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ready4-dev · Dec 23, 2022 · 39ad2a3 · 39ad2a3
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,113 +1,113 @@
-# Adapted from: https://github.com/ready4-dev/ready4class/runs/3657635374?check_suite_focus=true
-# NOTE: This workflow is overkill for most R packages
-# check-standard.yaml is likely a better choice
-# usethis::use_github_action("check-standard") will install it.
-#
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
-on:
- push:
- branches:
- - main
- - master
- pull_request:
- branches:
- - main
- - master
-
-name: R-CMD-check
-
-jobs:
- R-CMD-check:
- runs-on: ${{ matrix.config.os }}
-
- name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
- strategy:
- fail-fast: false
- matrix:
- config:
- - {os: macOS-latest, r: 'release'}
- - {os: windows-latest, r: 'release'}
- - {os: windows-latest, r: '3.6'}
- - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.0.0 (ubuntu-20.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
- - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-
- env:
- R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
- RSPM: ${{ matrix.config.rspm }}
- GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
- steps:
- - uses: actions/checkout@v2
-
- - uses: r-lib/actions/setup-r@master
- with:
- r-version: ${{ matrix.config.r }}
- http-user-agent: ${{ matrix.config.http-user-agent }}
-
- - uses: r-lib/actions/setup-pandoc@master
-
- - name: Query dependencies
- run: |
- install.packages('remotes')
- saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
- writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
- shell: Rscript {0}
-
- - name: Cache R packages
- if: runner.os != 'Windows' && !matrix.config.autobrew
- uses: actions/cache@v1
- with:
- path: ${{ env.R_LIBS_USER }}
- key: ${{ matrix.config.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
- restore-keys: ${{ matrix.config.os }}-${{ hashFiles('.github/R-version') }}-1-
-
- - name: Install system dependencies
- if: runner.os == 'Linux'
- run: |
- sudo apt-get install libharfbuzz-dev
- sudo apt-get install libfribidi-dev
- while read -r cmd
- do
- eval sudo $cmd
- done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
- - name: Install system dependencies
- if: runner.os == 'MacOS' && !matrix.config.autobrew
- run: brew install harfbuzz fribidi
-
- - name: Remove homebrew
- if: matrix.config.autobrew
- uses: autobrew/uninstall-homebrew@master
-
- - name: Install dependencies
- run: |
- remotes::install_deps(dependencies = TRUE)
- remotes::install_cran("rcmdcheck")
- shell: Rscript {0}
-
- - name: Session info
- run: |
- options(width = 100)
- pkgs <- installed.packages()[, "Package"]
- sessioninfo::session_info(pkgs, include_base = TRUE)
- shell: Rscript {0}
-
- - name: Check
- env:
- _R_CHECK_CRAN_INCOMING_: false
- run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
- shell: Rscript {0}
-
- - name: Show testthat output
- if: always()
- run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
- shell: bash
-
- - name: Upload check results
- if: failure()
- uses: actions/upload-artifact@main
- with:
- name: ${{ runner.os }}-r${{ matrix.config.r }}-results
- path: check
+# Adapted from: https://github.com/ready4-dev/ready4class/runs/3657635374?check_suite_focus=true
+# NOTE: This workflow is overkill for most R packages
+# check-standard.yaml is likely a better choice
+# usethis::use_github_action("check-standard") will install it.
