redo for updated dpcys

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

@@ -1,7 +1,4 @@
 # 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
@@ -29,85 +26,43 @@ jobs:
  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"}
+ - {os: ubuntu-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: actions/checkout@v3 #
  - uses: r-lib/actions/setup-r@v2
- with:
- r-version: ${{ matrix.config.r }}
- http-user-agent: ${{ matrix.config.http-user-agent }}
-
+ # with:
+ # r-version: ${{ matrix.config.r }}
+ # http-user-agent: ${{ matrix.config.http-user-agent }}
+ # use-public-rspm: true
+ - uses: r-lib/actions/setup-tinytex@v2
+ - run: tlmgr --version
  - uses: r-lib/actions/setup-pandoc@v2
-
- - name: Query dependencies
- run: |
- install.packages('remotes')
- saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
- writeLines(sprintf("R-%i.%i", getRversion()$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
+ pandoc-version: '2.17.1' # The pandoc version to download (if necessary) and use.
+ - run: echo "# Test" | pandoc -t html
+ # Addresses issue with incompatibility between libcurl4-gnutls-dev and libcurl4-openssl-dev
+ # Below fix is a customisation of approach outlined in https://github.com/r-hub/sysreqsdb/issues/77#issuecomment-620025428
+ - name: Install libraptor on Linux
  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
+ sudo add-apt-repository ppa:cran/librdf
+ sudo apt update
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::XML, any::rcmdcheck
+ needs: check
+ - uses: r-lib/actions/check-r-package@v2
  with:
- name: ${{ runner.os }}-r${{ matrix.config.r }}-results
- path: check
+ args: 'c("--no-manual", "--as-cran")'
+ error-on: '"error"'
+ check-dir: '"check"'

.github/workflows/pkgdown.yaml

@@ -19,15 +19,27 @@ jobs:
  group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
  env:
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ permissions:
+ contents: write
  steps:
  - uses: actions/checkout@v3
 
+ - uses: r-lib/actions/setup-tinytex@v2
+
  - uses: r-lib/actions/setup-pandoc@v2
 
  - uses: r-lib/actions/setup-r@v2
  with:
  use-public-rspm: true
 
+ # Addresses issue with incompatibility between libcurl4-gnutls-dev and libcurl4-openssl-dev
+ # Below fix is a customisation of approach outlined in https://github.com/r-hub/sysreqsdb/issues/77#issuecomment-620025428
+ - name: Install libraptor on Linux
+ if: runner.os == 'Linux'
+ run: |
+ sudo add-apt-repository ppa:cran/librdf
+ sudo apt update
+
  - uses: r-lib/actions/setup-r-dependencies@v2
  with:
  extra-packages: any::XML, any::pkgdown, local::.

LICENSE

@@ -1,4 +1,4 @@
-youthu - Transform Youth Outcomes to Health Utility Predictions with Ready4
+youthu - Transform Youth Outcomes to Health Utility Predictions
 Copyright (C) 2023 Orygen
 
 This program is free software: you can redistribute it and/or modify

README.md

@@ -1,21 +1,21 @@
 # youthu
 
-## Transform Youth Outcomes to Health Utility Predictions with Ready4
+## Transform Youth Outcomes to Health Utility Predictions
 
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
-[![ready4](https://img.shields.io/badge/ready4-prediction-forestgreen?style=flat&labelColor=black&logo=data:image/png;base64,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)](https://www.ready4-dev.com/toolkits/)
+[![ready4](https://img.shields.io/badge/ready4-prediction-forestgreen?style=flat&labelColor=black&logo=data:image/png;base64,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)](https://www.ready4-dev.com/docs/software/libraries/types/module/)
 [![R-CMD-check](https://github.com/ready4-dev/youthu/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ready4-dev/youthu/actions/workflows/R-CMD-check.yaml)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5646668.svg)](https://doi.org/10.5281/zenodo.5646668)
 <!-- badges: end -->
 
 Tools for mapping measures routinely collected in youth
 mental health services to Quality Adjusted Life Years (QALYs). Part of
 the ready4 youth mental health systems model
-(https://www.ready4-dev.com/). This development version of the youthu
-package has been made available as part of the process of testing and
-documenting the package. If you have any questions, please contact the
-authors (matthew.[email protected]).
+(https://www.ready4-dev.com/docs/model/). This development version of
+the youthu package has been made available as part of the process of
+testing and documenting the package. If you have any questions, please
+contact the authors (matthew.[email protected]).
 
