Merge branch 'master' into add-monthly-brackets-106

.Rbuildignore

@@ -1,13 +1,15 @@
+^.*\.Rproj$
+^CODE_OF_CONDUCT\.md$
+^LICENSE\.md$
 ^README\.Rmd$
 ^README_cache$
-^data-raw$
-^.*\.Rproj$
 ^\.Rproj\.user$
-^codecov\.yml$
 ^\.github$
+^\.pre-commit-config\.yaml$
 ^_pkgdown\.yml$
+^codecov\.yml$
+^data-raw$
 ^docs$
 ^pkgdown$
-^CODE_OF_CONDUCT\.md$
-^LICENSE\.md$
 ^touchstone$
+^paper$

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

@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,9 +41,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: |
-            any::rcmdcheck
-            any::XML
+          extra-packages: any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/pkgdown.yaml

@@ -1,33 +1,46 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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]
-    tags: ['*']
+  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@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: pkgdown
+          extra-packages: any::pkgdown, local::.
           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)'
+      - 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

.github/workflows/test-coverage.yaml

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
@@ -15,16 +15,36 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: covr
+          extra-packages: any::covr
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -5,4 +5,13 @@
 inst/doc
 .DS_Store
 docs
-README_cache
+README_cache
+.Rprofile
+.vscode/launch.json
+.pre-commit-config.yaml
+tests/README.md
+paper/*.html
+paper/*.pdf
+paper/paper_cache/
+paper/paper_files/
+chitra/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: conmat
 Title: Builds contact matrices using GAMs and population data
-Version: 0.0.0.9004
+Version: 0.0.2.9000
 Authors@R: c(
       person(given = "Nicholas",
              family = "Tierney",
@@ -17,6 +17,11 @@ Authors@R: c(
              role = c("aut"),
              email = "[email protected]",
              comment = c(ORCID = "https://orcid.org/0000-0002-6982-5989")),
+      person(given = "Michael",
+             family = "Lydeamore",
+             role = "aut",
+             email = "[email protected]",
+             comment = c(ORCID = "https://orcid.org/0000-0001-6515-827X")),
       person("Commonwealth of Australia", "AEC", role = c("cph")),
       person("Australian Bureau of Statistics", "ABS", role = c("cph"))
       )
@@ -25,35 +30,44 @@ Description: Builds contact matrices using GAMs and population data. This packag
   Electoral Commission and Australian Bureau of Statistics) 2020.
 License: MIT + file LICENSE
 Depends: 
-    R (>= 2.10)
+    R (>= 4.1.0)
 Suggests: 
     covr,
     knitr,
+    vdiffr,
     testthat (>= 3.0.0),
     rmarkdown,
-    future
+    future,
+    spelling,
+    deSolve
 VignetteBuilder: 
     knitr
 Config/testthat/edition: 3
 Encoding: UTF-8
-Language: en-GB
+Language: en-US
 LazyData: true
 LazyDataCompression: xz
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.2
 Imports: 
     mgcv,
-    dplyr,
+    dplyr (>= 1.0.9),
+    tidyr (>= 1.2.0),
+    cli,
     stats,
-    tidyr,
-    socialmixr,
+    socialmixr (>= 0.2.0),
     ggplot2,
-    tibble,
+    tibble (>= 3.1.8),
     patchwork,
     magrittr,
-    stringr,
-    rlang,
-    glue,
+    rlang (>= 1.0.4),
+    glue (>= 1.6.2),
     readr,
     furrr,
-    purrr
+    purrr (>= 1.0.1),
+    tidyselect,
+    vctrs,
+    scales,
+    english,
+    waldo,
+    stringr

