Merge pull request #95 from simon-smart88/master

Update to 0.4.0
aknandi · Nov 13, 2024 · 226b55e · 226b55e
2 parents cd7e7ef + d9e31a6
commit 226b55e
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diff --git a/.github/workflows/R-CMD-build.yaml b/.github/workflows/R-CMD-build.yaml
@@ -3,7 +3,7 @@
 on:
   push:
     branches:
-      'build' 
+      'build'
   pull_request:
     branches:
       - master
@@ -40,7 +40,6 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-          extra-repositories: "https://inla.r-inla-download.org/R/testing"
 
       - name: Install system dependencies on MacOS (X11, gdal)
         if: runner.os == 'macOS'
@@ -54,6 +53,7 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           sudo apt-get update -y && sudo apt-get install -y libglu1-mesa-dev
+          sudo apt-get install -y libproj-dev gdal-bin
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

diff --git a/.github/workflows/R-CMD-check-HTML5.yaml b/.github/workflows/R-CMD-check-HTML5.yaml
@@ -1,58 +1,56 @@
-# 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: [html5]
-  pull_request:
-    branches: [html5]
-
-name: R-CMD-check-html5
-
-
-jobs:
-  HTML5-check:
-    runs-on: ubuntu-latest
-    env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ matrix.config.r }}
-          extra-repositories: "https://inla.r-inla-download.org/R/stable"
-
-
-      - name: Install pdflatex
-        run: sudo apt-get install texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - name: Install system dependencies on MacOS (X11, gdal)
-        if: runner.os == 'macOS'
-        run: |
-          brew install --cask xquartz
-          brew install pkg-config
-          brew install proj@8
-          brew install gdal
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          dependencies: '"all"'
-          extra-packages: |
-             rcmdcheck
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - uses: r-lib/actions/check-r-package@v2
-        with:
-          args: '"--as-cran"'
-          build_args: 'character()'
-          #error-on: '"note"'
+# 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: [html5]
+  pull_request:
+    branches: [html5]
+
+name: R-CMD-check-html5
+
+
+jobs:
+  HTML5-check:
+    runs-on: ubuntu-latest
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - name: Install pdflatex
+        run: sudo apt-get install texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install system dependencies on MacOS (X11, gdal)
+        if: runner.os == 'macOS'
+        run: |
+          brew install --cask xquartz
+          brew install pkg-config
+          brew install proj@8
+          brew install gdal
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: '"all"'
+          extra-packages: |
+             rcmdcheck
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: '"--as-cran"'
+          build_args: 'character()'
+          #error-on: '"note"'
diff --git a/.github/workflows/R-CMD-check-no-suggests.yaml b/.github/workflows/R-CMD-check-no-suggests.yaml
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,9 +1,11 @@
 # 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
+
+# inspired by: https://github.com/r-spatial/sf/blob/main/.github/workflows/R-CMD-check.yaml
 on:
   push:
     branches:
-      '**' 
+      '**'
   pull_request:
     branches:
       - devel
@@ -21,23 +23,22 @@ jobs:
       fail-fast: false
       matrix:
         config:
-    #      - {os: windows-latest, r: 'release'}
-    #      - {os: macOS-latest, r: 'release'}
-          - {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"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {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'}
+          - {os: ubuntu-latest,   r: 'oldrel-2'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
 
     steps:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          extra-repositories: "https://inla.r-inla-download.org/R/stable"
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -46,21 +47,13 @@ jobs:
         run: |
           brew install --cask xquartz
           brew install pkg-config
-          brew install proj@8
+          brew install proj
           brew install gdal
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          dependencies: '"all"'
-          extra-packages: |
-             rcmdcheck
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         env:

diff --git a/.gitignore b/.gitignore
@@ -1,11 +1,11 @@
-inst/doc
-.Rproj.user
-.Rhistory
-.Rproj
-.RData
-*.o
-*.so
-vignettes/disaggregation_cache/*
-vignettes/disaggregation_files/*
-.github/workflows/R-CMD-check-HTML5.archyaml
-vignettes/spatio_temporal_disaggregation.Rmd
+inst/doc
+.Rproj.user
+.Rhistory
+*.Rproj
+.RData
+*.o
+*.so
+vignettes/disaggregation_cache/*
+vignettes/disaggregation_files/*
+.github/workflows/R-CMD-check-HTML5.archyaml
+vignettes/spatio_temporal_disaggregation.Rmd
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: disaggregation
 Type: Package
 Title: Disaggregation Modelling
-Version: 0.3.0
+Version: 0.4.0
 Authors@R: c(
     person("Anita", "Nandi", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-5087-2494")),
     person("Tim", "Lucas", email =  "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4694-8107")),
@@ -17,7 +17,7 @@ Description: Fits disaggregation regression models using 'TMB' ('Template Model
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Imports: 
     splancs,
     Matrix,
@@ -26,16 +26,15 @@ Imports:
     dplyr,
     ggplot2,
     cowplot,
+    rSPDE,
     sparseMVN,
     fmesher,
     tidyterra,
     terra,
     sf,
     utils
-Additional_repositories: https://inla.r-inla-download.org/R/stable
 Suggests: 
     testthat,
-    INLA,
     knitr,
     rmarkdown,
     SpatialEpi

diff --git a/NAMESPACE b/NAMESPACE
@@ -13,11 +13,11 @@ S3method(summary,disag_prediction)
 export(as.disag_data)
 export(build_mesh)
 export(disag_model)
-export(fit_model)
 export(getCovariateRasters)
 export(getPolygonData)
 export(getStartendindex)
 export(make_model_object)
+export(plot_disag_model_data)
 export(predict_model)
 export(predict_uncertainty)
 export(prepare_data)