Merge pull request #82 from timcdlucas/master

switch to sf, terra and fmesher

.Rbuildignore

@@ -1,10 +1,10 @@
-^.*\.Rproj$
-^\.Rproj\.user$
-^\.git*
-README.md
-.travis.yml
-vignettes/disaggregation_cache/*
-cran-comments.md
-^\.github$
-.github/workflows/R-CMD-check-HTML5.archyaml
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.git*
+README.md
+.travis.yml
+vignettes/disaggregation_cache/*
+cran-comments.md
+^\.github$
+.github/workflows/R-CMD-check-HTML5.archyaml
 vignettes/spatio_temporal_disaggregation.Rmd

.github/workflows/R-CMD-check-HTML5.yaml

@@ -1,58 +1,58 @@
-# 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 }}
+          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"'

.github/workflows/R-CMD-check-no-suggests.yaml

@@ -1,96 +1,96 @@
-# 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
-#
-# Largely copied from: https://github.com/inlabru-org/inlabru/blob/devel/.github/workflows/R-CMD-check-no-suggests.yaml
-# Want to test without suggests to ensure things don't fail on cran when INLA isn't there.
-
-on:
-  push:
-    branches:
-      '**' 
-  pull_request:
-    branches:
-      - devel
-      - master
-
-name: R-CMD-check-no-suggests
-
-jobs:
-  R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      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: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/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/testing"
-
-      - 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@9
-          brew install gdal
-      
-      - name: Has inla? Check.
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          "INLA" %in% pkgs
-        shell: Rscript {0}
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          dependencies: '"hard"'
-          extra-packages: |
-            rcmdcheck
-            testthat
-      
-      - name: Has inla? Check, and remove.
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          "INLA" %in% pkgs
-          if ("INLA" %in% pkgs) {
-            remove.packages("INLA")
-          }
-        shell: Rscript {0}
-
-      - 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
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-          _R_CHECK_FORCE_SUGGESTS_: false
-        with:
-          build_args: 'c("--no-manual", "--no-build-vignettes")'
-          args: 'c("--no-manual", "--ignore-vignettes", "--as-cran")'
-
-
-
+# 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
+#
+# Largely copied from: https://github.com/inlabru-org/inlabru/blob/devel/.github/workflows/R-CMD-check-no-suggests.yaml
+# Want to test without suggests to ensure things don't fail on cran when INLA isn't there.
+
+on:
+  push:
+    branches:
+      '**' 
+  pull_request:
+    branches:
+      - devel
+      - master
+
+name: R-CMD-check-no-suggests
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      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: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/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/testing"
+
+      - 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@9
+          brew install gdal
+      
+      - name: Has inla? Check.
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          "INLA" %in% pkgs
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: '"hard"'
+          extra-packages: |
+            rcmdcheck
+            testthat
+      
+      - name: Has inla? Check, and remove.
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          "INLA" %in% pkgs
+          if ("INLA" %in% pkgs) {
+            remove.packages("INLA")
+          }
+        shell: Rscript {0}
+
+      - 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
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+        with:
+          build_args: 'c("--no-manual", "--no-build-vignettes")'
+          args: 'c("--no-manual", "--ignore-vignettes", "--as-cran")'
+
+
+
 

.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
+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

DESCRIPTION

@@ -1,12 +1,13 @@
 Package: disaggregation
 Type: Package
 Title: Disaggregation Modelling
-Version: 0.2.1
+Version: 0.3.0
 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")),
     person("Rohan", "Arambepola", email = "[email protected]", role = "aut"),
-    person("Andre", "Python", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0001-8094-7226"))
+    person("Andre", "Python", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0001-8094-7226")),
+    person("Simon", "Smart", email = "[email protected]", role = "ctb")
     )
 Description: Fits disaggregation regression models using 'TMB' ('Template Model
     Builder'). When the response data are aggregated to polygon level but
@@ -18,12 +19,6 @@ Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.3
 Imports: 
-    raster,
-    foreach,
-    sp,
-    sf,
-    parallel,
-    doParallel,
     splancs,
     Matrix,
     stats,
@@ -32,6 +27,10 @@ Imports:
     ggplot2,
     cowplot,
     sparseMVN,
+    fmesher,
+    tidyterra,
+    terra,
+    sf,
     utils
 Additional_repositories: https://inla.r-inla-download.org/R/stable
 Suggests: