Merge branch 'devel' into 1960_enhance_derive_extreme_event@devel

.github/workflows/stale-bot.yml

@@ -0,0 +1,25 @@
+# https://github.com/actions/stale
+
+name: Close Inactive Issues and Pull Requests
+on:
+  schedule:
+    - cron: "30 1 * * *"
+
+jobs:
+  close-issues:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v8
+        with:
+          days-before-issue-stale: 90
+          days-before-issue-close: -1
+          stale-issue-label: "stale"
+          stale-issue-message: "This issue is stale because it has been open for 90 days with no activity."
+          days-before-pr-stale: 15
+          days-before-pr-close: -1
+          stale-pr-label: "stale"
+          stale-pr-message: "This Pull Request is stale because it has not been worked on in 15 days."
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.lycheeignore

@@ -3,4 +3,3 @@ https://github.com/pharmaverse/admiral/blob/main/
 https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adxx.R
 irongut/[email protected]
 https://packagemanager.rstudio.com/cran/__linux__/focal/latest
-https://pharmaverse.github.io/admiral/articles/higher_order.html

R/derive_param_tte.R

@@ -8,7 +8,7 @@
 #'
 #' @param dataset_adsl ADSL input dataset
 #'
-#'   The variables specified for `start_date`, `start_imputation_flag`, and
+#'   The variables specified for `start_date`, and
 #'   `subject_keys` are expected.
 #'
 #' @param source_datasets Source datasets
@@ -35,9 +35,6 @@
 #'   If the event or censoring date is before the origin date, `ADT` is set to
 #'   the origin date.
 #'
-#'   If the specified variable is imputed, the corresponding date imputation
-#'   flag must specified for `start_imputation_flag`.
-#'
 #' @param event_conditions Sources and conditions defining events
 #'
 #'   A list of `event_source()` objects is expected.
@@ -112,8 +109,8 @@
 #'   selected. Otherwise the censoring observation is selected.
 #'
 #'   Finally:
-#'   1. The variables specified for `start_date` and `start_imputation_flag` are
-#'   joined from the ADSL dataset. Only subjects in both datasets are kept,
+#'   1. The variable specified for `start_date` is joined from the
+#'   ADSL dataset. Only subjects in both datasets are kept,
 #'   i.e., subjects with both an event or censoring and an observation in
 #'   `dataset_adsl`.
 #'   1. The variables as defined by the `set_values_to` parameter are added.

README.md

@@ -33,21 +33,24 @@ remotes::install_github("pharmaverse/admiral")
 
 ## Release Schedule
 
-`{admiral}` releases are targeted for the first Monday of the last month of each quarter.  Pull Requests will be frozen the week before a release.
-The `admiral` family has several downstream and upstream dependencies and so this release shall be done in three
+[{admiral}](https://pharmaverse.github.io/admiral/cran-release/)` releases are targeted for the first Monday of the last month of each quarter.  Pull Requests will be frozen the week before a release.
+The {admiral} family has several downstream and upstream dependencies and so this release shall be done in three
 Phases:
 
-* Phase 1 release is for `{admiraldev}`, `{admiral.test}`, and `{admiral}` core
-* Phase 2 release is extension packages, e.g. `{admiralonco}`, `admiralophtha`
-
-| Release Schedule | Phase 1- Date and Packages      | Phase 2- Date and Packages |
-| ---------------- | ------------------------------- | -------------------------- |
-| Q3-2023          | September 4th                   | September 11th             |
-|                  | `{admiraldev}` `{admiral.test}` | `{admiralonco}`            |
-|                  | `{admiral}`                     | `{admiralophtha}`          |
-| Q4-2023          | December 4th                    | December 11th              |
-|                  | `{admiraldev}` `{admiral.test}` | `{admiralonco}`            |
-|                  | `{admiral}`                     | `{admiralophtha}`          |
+* Phase 1 release is for [{admiraldev}](https://pharmaverse.github.io/admiraldev/main/), {admiral.test}, and [{admiral}](https://pharmaverse.github.io/admiral/cran-release/) core 
+* Phase 2 release is extension packages, e.g. [{admiralonco}](https://pharmaverse.github.io/admiralonco/main/), [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/main/), [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/main/)
+
+
+|Release Schedule | Phase 1- Date and Packages                                        | Phase 2- Date and Packages                                                    |
+|---------------- | --------------------------                                        | --------------------------                                                    |   
+| Q3-2023         | September 4th                                                     | September 11th                                                                | 
+|                 | [{admiraldev}](https://pharmaverse.github.io/admiraldev/main/)    | [{admiralonco}](https://pharmaverse.github.io/admiralonco/main/)              | 
+|                 | {admiral.test}                                                    | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/main/)          | 
+|                 | [{admiral}](https://pharmaverse.github.io/admiral/main/)          | [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/main/)        | 
+| Q4-2023         | December 4th                                                      | December 11th                                                                 | 
+|                 | [{admiraldev}](https://pharmaverse.github.io/admiraldev/main/)    | [{admiralonco}](https://pharmaverse.github.io/admiralonco/main/)              |
+|                 | {admiral.test}                                                    | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/main/)          |  
+|                 | [{admiral}](https://pharmaverse.github.io/admiral/main/)          | [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/main/)        | 
 
 ## Main Goal
 

inst/WORDLIST

@@ -336,3 +336,7 @@ xportr
 xpt
 α
 κ
+admiraldev
+admiralophtha
+admiralvaccine
+