[skip vbump] Closes #2635: 1.2 Release

DESCRIPTION

@@ -40,9 +40,9 @@ URL: https://pharmaverse.github.io/admiral/,
     https://github.com/pharmaverse/admiral
 BugReports: https://github.com/pharmaverse/admiral/issues
 Depends: 
-    R (>= 4.0)
+    R (>= 4.1)
 Imports:
-    admiraldev (>= 1.1.0.9007),
+    admiraldev (>= 1.2.0),
     cli (>= 3.6.2),
     dplyr (>= 1.0.5),
     hms (>= 0.5.3),

NEWS.md

@@ -8,19 +8,16 @@
 (`CRITy`, `CRITyFL`, `CRITyFN`). (#2468)
 - New function `transform_range()`  to transform values from a source range to a
 target range. (#2571)
-- Replace use of `data("sdtm")` with `sdtm <- pharmaverse::sdtm` in templates and vignettes. (#2498)
-
-- Remove `dthcaus_source()` calls in `ADSL` template because they are deprecated. (#2517)
-- Update `ADEG` template to flag `ABLFL` and `ANL01FL` based on `DTYPE == "AVERAGE"` records. (#2561)
 
 ## Updates of Existing Functions
-- added `"message"` as option for `check_type` argument in `derive_var_obs_number()` function. (#2481)
 
-- added `"message"` as option for `check_type` argument in `filter_extreme()` function. (#2481)
+- Added `"message"` as option for `check_type` argument in `derive_var_obs_number()` function. (#2481)
+
+- Added `"message"` as option for `check_type` argument in `filter_extreme()` function. (#2481)
 
 - Users can now specify how duplicate records are handled in `derive_param_tte()` using the `check_type` argument, with options including `"error"`, `"warning"`, `"message"`, or `"none"`, allowing for greater flexibility in managing duplicate data scenarios. (#2481)
 
-- `order` argument has been added to `event_source()` and `censor_source()` and  
+- The `order` argument has been added to `event_source()` and `censor_source()` and  
   defaulted to `NULL` to allow specifying variables in addition to the date variable. This can be used to ensure the uniqueness of the select records if there is more than one record per date.  (#2481)  
 
 - NCICTCAEv5 grading criteria (`atoxgr_criteria_ctcv5`):
@@ -47,7 +44,7 @@ or that the queries dataset contains duplicates. (#2543)
 
 - `derive_vars_atc()` and `create_single_dose_dataset()` `by_vars` argument updated to use `get_admiral_option("subject_keys")` instead of  `USUBJID` or `STUDYID` in `bds_exposure.Rmd`. (#2501)
 
-- test scripts, R, and markdown files for `create_single_dose_dataset` and `occds.Rmd` updated to include a `STUDYID` column because of `get_admiral_option("subject_keys")` update above. (#2501)
+- The test scripts, R, and markdown files for `create_single_dose_dataset()` and `occds.Rmd` updated to include a `STUDYID` column because of `get_admiral_option("subject_keys")` update above. (#2501)
 
 - Update `derive_vars_period()` to make it work when there is only one new variable. (#2582)
 
@@ -118,6 +115,10 @@ one in `censor_conditions`). (#2639)
 
 ## Various
 
+- Replace use of `data("sdtm")` with `sdtm <- pharmaverse::sdtm` in templates and vignettes. (#2498)
+- Remove `dthcaus_source()` calls in `ADSL` template because they are deprecated. (#2517)
+- Update `ADEG` template to flag `ABLFL` and `ANL01FL` based on `DTYPE == "AVERAGE"` records. (#2561)
+
 <details>
 <summary>Developer Notes</summary>
 

R/data.R

@@ -4,7 +4,7 @@
 #' @keywords datasets
 #' @family datasets
 #' @source
-#' Derived from the `ex` dataset using `{admiral}` and `{dplyr}` (\url{https://github.com/pharmaverse/admiral/blob/main/inst/example_scripts/derive_single_dose.R})
+#' Derived from the `ex` dataset using `{admiral}` and `{dplyr}` (\url{https://github.com/pharmaverse/admiral/blob/main/data-raw/create_ex_single.R})
 "ex_single"
 
