@ -52,9 +64,9 @@
 #' `dataset` and returned to the user.
 #'
 #' This function only works correctly for EX dataset with a structure of single dose per row.
-#' If your study EX dataset has multiple doses per row, use `expansion_function_name??` to
+#' If your study EX dataset has multiple doses per row, use [`create_single_dose_dataset()`] to
 #' transform the EX dataset into single dose per row structure before calling
-#' `derive_vars_last_dose`.
+#' `derive_vars_last_dose()`.
 #'
 #' If variables (other than those specified in `by_vars`) exist in both `dataset` and `dataset_ex`,
 #' then join cannot be performed properly and an error is issued. To resolve the error, use
@@ -109,7 +121,7 @@ derive_vars_last_dose <- function(dataset,
                                   dose_id = vars(),
                                   dose_date,
                                   analysis_date,
-                                  single_dose_condition = (EXDOSFRQ == "ONCE"),
+                                  single_dose_condition = EXDOSFRQ == "ONCE",
                                   new_vars = NULL,
                                   traceability_vars = NULL) {
   filter_ex <- assert_filter_cond(enquo(filter_ex), optional = TRUE)
@@ -121,10 +133,12 @@ derive_vars_last_dose <- function(dataset,
   assert_varval_list(new_vars, optional = TRUE, accept_var = TRUE)
   assert_varval_list(traceability_vars, optional = TRUE)
   assert_data_frame(dataset, quo_c(by_vars, analysis_date))
-  assert_data_frame(dataset_ex, quo_c(
-    by_vars, dose_date, new_vars,
-    get_source_vars(traceability_vars)
-  ))
+  if (as_name(dose_date) %in% names(new_vars)) {
+    required_vars <- quo_c(by_vars, new_vars, get_source_vars(traceability_vars))
+  } else {
+    required_vars <- quo_c(by_vars, dose_date, new_vars, get_source_vars(traceability_vars))
+  }
+  assert_data_frame(dataset_ex, required_vars)
 
   # vars converted to string
   by_vars_str <- vars2chr(by_vars)
@@ -136,15 +150,22 @@ derive_vars_last_dose <- function(dataset,
     all()
 
   if (!single_dose_eval) {
-    stop("Specified single_dose_condition is not satisfied.")
+    stop("Specified `single_dose_condition` is not satisfied.")
   }
 
-  # check if doses are unique based on dose_date and dose_id
+  # check if doses are unique based on `dose_date` and `dose_id`
+  if (as_name(dose_date) %in% names(new_vars)) {
+    unique_by <- c(by_vars, new_vars[[as_name(dose_date)]], dose_id)
+  } else {
+    unique_by <- c(by_vars, dose_date, dose_id)
+  }
   signal_duplicate_records(
-    dataset_ex, c(by_vars, dose_date, dose_id),
-    "Multiple doses exist for the same dose_date. Update dose_id to identify unique doses."
+    dataset_ex,
+    unique_by,
+    "Multiple doses exist for the same `dose_date`. Update `dose_id` to identify unique doses."
   )
 
+
   # filter EX based on user-specified condition
   if (!is.null(quo_get_expr(filter_ex))) {
     dataset_ex <- dataset_ex %>%