Merge pull request #28 from larmarange/dev_v5

Development of a version 5 based on `sf`

.Rbuildignore

@@ -12,3 +12,5 @@ gps.dbf
 ^revdep$
 ^\.github$
 ^CRAN-SUBMISSION$
+.lintr
+LICENSE.md

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

@@ -1,9 +1,5 @@
 # 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
-#
-# NOTE: This workflow is overkill for most R packages and
-# check-standard.yaml is likely a better choice.
-# usethis::use_github_action("check-standard") will install it.
 on:
   push:
     branches: [main, master]
@@ -22,23 +18,18 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
-
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
-
-          # Use older ubuntu to maximise backward compatibility
-          - {os: ubuntu-18.04,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-18.04,   r: 'release'}
-          - {os: ubuntu-18.04,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/test-coverage.yaml → .github/workflows/lint.yaml

@@ -6,26 +6,27 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: lint
 
 jobs:
-  test-coverage:
+  lint:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - 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
-          needs: coverage
+          extra-packages: any::lintr, local::.
+          needs: lint
 
-      - name: Test coverage
-        run: covr::codecov(quiet = FALSE)
+      - name: Lint
+        run: lintr::lint_package()
         shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.lintr

@@ -0,0 +1,2 @@
+linters: linters_with_defaults(object_name_linter = NULL, cyclocomp_linter = NULL) # see vignette("lintr")
+encoding: "UTF-8"

DESCRIPTION

@@ -20,49 +20,22 @@ LazyData: yes
 Depends:
     R (>= 3.5.0)
 Imports:
-    sp,
-    rgdal (>= 0.7),
-    ggplot2,
     directlabels,
+    ggplot2,
+    gstat,
     KernSmooth,
     fields,
-    gstat,
     foreign,
-    maptools,
-    methods
+    methods,
+    sf,
+    stars
 Suggests:
+    grDevices,
     knitr,
-    rmarkdown
+    rmarkdown,
+    spelling,
+    terra
 Encoding: UTF-8
-Collate:
-    'prevR-package.r'
-    'setClass.prevR.r'
-    'is.prevR.r'
-    'as.prevR.r'
-    'onAttach.r'
-    'isInputOk.prevR.r'
-    'changeproj.prevR.r'
-    'colors.prevR.r'
-    'as.data.frame.prevR.r'
-    'plot.prevR.r'
-    'show.prevR.r'
-    'print.prevR.r'
-    'summary.prevR.r'
-    'rings.prevR.r'
-    'as.SpatialGrid.prevR.r'
-    'create.boundary.prevR.r'
-    'export.prevR.r'
-    'import.dhs.prevR.r'
-    'point.in.SpatialPolygons.prevR.r'
-    'NA.outside.SpatialPolygons.prevR.r'
-    'xyz2dataframe.prevR.r'
-    'init.exp.model.variogram.r'
-    'krige.prevR.r'
-    'kde.prevR.r'
-    'Noptim.r'
-    'theme_prevR.r'
-    'direct.label_prevR.r'
-    'quick.prevR.r'
 VignetteBuilder: knitr
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,14 +1,13 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(as.data.frame,prevR)
-export(NA.outside.SpatialPolygons)
 export(Noptim)
 export(as.prevR)
 export(create.boundary)
 export(direct.label_prevR)
 export(import.dhs)
 export(is.prevR)
-export(point.in.SpatialPolygons)
+export(make.grid.prevR)
 export(prevR.colors.blue)
 export(prevR.colors.blue.inverse)
 export(prevR.colors.gray)
@@ -20,11 +19,12 @@ export(prevR.colors.red)
 export(prevR.colors.red.inverse)
 export(prevR.demo.pal)
 export(quick.prevR)
+export(st_filter_prevR)
 export(theme_prevR)
 export(theme_prevR_light)
+export(update_prevR)
 export(xyz2dataframe)
 exportClasses(prevR)
-exportMethods(as.SpatialGrid)
 exportMethods(changeproj)
 exportMethods(export)
 exportMethods(idw)
@@ -36,7 +36,6 @@ exportMethods(rings)
 exportMethods(show)
 exportMethods(summary)
 import(ggplot2)
-import(sp)
 importFrom(KernSmooth,bkde2D)
 importFrom(directlabels,default.picker)
 importFrom(directlabels,geom_dl)
@@ -46,6 +45,10 @@ importFrom(foreign,read.dbf)
 importFrom(foreign,read.spss)
 importFrom(foreign,write.dbf)
 importFrom(ggplot2,'%+replace%')
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_grey)
+importFrom(ggplot2,unit)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,dev.new)
 importFrom(grDevices,gray)
@@ -56,25 +59,29 @@ importFrom(graphics,rect)
 importFrom(graphics,sunflowerplot)
 importFrom(graphics,text)
 importFrom(graphics,title)
-importFrom(gstat,as.vgm.variomodel)
 importFrom(gstat,fit.variogram)
 importFrom(gstat,idw)
-importFrom(gstat,krige)
 importFrom(gstat,variogram)
 importFrom(gstat,vgm)
-importFrom(maptools,writePointsShape)
-importFrom(maptools,writePolyShape)
-importFrom(methods,"slot<-")
+importFrom(methods,`slot<-`)
 importFrom(methods,as)
-importFrom(methods,is)
 importFrom(methods,new)
-importFrom(methods,setClass)
-importFrom(methods,setGeneric)
-importFrom(methods,setMethod)
+importFrom(methods,show)
 importFrom(methods,slot)
 importFrom(methods,slotNames)
-importFrom(rgdal,writeOGR)
-importFrom(sp,plot)
+importFrom(sf,st_as_s2)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_bbox)
+importFrom(sf,st_coordinates)
+importFrom(sf,st_crs)
+importFrom(sf,st_drop_geometry)
+importFrom(sf,st_filter)
+importFrom(sf,st_polygon)
+importFrom(sf,st_sf)
+importFrom(sf,st_sfc)
+importFrom(sf,st_transform)
+importFrom(sf,st_write)
+importFrom(stars,st_rasterize)
 importFrom(stats,na.omit)
 importFrom(stats,optim)
 importFrom(stats,quantile)

NEWS.md

@@ -1,5 +1,16 @@
 # prevR (development version)
 
+**BREAKING CHANGE:**
+
+* `prevR` objects now use `sf` spatial classes instead of those from `sp` (#27)
+* you can use `update_prevR()` to update a `prevR` object created with a
+  previous version of the package
+* `as.SpatialGrid()` method has been removed: use `make.grid.prevR()` instead
+* `point.in.SpatialPolygons()` and `NA.outside.SpatialPolygons()` have been
+  removed, see `st_filter_prevR()` instead
+* `kde()` and `krige()` methods now return results as an `sf` object, see
+  documentation for examples for plotting or exporting
+
 # prevR 4.0.1
 
 * Compatibility with `rlang` 0.3.0 and `ggplot2` 3.4.0 (#24)