citation and redo

ready4-dev · Sep 13, 2022 · 14456c4 · 14456c4
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,77 +1,77 @@
-^youthu\.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/youthu_DATASET\.R$
-^\.github$
-^data-raw/csvs/AQoL_6D_Dim_Scaling\.csv$
-^data-raw/csvs/aqol_valid_stata\.csv$
-^data-raw/csvs/adol_dim_scalg_eqs_lup\.csv$
-^data-raw/R-CMD-check_BUP\.txt$
-^data-raw/gnrcs/generics\.R$
-^data-raw/abbreviations_lup\.csv$
-^data-raw/adol_dim_scalg_eqs_lup\.csv$
-^data-raw/aqol_scrg_dict_r3\.csv$
-^data-raw/aqol6d_adult_disv_lup_tb\.csv$
-^data-raw/aqol6d_adult_itm_wrst_wts_lup_tb\.csv$
-^data-raw/aqol6d_adult_vldn_pop_with_STATA_scores_tb\.csv$
-^data-raw/aqol6d_dim_sclg_con_lup_tb\.csv$
-^data-raw/aqol6d_domain_qs_lup_tb\.csv$
-^data-raw/aqol6d_from_8d_coefs_lup_tb\.csv$
-^data-raw/predictors_lup\.csv$
-^data-raw/fn_types_lup\.csv$
-^data-raw/fns_dmt_tb\.csv$
-^data-raw/prototype_lup\.csv$
-^data-raw/replication_popl_tb\.csv$
-^data-raw/repln_ds_dict_r3\.csv$
-^initial_setup\.R$
-^data-raw/vignettes/TA_Tools_Data_Integrity\.Rmd$
-^data-raw/vignettes/TA_Tools_Replication_DS\.Rmd$
-^data-raw/vignettes/TA_Tools_Scoring\.Rmd$
-^data-raw/youthu_DATASET\.R$
-^data-raw/fake_pop_tb\.csv$
-^data-raw/fns/rename\.R$
-^data-raw/candidate_predrs_lup\.csv$
-^data-raw/inst/models/example_mdl\.RDS$
-^data-raw/fns/update\.R$
-^data-raw/vignettes/_AQoL_6D_Syn_Pop\.Rmd$
-^doc$
-^Meta$
-^data-raw/vignettes/_Clippings\.Rmd$
-^data-raw/dataverse/fn_types_lup/fn_types_lup\.csv$
-^data-raw/dataverse/fn_types_lup/fn_types_lup\.RDS$
-^data-raw/MAKE_HOUSESTYLE_DSS\.R$
-^data-raw/dataverse/abbreviations_lup/abbreviations_lup\.csv$
-^data-raw/dataverse/abbreviations_lup/abbreviations_lup\.RDS$
-^data-raw/dataverse/object_type_lup/object_type_lup\.csv$
-^data-raw/dataverse/object_type_lup/object_type_lup\.RDS$
-^data-raw/dataverse/seed_obj_lup_tb/seed_obj_lup_tb\.csv$
-^data-raw/dataverse/seed_obj_lup_tb/seed_obj_lup_tb\.RDS$
-^data-raw/name_changes\.txt$
-^data-raw/safety\.txt$
-^data-raw/vignette_pts/_clipped_fake_ds\.Rmd$
-^data-raw/dataverse/fn_type_lup_tb/fn_type_lup_tb\.csv$
-^data-raw/dataverse/fn_type_lup_tb/fn_type_lup_tb\.RDS$
-^data-raw/NOTES\.R$
+^youthu\.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/youthu_DATASET\.R$
+^\.github$
+^data-raw/csvs/AQoL_6D_Dim_Scaling\.csv$
+^data-raw/csvs/aqol_valid_stata\.csv$
+^data-raw/csvs/adol_dim_scalg_eqs_lup\.csv$
+^data-raw/R-CMD-check_BUP\.txt$
+^data-raw/gnrcs/generics\.R$
+^data-raw/abbreviations_lup\.csv$
+^data-raw/adol_dim_scalg_eqs_lup\.csv$
+^data-raw/aqol_scrg_dict_r3\.csv$
+^data-raw/aqol6d_adult_disv_lup_tb\.csv$
+^data-raw/aqol6d_adult_itm_wrst_wts_lup_tb\.csv$
+^data-raw/aqol6d_adult_vldn_pop_with_STATA_scores_tb\.csv$
+^data-raw/aqol6d_dim_sclg_con_lup_tb\.csv$
+^data-raw/aqol6d_domain_qs_lup_tb\.csv$
+^data-raw/aqol6d_from_8d_coefs_lup_tb\.csv$
+^data-raw/predictors_lup\.csv$
+^data-raw/fn_types_lup\.csv$
+^data-raw/fns_dmt_tb\.csv$
+^data-raw/prototype_lup\.csv$
+^data-raw/replication_popl_tb\.csv$
+^data-raw/repln_ds_dict_r3\.csv$
+^initial_setup\.R$
+^data-raw/vignettes/TA_Tools_Data_Integrity\.Rmd$
+^data-raw/vignettes/TA_Tools_Replication_DS\.Rmd$
+^data-raw/vignettes/TA_Tools_Scoring\.Rmd$
+^data-raw/youthu_DATASET\.R$
+^data-raw/fake_pop_tb\.csv$
+^data-raw/fns/rename\.R$
+^data-raw/candidate_predrs_lup\.csv$
+^data-raw/inst/models/example_mdl\.RDS$
+^data-raw/fns/update\.R$
+^data-raw/vignettes/_AQoL_6D_Syn_Pop\.Rmd$
+^doc$
+^Meta$
+^data-raw/vignettes/_Clippings\.Rmd$
+^data-raw/dataverse/fn_types_lup/fn_types_lup\.csv$
+^data-raw/dataverse/fn_types_lup/fn_types_lup\.RDS$
+^data-raw/MAKE_HOUSESTYLE_DSS\.R$
+^data-raw/dataverse/abbreviations_lup/abbreviations_lup\.csv$
+^data-raw/dataverse/abbreviations_lup/abbreviations_lup\.RDS$
+^data-raw/dataverse/object_type_lup/object_type_lup\.csv$
+^data-raw/dataverse/object_type_lup/object_type_lup\.RDS$
+^data-raw/dataverse/seed_obj_lup_tb/seed_obj_lup_tb\.csv$
+^data-raw/dataverse/seed_obj_lup_tb/seed_obj_lup_tb\.RDS$
+^data-raw/name_changes\.txt$
+^data-raw/safety\.txt$
+^data-raw/vignette_pts/_clipped_fake_ds\.Rmd$
+^data-raw/dataverse/fn_type_lup_tb/fn_type_lup_tb\.csv$
+^data-raw/dataverse/fn_type_lup_tb/fn_type_lup_tb\.RDS$
+^data-raw/NOTES\.R$
diff --git a/.github/.gitignore b/.github/.gitignore
@@ -1 +1 @@
-*.html
+*.html
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@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