Merge pull request #19 from JGCRI/dev-pop

Dev pop

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

@@ -0,0 +1,51 @@
+name: R-CMD-check
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions: read-all
+
+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: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.PAT }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          error-on: '"error"'

.github/workflows/test_coverage.yaml

@@ -0,0 +1,60 @@
+name: test_coverage
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.PAT }}
+
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

R/hdcd.R

@@ -203,6 +203,8 @@ hdcd <- function(ncdf = NULL,
             print('Starting population weighting ...')
 
             population_j_weighted <- population_j_grid %>%
+              dplyr::filter(lat %in% grid_intersect$lat,
+                            lon %in% grid_intersect$lon) %>%
               dplyr::group_by(region, ID, subRegion, year) %>%
               dplyr::mutate(subRegion_total_value = sum(value, na.rm = T),
                             value = ifelse(is.na(value), 0, value)) %>%
@@ -221,8 +223,9 @@ hdcd <- function(ncdf = NULL,
               dplyr::left_join(population_j_weighted %>%
                                  dplyr::select(-value, -subRegion_total_value),
                                by = c('ID', 'region', 'subRegion', 'lat', 'lon', 'year')) %>%
-              dplyr::mutate(value = (((value - 273.15) * 9/5) + 32) - reference_temp_F,
-                            value = dplyr::if_else(is.na(pop_weight), value, value * pop_weight))
+              dplyr::mutate(pop_weight = ifelse(is.na(pop_weight), 0, pop_weight),
+                            value = (((value - 273.15) * 9/5) + 32) - reference_temp_F,
+                            value = value * pop_weight)
 
           } else {
             print(paste0('Population data years: ', paste(names(population_j_grid)[!grepl('RID|lat|lon', names(population_j_grid))], collapse = ',')))
@@ -246,13 +249,10 @@ hdcd <- function(ncdf = NULL,
             hdcd_region <- ncdf_hdcd_pop_weighted %>%
               dplyr::filter(!is.na(subRegion)) %>%
               dplyr::select(-lat, -lon) %>%
-              dplyr::group_by(region, subRegion, ID, year, datetime) %>%
-              dplyr::summarise(value = dplyr::if_else(any(is.na(pop_weight)), mean(value), sum(value))) %>%
-              dplyr::ungroup()
-
-            # Assign HDCD categories
-            hdcd_region <- hdcd_region %>%
               dplyr::mutate(HDCD = dplyr::if_else(value < 0, 'HD', 'CD')) %>%
+              dplyr::group_by(region, subRegion, ID, year, datetime, HDCD) %>%
+              dplyr::summarise(value = sum(value)) %>%
+              dplyr::ungroup() %>%
               dplyr::filter(value != 0)
 
             #......................

README.md

@@ -1,9 +1,8 @@
 <!-- badges: start -->
-[![build](https://github.com/JGCRI/helios/actions/workflows/build.yml/badge.svg?branch=main)](https://github.com/JGCRI/helios/actions/workflows/build.yml)
-[![test_coverage](https://github.com/JGCRI/helios/actions/workflows/test_coverage.yml/badge.svg?branch=main)](https://github.com/JGCRI/helios/actions/workflows/test_coverage.yml)
+[![R-CMD-check](https://github.com/JGCRI/helios/actions/workflows/R-CDM-check.yaml/badge.svg?branch=main)](https://github.com/JGCRI/helios/actions/workflows/R-CDM-check.yaml)
+[![test-coverage](https://github.com/JGCRI/helios/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/JGCRI/helios/actions/workflows/test-coverage.yaml)
 [![docs](https://github.com/JGCRI/helios/actions/workflows/docs.yaml/badge.svg?branch=main)](https://github.com/JGCRI/helios/actions/workflows/docs.yaml)
 [![codecov](https://codecov.io/gh/JGCRI/helios/branch/main/graph/badge.svg?token=XQ913U4IYM)](https://codecov.io/gh/JGCRI/helios) 
-[![Github All Releases](https://img.shields.io/github/downloads/JGCRI/helios/total.svg)]()
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.06033/status.svg)](https://doi.org/10.21105/joss.06033)
 [![DOI](https://zenodo.org/badge/429143355.svg)](https://zenodo.org/doi/10.5281/zenodo.8170310)
 <!-- badges: end -->