NAMESPACE

@@ -1,42 +1,124 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(age_breaks,array)
+S3method(age_breaks,conmat_age_matrix)
+S3method(age_breaks,conmat_setting_prediction_matrix)
+S3method(age_breaks,default)
+S3method(age_breaks,matrix)
+S3method(age_breaks,ngm_setting_matrix)
+S3method(age_breaks,numeric)
+S3method(age_breaks,predicted_contacts)
+S3method(age_breaks,setting_contact_model)
+S3method(age_breaks,setting_data)
+S3method(age_breaks,setting_vaccination_matrix)
+S3method(age_breaks,transmission_probability_matrix)
+S3method(age_label,conmat_population)
+S3method(age_label,default)
+S3method(as_conmat_population,"NULL")
+S3method(as_conmat_population,data.frame)
+S3method(as_conmat_population,default)
+S3method(as_conmat_population,grouped_df)
+S3method(as_conmat_population,list)
+S3method(as_setting_prediction_matrix,conmat_setting_prediction_matrix)
+S3method(as_setting_prediction_matrix,default)
+S3method(as_setting_prediction_matrix,list)
+S3method(autoplot,conmat_age_matrix)
+S3method(autoplot,conmat_setting_prediction_matrix)
+S3method(autoplot,ngm_setting_matrix)
+S3method(autoplot,setting_vaccination_matrix)
+S3method(autoplot,transmission_probability_matrix)
+S3method(generate_ngm,conmat_population)
+S3method(generate_ngm,conmat_setting_prediction_matrix)
+S3method(get_age_population_function,conmat_population)
+S3method(get_age_population_function,data.frame)
+S3method(population_label,conmat_population)
+S3method(population_label,default)
+S3method(predictions_to_matrix,predicted_contacts)
+S3method(print,conmat_age_matrix)
+S3method(print,conmat_population)
+S3method(print,conmat_setting_prediction_matrix)
+S3method(print,ngm_setting_matrix)
+S3method(print,setting_contact_model)
+S3method(print,setting_data)
+S3method(print,setting_vaccination_matrix)
+S3method(print,transmission_probability_matrix)
 export("%>%")
-export(abbreviate_states)
+export(abs_abbreviate_states)
+export(abs_age_education_lga)
+export(abs_age_education_state)
 export(abs_age_lga)
 export(abs_age_state)
+export(abs_age_work_lga)
+export(abs_age_work_state)
+export(abs_unabbreviate_states)
+export(add_age_partial_sum)
 export(add_intergenerational)
 export(add_modelling_features)
 export(add_offset)
 export(add_population_age_to)
 export(add_school_work_participation)
+export(add_symmetrical_features)
+export(age)
+export(age_breaks)
+export(age_label)
 export(age_population)
 export(aggregate_predicted_contacts)
 export(apply_vaccination)
-export(check_lga_name)
+export(as_conmat_population)
+export(as_setting_prediction_matrix)
+export(autoplot)
+export(clean_term_names)
+export(conmat_population)
+export(create_age_grid)
 export(estimate_setting_contacts)
+export(extract_term_names)
 export(extrapolate_polymod)
 export(fit_setting_contacts)
 export(fit_single_contact_model)
 export(generate_ngm)
+export(generate_ngm_oz)
+export(get_abs_household_size_distribution)
+export(get_abs_household_size_population)
+export(get_abs_per_capita_household_size)
+export(get_abs_per_capita_household_size_lga)
+export(get_abs_per_capita_household_size_state)
 export(get_age_population_function)
-export(get_data_abs_age_education)
-export(get_data_abs_age_work)
-export(get_household_size_distribution)
-export(get_per_capita_household_size)
 export(get_polymod_contact_data)
 export(get_polymod_per_capita_household_size)
 export(get_polymod_population)
 export(get_polymod_setting_data)
 export(get_setting_transmission_matrices)
+export(gg_age_partial_pred_long)
+export(gg_age_partial_sum)
+export(gg_age_terms_settings)
 export(matrix_to_predictions)
+export(new_age_matrix)
+export(new_ngm_setting_matrix)
+export(new_setting_data)
 export(per_capita_household_size)
-export(plot_matrix)
-export(plot_setting_matrices)
+export(pivot_longer_age_preds)
 export(polymod)
+export(population)
+export(population_label)
 export(predict_contacts)
 export(predict_contacts_1y)
+export(predict_individual_terms)
 export(predict_setting_contacts)
 export(predictions_to_matrix)
-export(unabbreviate_states)
+export(prepare_population_for_modelling)
+export(raw_eigenvalue)
+export(scaling)
+export(setting_prediction_matrix)
+export(transmission_probability_matrix)
+import(rlang)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,autoplot)
+importFrom(ggplot2,coord_fixed)
+importFrom(ggplot2,facet_grid)
+importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_tile)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,scale_fill_viridis_c)
+importFrom(ggplot2,theme_minimal)
 importFrom(magrittr,"%>%")
 importFrom(stats,predict)