migration in from fbaqol

.Rbuildignore

@@ -0,0 +1,28 @@
+^map2aqol\.Rproj$
+^\.Rproj\.user$
+^data-raw$
+^LICENSE\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^data-raw/DATASET\.R$
+^data-raw/fns/add\.R$
+^data-raw/fns/calculate\.R$
+^data-raw/fns/extract\.R$
+^data-raw/fns/fit\.R$
+^data-raw/fns/force\.R$
+^data-raw/fns/get\.R$
+^data-raw/fns/impute\.R$
+^data-raw/fns/knit\.R$
+^data-raw/fns/make\.R$
+^data-raw/fns/plot\.R$
+^data-raw/fns/predict\.R$
+^data-raw/fns/print\.R$
+^data-raw/fns/randomise\.R$
+^data-raw/fns/reorder\.R$
+^data-raw/fns/replace\.R$
+^data-raw/fns/scramble\.R$
+^data-raw/fns/transform\.R$
+^data-raw/fns/write\.R$
+^data-raw/map2aqol_DATASET\.R$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

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+# 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: windows-latest, r: 'release'}
+ - {os: macOS-latest, r: 'release'}
+ - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+ - {os: ubuntu-20.04, r: 'devel', 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@v1
+ with:
+ r-version: ${{ matrix.config.r }}
+
+ - uses: r-lib/actions/setup-pandoc@v1
+
+ - name: Query dependencies
+ run: |
+ install.packages('remotes')
+ saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+ writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+ shell: Rscript {0}
+
+ - name: Cache R packages
+ if: runner.os != 'Windows'
+ uses: actions/cache@v2
+ with:
+ path: ${{ env.R_LIBS_USER }}
+ key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+ restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+ - name: Install system dependencies
+ if: runner.os == 'Linux'
+ run: |
+ while read -r cmd
+ do
+ eval sudo $cmd
+ done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+ - name: Install dependencies
+ run: |
+ remotes::install_deps(dependencies = TRUE)
+ remotes::install_cran("rcmdcheck")
+ shell: Rscript {0}
+
+ - name: Check
+ env:
+ _R_CHECK_CRAN_INCOMING_REMOTE_: false
+ run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+ shell: Rscript {0}
+
+ - name: Upload check results
+ if: failure()
+ uses: actions/upload-artifact@main
+ with:
+ name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+ path: check

.github/workflows/pkgdown.yaml

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+on:
+ push:
+ branches:
+ - main
+ - master
+
+name: pkgdown
+
+jobs:
+ pkgdown:
+ runs-on: macOS-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v2
+
+ - uses: r-lib/actions/setup-r@v1
+
+ - uses: r-lib/actions/setup-pandoc@v1
+
+ - name: Query dependencies
+ run: |
+ install.packages('remotes')
+ saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+ writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+ shell: Rscript {0}
+
+ - name: Cache R packages
+ uses: actions/cache@v2
+ with:
+ path: ${{ env.R_LIBS_USER }}
+ key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+ restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+ - name: Install dependencies
+ run: |
+ remotes::install_deps(dependencies = TRUE)
+ install.packages("pkgdown", type = "binary")
+ shell: Rscript {0}
+
+ - name: Install package
+ run: R CMD INSTALL .
+
+ - name: Deploy package
+ run: |
+ git config --local user.email "[email protected]"
+ git config --local user.name "GitHub Actions"
+ Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

DESCRIPTION

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+Package: map2aqol
+Title: Map Measures Routinely Collected in Mental Health
+ Services To AQOL 6D Health Utility.
+Version: 0.0.0.9001
+Authors@R: 
+ c(person(given = "Caroline",
+ family = "Gao",
+ role = "aut",
+ email = "[email protected]",
+ comment = c(ORCID = "0000-0002-0987-2759")),
+ person(given = "Matthew",
+ family = "Hamilton",
+ role = c("aut", "cre"),
+ email = "[email protected]",
+ comment = c(ORCID = "0000-0001-7407-9194")),
+ person(given = "Orygen",
+ role = c("cph", "fnd")),
+ person(given = "Headspace",
+ role = "fnd"),
+ person(given = "National Health and Medical Research Council",
+ role = "fnd"))
+Description: Tools for mapping measures routinely collected in
+ youth mental health services to AQOL 6D Health Utility. Part of the
+ First Bounce model of primary youth mental health services. This
+ development version of the map2aqol package has been made available as
+ part of the process of testing and documenting the package. The tools
+ contained in this development release automate a number of tasks which
+ MODIFY THE DIRECTORY STRUCTURE OF YOUR LOCAL MACHINE. Therefore you
+ should only trial this software if you feel confident that you
+ understand what it does and have created a sandpit area in which you
+ can safely undertake testing. If you have any questions, please
+ contact the authors ([email protected]). The
+ documentation for this package has been automatically generated by the
+ ready4fun package and is therefore quite rudimentary. Human authored
+ documentation will follow in 2021.
+License: GPL-3 + file LICENSE
+URL: https://ready4-dev.github.io/map2aqol/,
+ https://github.com/ready4-dev/map2aqol,
+ https://ready4-dev.github.io/ready4/
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.1
+Imports: 
+ testthat,
+ knitr,
+ lifecycle,
+ ready4fun (>= 0.0.0.9255),
+ brms,
+ caret,
+ dplyr,
+ flextable,
+ ggalt,
+ ggplot2,
+ Hmisc,
+ hutils,
+ kableExtra,
+ magrittr,
+ MASS,
+ Matrix,
+ matrixcalc,
+ methods,
+ mice,
+ officer,
+ psych,
+ purrr,
+ rlang,
+ rmarkdown,
+ simstudy,
+ stats,
+ stringr,
+ Surrogate,
+ tibble,
+ tidyr,
+ tidyselect,
+ utils,
+ viridis,
+ xtable
+VignetteBuilder: knitr
+RdMacros: lifecycle
+Depends: 
+ R (>= 2.10)
+Remotes: 
+ ready4-dev/ready4fun