ctry-specific model

.github/workflows/build.yaml

@@ -1,49 +1,74 @@
 name: build
-
 on:
   push:
     branches: [main, k_dev]
   pull_request:
     branches: [main, k_dev]
-
 jobs:
   R-CMD:
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
     strategy:
       fail-fast: false
       matrix:
         config:
         - { os: ubuntu-latest, r: 'devel', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
-
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       GITHUB_PAT: ${{ secrets.GH_RHAP_TOKEN}}
-
     steps:
-      - uses: actions/checkout@v1
-      - uses: r-lib/actions/setup-r@v2-branch
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: '4.1'
-      - uses: r-lib/actions/setup-pandoc@v2-branch
-      - uses: r-lib/actions/setup-tinytex@v2-branch
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Install libraries
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - name: Install system libraries
         if: startsWith(matrix.config.os, 'ubuntu')
         run: |
-          sudo apt-add-repository ppa:ubuntugis/ubuntugis-unstable
           sudo apt-get update
-          sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev libudunits2-dev libgdal-dev libgeos-dev libproj-dev libmagick++-dev libavfilter-dev libharfbuzz-dev libfribidi-dev
+          sudo apt-get install -y \
+            libcurl4-openssl-dev libssl-dev libxml2-dev \
+            libudunits2-dev libgdal-dev libgeos-dev libproj-dev \
+            libmagick++-dev libavfilter-dev \
+            libharfbuzz-dev libfribidi-dev \
+            libfontconfig1-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev \
+            libuv1-dev
 
-      - name: Install dependencies
+      - name: Install R dependencies
         run: |
-          install.packages(c("remotes","rcmdcheck","stringi"), repos = "https://cloud.r-project.org")
-          install.packages(c("evaluate"), repos = "https://cloud.r-project.org")
-          install.packages(c("knitr","rmarkdown","htmlwidgets", "plm"), repos = "https://cloud.r-project.org")
-          remotes::install_deps(dependencies = TRUE)
+          options(Ncpus = parallel::detectCores())
+          options(repos = c(CRAN = "https://cloud.r-project.org"))
+          install.packages(c("remotes", "rcmdcheck", "covr", "fs", "usethis", "testthat"))
+          remotes::install_deps(dependencies = TRUE, upgrade = "never")
+        shell: Rscript {0}
+
+      - name: Install the package
+        run: remotes::install_local(".")
         shell: Rscript {0}
 
+      # - name: Install dependencies
+      #   run: |
+      #     install.packages(c("remotes", "rcmdcheck", "stringi", "devtools"), repos = "https://cloud.r-project.org")
+      #     install.packages(c("evaluate"), repos = "https://cloud.r-project.org")
+      #     install.packages(c("knitr", "rmarkdown", "htmlwidgets", "plm"), repos = "https://cloud.r-project.org")
+      #     remotes::install_deps(dependencies = TRUE)
+      #   shell: Rscript {0}
+      #
+      # - name: Install GitHub packages
+      #   run: |
+      #     remotes::install_github("JGCRI/rmap")
+      #     remotes::install_github("JGCRI/gcamdata")
+      #   shell: Rscript {0}
+
       - name: Check
         run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--ignore-vignettes", "--no-build-vignettes"), build_args = c("--no-manual", "--ignore-vignettes", "--no-build-vignettes"), error_on = "error")
         shell: Rscript {0}
+
+      - name: Run tests
+        run: testthat::test_local()
+        shell: Rscript {0}

.github/workflows/test_coverage.yaml

@@ -1,26 +1,21 @@
 name: test_coverage
-
 on:
   push:
     branches: [main]
   pull_request:
     branches: [main]
-
 jobs:
   R-CMD:
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
     strategy:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest" }
-
+          - { os: ubuntu-latest, r: 'release' }
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       GITHUB_PAT: ${{ secrets.GH_RHAP_TOKEN }}
-
     steps:
       - uses: actions/checkout@v4
 
@@ -29,27 +24,31 @@ jobs:
           r-version: ${{ matrix.config.r }}
 
       - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-tinytex@v2
 
       - name: Install system libraries
         if: startsWith(matrix.config.os, 'ubuntu')
         run: |
-          sudo apt-add-repository ppa:ubuntugis/ubuntugis-unstable
           sudo apt-get update
           sudo apt-get install -y \
             libcurl4-openssl-dev libssl-dev libxml2-dev \
             libudunits2-dev libgdal-dev libgeos-dev libproj-dev \
-            libmagick++-dev libavfilter-dev libharfbuzz-dev libfribidi-dev
+            libmagick++-dev libavfilter-dev \
+            libharfbuzz-dev libfribidi-dev \
+            libfontconfig1-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev \
+            libuv1-dev
 
       - name: Install R dependencies
         run: |
-          install.packages(c("remotes", "rcmdcheck", "covr"), repos = "https://cloud.r-project.org")
-          remotes::install_deps(dependencies = TRUE)
+          options(Ncpus = parallel::detectCores())
+          options(repos = c(CRAN = "https://cloud.r-project.org"))
+          install.packages(c("remotes", "rcmdcheck", "covr", "fs", "usethis", "testthat"))
+          remotes::install_deps(dependencies = TRUE, upgrade = "never")
         shell: Rscript {0}
 