 #' Example `QS` Dataset
@@ -17,7 +17,7 @@
 #' @keywords datasets
 #' @family datasets
 #' @source
-#' Created by (\url{https://github.com/pharmaverse/admiral/blob/main/inst/example_scripts/example_qs.R})
+#' Created by (\url{https://github.com/pharmaverse/admiral/blob/main/data-raw/create_example_qs.R})
 "example_qs"
 
 #' Queries Dataset

README.md

@@ -26,8 +26,7 @@ install.packages("admiral")
 To install the development version of the package from GitHub run:
 
 ```r
-# install.packages("devtools")
-devtools::install_github("pharmaverse/admiral")
+pak::pkg_install("admiral", dependencies = TRUE)
 ```
 
 ## Cheat Sheet
@@ -41,18 +40,22 @@ The `{admiral}` family has several downstream and upstream dependencies and so r
 * Phase 1 release is for [{admiraldev}](https://pharmaverse.github.io/admiraldev/), [{pharmaversesdtm}](https://pharmaverse.github.io/pharmaversesdtm/), and [{admiral}](https://pharmaverse.github.io/admiral/) core
 * Phase 2 release is extension packages, e.g. [{admiralonco}](https://pharmaverse.github.io/admiralonco/), [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/), [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/) and [{pharmaverseadam}](https://pharmaverse.github.io/pharmaverseadam/).
 
-| Release Schedule | Phase 1- Date and Packages                                               | Phase 2- Date and Packages                                        |
-| ---------------- | ------------------------------------------------------------------------ | ----------------------------------------------------------------- |
-|                  |                                                                          |                                                                   |
-| Q4-2024          | December 2nd                                                             | December 9th                                                      |
-|                  | [{pharmaversesdtm}](https://pharmaverse.github.io/pharmaversesdtm/)      | [{admiralonco}](https://pharmaverse.github.io/admiralonco/)       |
-|                  | [{admiraldev}](https://pharmaverse.github.io/admiraldev/)                | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/)   |
-|                  | [{admiral}](https://pharmaverse.github.io/admiral/)                      | [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/) |                        |                  |                                                                          | [{pharmaverseadam}](https://pharmaverse.github.io/pharmaverseadam/)  |
-|                  |                                                                          |                                                                   | 
-| Q2-2025          | June 2nd                                                                 | June 10th                                                      |
-|                  | [{pharmaversesdtm}](https://pharmaverse.github.io/pharmaversesdtm/)      | [{admiralonco}](https://pharmaverse.github.io/admiralonco/)       |
-|                  | [{admiraldev}](https://pharmaverse.github.io/admiraldev/)                | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/)   |
-|                  | [{admiral}](https://pharmaverse.github.io/admiral/)                      | [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/) |                        |                  |                                                                          | [{pharmaverseadam}](https://pharmaverse.github.io/pharmaverseadam/)   |                                                                       
+__NB:__ We strive for a regular 6 month release schedule.
+
+| Release Schedule | Phase 1- Date and Packages                                               | Phase 2- Date and Packages                                         |
+| ---------------- | ------------------------------------------------------------------------ | ------------------------------------------------------------------ |
+|                  |                                                                          |                                                                    |
+| Q2-2025          | mid-June                                                                 | mid-June                                                           |
+|                  | [{pharmaversesdtm}](https://pharmaverse.github.io/pharmaversesdtm/)      | [{admiralonco}](https://pharmaverse.github.io/admiralonco/)        |
+|                  | [{admiraldev}](https://pharmaverse.github.io/admiraldev/)                | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/)    |
+|                  | [{admiral}](https://pharmaverse.github.io/admiral/)                      | [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/)  |                        
+|                  |                                                                          | [{pharmaverseadam}](https://pharmaverse.github.io/pharmaverseadam/)|
+|                  |                                                                          |                                                                    | 
+| Q4-2025/Q1 2026  | late December 2025/early January 2026                                    | late December 2025/early January 2026                              |
+|                  | [{pharmaversesdtm}](https://pharmaverse.github.io/pharmaversesdtm/)      | [{admiralonco}](https://pharmaverse.github.io/admiralonco/)        |
+|                  | [{admiraldev}](https://pharmaverse.github.io/admiraldev/)                | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/)    |
+|                  | [{admiral}](https://pharmaverse.github.io/admiral/)                      | [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/)  |                        
+|                  |                                                                          | [{pharmaverseadam}](https://pharmaverse.github.io/pharmaverseadam/)|                                                                       
 
