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