       - name: Install the package
-        run: |
-          remotes::install_local(".")
+        run: remotes::install_local(".")
         shell: Rscript {0}
 
       - name: Run tests and generate coverage
@@ -60,7 +59,6 @@ jobs:
 
       - uses: codecov/codecov-action@v4.0.1
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}  # Optional if repo is public
+          token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage.xml
           verbose: true
-

.gitignore

@@ -8,3 +8,7 @@ R/*.txt
 /tests/testthat/testInputs/database_basexdb_ref/*
 /tests/testthat/output
 inst/doc
+/output_esp
+plot*
+*pptx
+*check*

DESCRIPTION

@@ -19,7 +19,7 @@ Depends: R (>= 3.5)
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Imports:
     usethis,
     ggplot2,

NAMESPACE

@@ -2,9 +2,12 @@
 
 export(calc_ResidEm_grp)
 export(calc_hap_impacts)
+export(calc_hap_impacts_predict)
+export(calc_hap_impacts_preproces)
 export(calc_hia_adder)
 export(create_panel)
 export(fit_model)
 export(get_gdp_ctry)
 export(get_pop_ctry)
+export(listYears)
 importFrom(magrittr,"%>%")

R/calc_ResidEm_grp.R

@@ -34,26 +34,6 @@ calc_ResidEm_grp <- function(db_path = NULL, query_path = "./inst/extdata", db_n
   if (length(pollutant) != 1) stop("Error: Please provide a single pollutant as input to the `calc_ResidEm_grp` function.")
   if (length(region) != 1) stop("Error: Please provide a single region as input to the `calc_ResidEm_grp` function.")
 
-  year <- as.numeric(as.character(year))
-  if (!year %in% seq(2020, 2100, 5)) {
-    stop(sprintf(
-      "Error: The specified year '%s' is invalid. Accepted years are: %s. Please rerun the `calc_ResidEm_grp` function with a valid year.",
-      year, paste(seq(2020, 2100, 5), collapse = ", ")
-    ))
-  }
-  if (!pollutant %in% rhap::all_pollutants) {
-    stop(sprintf(
-      "Error: The specified pollutant '%s' is invalid. Accepted pollutants are: %s. Please rerun the `calc_ResidEm_grp` function with a valid pollutant.",
-      pollutant, paste(rhap::all_pollutants, collapse = ", ")
-    ))
-  }
-  if (!region %in% rhap::gcam_regions) {
-    stop(sprintf(
-      "Error: The specified region '%s' is invalid. Accepted regions are: %s. Please rerun the `calc_ResidEm_grp` function with a valid region.",
-      region, paste(rhap::gcam_regions, collapse = ", ")
-    ))
-  }
-
 
   # Then, load the rgcam project if prj not passed as a parameter:
   if (!is.null(db_path) & !is.null(db_name)) {
@@ -79,11 +59,39 @@ calc_ResidEm_grp <- function(db_path = NULL, query_path = "./inst/extdata", db_n
     final_db_year,
     max(rgcam::getQuery(prj, "nonCO2 emissions by sector (excluding resource production)")$year)
   )
+  # Find last historical year
+  years_in_prj  <- listYears(prj)
+  years_in_prj  <- years_in_prj[!is.na(years_in_prj)]
+  years_in_prj  <- setdiff(years_in_prj, NA)
+  base_year     <- dplyr::if_else(2021 %in% years_in_prj, 2021, 2015)
+  base_year_p   <- dplyr::if_else(base_year == 2021, base_year, 2020)
+
+  # More checks
+  year <- as.numeric(as.character(year))
+  if (!year %in% c(base_year_p, seq(2025, 2100, 5))) {
+    stop(sprintf(
+      "Error: The specified year '%s' is invalid. Accepted years are: %s. Please rerun the `calc_ResidEm_grp` function with a valid year.",
+      year, paste(c(base_year_p, seq(2025, 2100, 5)), collapse = ", ")
+    ))
+  }
+  if (!pollutant %in% rhap::all_pollutants) {
+    stop(sprintf(
+      "Error: The specified pollutant '%s' is invalid. Accepted pollutants are: %s. Please rerun the `calc_ResidEm_grp` function with a valid pollutant.",
+      pollutant, paste(rhap::all_pollutants, collapse = ", ")
+    ))
+  }
+  if (!region %in% rhap::gcam_regions) {
+    stop(sprintf(
+      "Error: The specified region '%s' is invalid. Accepted regions are: %s. Please rerun the `calc_ResidEm_grp` function with a valid region.",
+      region, paste(rhap::gcam_regions, collapse = ", ")
+    ))
+  }
+
 
   if (year > final_db_year) {
     stop(sprintf(
       "Error: The specified year '%s' is invalid. The database only contains data up to %s. Accepted years are: %s. Please rerun the `calc_ResidEm_grp` function with a valid year.",
-      year, final_db_year, paste(seq(2020, final_db_year, 5), collapse = ", ")
+      year, final_db_year, paste(c(base_year_p, seq(2025, final_db_year, 5)), collapse = ", ")
     ))
   }