 ## Main Goal
 

vignettes/faq.Rmd

@@ -50,7 +50,7 @@ knitr::opts_chunk$set(
 ##### Admiral offers a **toolbox of functions to facilitate ADaM**. What does that mean?
 
 * Functions are usually parameter driven: 
-    * e.g. the `derive_vars_aage` has a parameterized start and end-date and a unit.
+    * e.g. the `derive_vars_aage()` has a parameterized start and end-date and a unit.
     * Depending on the parameters results may vary as does the specification.
     * Functions serve as a toolbox so the user can create their ADaM according to the requirements.
     * The principles, programming strategy and documentation of `{admiral}` are considered as a framework for users to contribute.
@@ -65,6 +65,8 @@ knitr::opts_chunk$set(
 
 * A [Cheat Sheet](https://github.com/pharmaverse/admiral/blob/main/inst/cheatsheet/admiral_cheatsheet.pdf) is available, providing some examples of the many `{admiral}` functions. 
 * For more detailed description, please refer to the [Reference section](https://pharmaverse.github.io/admiral/reference/index.html). 
+* [admiraldiscovery](https://pharmaverse.github.io/admiraldiscovery/articles/reactable.html) provides
+a way to look up common ADaM variables with recommended `{admiral}` functions to complete the derivation.
 
 ##### Would `{admiral}` **create a whole** ADaM  dataset?
 

vignettes/lab_grading.Rmd

@@ -482,12 +482,12 @@ atoxgr_criteria_ctcv4 %>%
 
 Grading is implemented for those lab tests where a lab value is included in the grading definition,
 `{admiral}` does NOT try to read any other data to determine the grade, and only the `ADLB` dataset is used.
-The following CTCAE v5.0 SOC values were identified for grading, these are “Investigations", 
-“Metabolism and nutrition disorders” and “Blood and lymphatic system disorders”.
+The following CTCAE v5.0 SOC values were identified for grading, these are "Investigations", 
+"Metabolism and nutrition disorders" and "Blood and lymphatic system disorders".
 
 From these SOC values the following terms criteria is implemented in `{admiral}` 
 
-From SOC = “Investigations" there are 21 CTCAE v5.0 Terms:
+From SOC = "Investigations" there are 21 CTCAE v5.0 Terms:
 
   + Activated partial thromboplastin time prolonged
   + Alanine aminotransferase increased
@@ -513,7 +513,7 @@ From SOC = “Investigations" there are 21 CTCAE v5.0 Terms:
 
 Note: These are the same terms identified for NCI-CTCAEv4.
 
-From the SOC =  “Metabolism and nutrition disorders” there are 12 CTCAE v4.0 Terms:
+From the SOC =  "Metabolism and nutrition disorders" there are 12 CTCAE v4.0 Terms:
 
   + Hypercalcemia
   + Hyperkalemia
@@ -531,7 +531,7 @@ From the SOC =  “Metabolism and nutrition disorders” there are 12 CTCAE v4.0
 Note: These are the same terms identified for NCI-CTCAEv4, except "Hypophosphatemia"
 and "Hyperglycemia" which are not in NCICTCAEv5 grading criteria.
 
-From the SOC =  “Blood and lymphatic system disorders” there are 2 CTCAE v4.0 Terms:
+From the SOC =  "Blood and lymphatic system disorders" there are 2 CTCAE v4.0 Terms:
 
   + Anemia
   + Leukocytosis