+#
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+ push:
+ branches:
+ - main
+ - master
+ pull_request:
+ branches:
+ - main
+ - master
+
+name: R-CMD-check
+
+jobs:
+ R-CMD-check:
+ runs-on: ${{ matrix.config.os }}
+
+ name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - {os: macOS-latest, r: 'release'}
+ - {os: windows-latest, r: 'release'}
+ - {os: windows-latest, r: '3.6'}
+ - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.0.0 (ubuntu-20.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+ - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+ - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+ env:
+ R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+ RSPM: ${{ matrix.config.rspm }}
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+ steps:
+ - uses: actions/checkout@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: ${{ matrix.config.r }}
+ http-user-agent: ${{ matrix.config.http-user-agent }}
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - name: Query dependencies
+ run: |
+ install.packages('remotes')
+ saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+ writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+ shell: Rscript {0}
+
+ - name: Cache R packages
+ if: runner.os != 'Windows' && !matrix.config.autobrew
+ uses: actions/cache@v1
+ with:
+ path: ${{ env.R_LIBS_USER }}
+ key: ${{ matrix.config.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+ restore-keys: ${{ matrix.config.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+ - name: Install system dependencies
+ if: runner.os == 'Linux'
+ run: |
+ sudo apt-get install libharfbuzz-dev
+ sudo apt-get install libfribidi-dev
+ while read -r cmd
+ do
+ eval sudo $cmd
+ done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
+ - name: Install system dependencies
+ if: runner.os == 'MacOS' && !matrix.config.autobrew
+ run: brew install harfbuzz fribidi
+
+ - name: Remove homebrew
+ if: matrix.config.autobrew
+ uses: autobrew/uninstall-homebrew@master
+
+ - name: Install dependencies
+ run: |
+ remotes::install_deps(dependencies = TRUE)
+ remotes::install_cran("rcmdcheck")
+ shell: Rscript {0}
+
+ - name: Session info
+ run: |
+ options(width = 100)
+ pkgs <- installed.packages()[, "Package"]
+ sessioninfo::session_info(pkgs, include_base = TRUE)
+ shell: Rscript {0}
+
+ - name: Check
+ env:
+ _R_CHECK_CRAN_INCOMING_: false
+ run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+ shell: Rscript {0}
+
+ - name: Show testthat output
+ if: always()
+ run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+ shell: bash
+
+ - name: Upload check results
+ if: failure()
+ uses: actions/upload-artifact@main
+ with:
+ name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+ path: check
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,35 +1,46 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
-# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
-on:
- push:
- branches: [main, master]
- release:
- types: [published]
- workflow_dispatch:
-
-name: pkgdown
-
-jobs:
- pkgdown:
- runs-on: ubuntu-latest
- env:
- GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
- steps:
- - uses: actions/checkout@v2
-
- - uses: r-lib/actions/setup-pandoc@v1
-
- - uses: r-lib/actions/setup-r@v1
- with:
- use-public-rspm: true
-
- - uses: r-lib/actions/setup-r-dependencies@v1
- with:
- extra-packages: pkgdown
- needs: website
-
- - name: Deploy package
- run: |
- git config --local user.name "$GITHUB_ACTOR"
- git config --local user.email "[email protected]"
- Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+ release:
+ types: [published]
+ workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+ pkgdown:
+ runs-on: ubuntu-latest
+ # Only restrict concurrency for non-PR jobs
+ concurrency:
+ group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v3
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::XML, any::pkgdown, local::.
+ needs: website
+
+ - name: Build site
+ run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+ shell: Rscript {0}
+
+ - name: Deploy to GitHub pages 🚀
+ if: github.event_name != 'pull_request'
+ uses: JamesIves/[email protected]
+ with:
+ clean: false
+ branch: gh-pages
+ folder: docs
diff --git a/LICENSE b/LICENSE
@@ -1,15 +1,15 @@
-youthu - Transform Youth Outcomes to Health Utility Predictions
-Copyright (C) 2022 Orygen
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http:https://www.gnu.org/licenses/>.
+youthu - Transform Youth Outcomes to Health Utility Predictions with Ready4
+Copyright (C) 2022 Orygen
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http:https://www.gnu.org/licenses/>.
diff --git a/R/db_mdls_lup.R b/R/db_mdls_lup.R
@@ -1,14 +1,14 @@
-#' Lookup table of prediction models
-#' 
-#' A summary of the key descriptive features of the prediction models included in the youthu package.
-#' 
-#' A tibble
-#' 
-#' \describe{
-#' \item{mdl_nms_chr}{Model names (a character vector)}
-#' \item{predrs_ls}{Predictors (a list)}
-#' \item{mdl_type_chr}{Model type (a character vector)}
-#' \item{tfmn_chr}{Transformation (a character vector)}
-#' \item{source_chr}{Source (a character vector)}
-#' }
-"mdls_lup"
+#' Lookup table of prediction models
+#' 
+#' A summary of the key descriptive features of the prediction models included in the youthu package.
+#' 
+#' A tibble
+#' 
+#' \describe{
+#' \item{mdl_nms_chr}{Model names (a character vector)}
+#' \item{predrs_ls}{Predictors (a list)}
+#' \item{mdl_type_chr}{Model type (a character vector)}
+#' \item{tfmn_chr}{Transformation (a character vector)}
+#' \item{source_chr}{Source (a character vector)}
+#' }
+"mdls_lup"