diff --git a/.github/workflows/stale-bot.yml b/.github/workflows/stale-bot.yml new file mode 100644 index 0000000000..d25d15ba91 --- /dev/null +++ b/.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 }} diff --git a/.lycheeignore b/.lycheeignore index 7dbdbcd3c2..5774d2a153 100644 --- a/.lycheeignore +++ b/.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/CodeCoverageSummary@v1.2.0 https://packagemanager.rstudio.com/cran/__linux__/focal/latest -https://pharmaverse.github.io/admiral/articles/higher_order.html diff --git a/R/derive_param_tte.R b/R/derive_param_tte.R index bbc9526fad..9b5069813d 100644 --- a/R/derive_param_tte.R +++ b/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. diff --git a/README.md b/README.md index 1c1ec08ec0..392bec6e79 100644 --- a/README.md +++ b/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 diff --git a/inst/WORDLIST b/inst/WORDLIST index d7b74865a6..6b3eb2fcc9 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -336,3 +336,7 @@ xportr xpt α κ +admiraldev +admiralophtha +admiralvaccine + diff --git a/man/derive_param_tte.Rd b/man/derive_param_tte.Rd index 8edb228af9..4177cbf61f 100644 --- a/man/derive_param_tte.Rd +++ b/man/derive_param_tte.Rd @@ -24,7 +24,7 @@ The \code{PARAMCD} variable is expected.} \item{dataset_adsl}{ADSL input dataset -The variables specified for \code{start_date}, \code{start_imputation_flag}, and +The variables specified for \code{start_date}, and \code{subject_keys} are expected.} \item{source_datasets}{Source datasets @@ -49,10 +49,7 @@ The variable \code{STARTDT} is set to the specified date. The value is taken from the ADSL dataset. If the event or censoring date is before the origin date, \code{ADT} is set to -the origin date. - -If the specified variable is imputed, the corresponding date imputation -flag must specified for \code{start_imputation_flag}.} +the origin date.} \item{event_conditions}{Sources and conditions defining events @@ -136,8 +133,8 @@ selected. Otherwise the censoring observation is selected. Finally: \enumerate{ -\item The variables specified for \code{start_date} and \code{start_imputation_flag} are -joined from the ADSL dataset. Only subjects in both datasets are kept, +\item The variable specified for \code{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 \code{dataset_adsl}. \item The variables as defined by the \code{set_values_to} parameter are added.