 To install a development version of this software, run the following commands in your R console:
 

_pkgdown.yml

@@ -10,7 +10,7 @@ home:
  href: https://github.com/ready4-dev/youthu/releases/download/Documentation_0.0/youthu_User.pdf
  - text: Manual - Developer (PDF)
  href: https://github.com/ready4-dev/youthu/releases/download/Documentation_0.0/youthu_Developer.pdf
- - text: Model
+ - text: Framework & Model
  href: https://www.ready4-dev.com/
 development:
  mode: auto

data-raw/DATASET.R

@@ -1,18 +1,18 @@
-library(generics)
+#library(generics)
 library(ready4)
 library(ready4show)
 library(ready4use)
 library(youthvars)
-library(scorz)
+#library(scorz)
 library(specific)
 ready4fun::write_fn_type_dirs()
 # MANUAL STEP. Write all your functions to R files in the new "fns" directory.
 fns_env_ls <- ready4fun::read_fns(c("data-raw/fns/","data-raw/mthds/"),
  fns_env = new.env(parent = globalenv()))
-x <- ready4fun::make_pkg_desc_ls(pkg_title_1L_chr = "Transform Youth Outcomes to Health Utility Predictions With Ready4",
- pkg_desc_1L_chr = "Tools for mapping measures routinely collected in youth mental health services to Quality Adjusted Life Years (QALYs). Part of the ready4 youth mental health systems model (https://www.ready4-dev.com/).
- This development version of the youthu package has been made available as part of the process of testing and documenting the package. If you have any questions, please contact the authors (matthew.[email protected]).",
- authors_prsn = c(utils::person(given = "Matthew",family = "Hamilton",email = "matthew.[email protected]", role = c("aut", "cre"),comment = c(ORCID = "0000-0001-7407-9194")),
+x <- ready4fun::make_pkg_desc_ls(pkg_title_1L_chr = "Transform Youth Outcomes to Health Utility Predictions",
+ pkg_desc_1L_chr = "Tools for mapping measures routinely collected in youth mental health services to Quality Adjusted Life Years (QALYs). Part of the ready4 youth mental health systems model (https://www.ready4-dev.com/docs/model/).
+ This development version of the youthu package has been made available as part of the process of testing and documenting the package. If you have any questions, please contact the authors (matthew.[email protected]).",
+ authors_prsn = c(utils::person(given = "Matthew",family = "Hamilton",email = "matthew.[email protected]", role = c("aut", "cre"),comment = c(ORCID = "0000-0001-7407-9194")),
  utils::person(given = "Caroline",family = "Gao",email = "[email protected]", role = c("aut"),comment = c(ORCID = "0000-0002-0987-2759")),
  utils::person("Orygen", role = c("cph", "fnd")),
  utils::person("Headspace", role = c( "fnd")),
@@ -54,7 +54,11 @@ z <- ready4pack::make_pt_ready4pack_manifest(x,
  pkg_ds_ls_ls = datasets_ls) %>%
  ready4pack::ready4pack_manifest()
 z <- ready4::author(z)
-ready4::write_extra_pkgs_to_actions()
+ready4::write_extra_pkgs_to_actions(consent_1L_chr = "Y")
+write_to_edit_workflow("pkgdown.yaml", consent_1L_chr = "Y") # In other packages, run for "test-coverage.yaml" as well.
+readLines("_pkgdown.yml") %>%
+ stringr::str_replace_all(" - text: Model", " - text: Framework & Model") %>%
+ writeLines(con = "_pkgdown.yml")
 devtools::build_vignettes()
 # ready4::write_citation_cff(packageDescription("youthu"),
 # citation_chr = readLines("inst/CITATION"))

inst/CITATION

@@ -4,11 +4,11 @@ citEntry(
  entry = "Manual",
  doi = "10.5281/zenodo.5646668",
  title = paste0(meta$Package,": ",meta$Title),
- author = c(person("Matthew Hamilton <matthew.[email protected]> [aut, cre]", "(<https://orcid.org/0000-0001-7407-9194>)"), person("Caroline Gao <[email protected]> [aut]", "(<https://orcid.org/0000-0002-0987-2759>)")),
+ author = c(person("Matthew Hamilton <matthew.[email protected]> [aut, cre]", "(<https://orcid.org/0000-0001-7407-9194>)"), person("Caroline Gao <[email protected]> [aut]", "(<https://orcid.org/0000-0002-0987-2759>)")),
  year = "2023",
  note = sprintf("R package version %s", meta$Version),
  url = "https://ready4-dev.github.io/youthu/",
- textVersion = paste("Matthew Hamilton <matthew.[email protected]> [aut, cre] (<https://orcid.org/0000-0001-7407-9194>) and Caroline Gao <[email protected]> [aut] (<https://orcid.org/0000-0002-0987-2759>) ",
+ textVersion = paste("Matthew Hamilton <matthew.[email protected]> [aut, cre] (<https://orcid.org/0000-0001-7407-9194>) and Caroline Gao <[email protected]> [aut] (<https://orcid.org/0000-0002-0987-2759>) ",
  "(2023).",
  paste0(meta$Package,": ",meta$Title,
  "."),