Fix issues related to migration to **terra** (#174)

* Edits

* Fix typos and outdated URLs

* First saveRDS & readRDS methods (#172)

* PrecipBrickDE: raster -> terra

* isomultiscape was broken

* Methods for saveRDS and readRDS

* Remove pdf after test

* Add bookdown link

* Adapt to new IsoriX

* Omnibus saveRDS fn

* Omnibus saveRDS fn

* Use distinct Rproj for bookdown and package

* Add comment on terra

* `terra::aggregate()` does not na.rm by default (unlike `raster::aggregate`)

* Minor edits for consistency

* Fix typo(s)

* NEWS moved to md

* Update spelling

* Fix typo(s)

* Reoxygenise

* Minor edit

* Reformatting

* Update README

* Fix wrong index in tests

* Capture spaMM warnings and messages

* New IsoriX options for reviving spaMM warnings and messages

* Fix typo(s)

* Better handle NAs in predictions

* `terra::aggregate()` does not na.rm by default (unlike `raster::aggregate`)

* Outdated?

* Reformating

* Add local tests

* Update README

* Better handle NAs

* Add info origin def

* Add bullet points to issue template

* Add missing namespace

* `styler:::style_active_pkg()` and `lintr::lint_package()`

* Add path in example

* Revise spacing

* Local test for RDS

* Solve S3/S4 remaining issues

* Complete NEWS

* Polish links

* Update URL

* `usethis::use_spell_check(lang = "en-GB")`

* `styler:::style_active_pkg()`

* `usethis::use_cran_comments()`

* Add steps

* Update CRAN comment

* More steps

* Bump version number

IsoriX/.Rbuildignore

@@ -3,3 +3,6 @@ R/testpackage\.R
 man/isosim\.Rd
 README\.md
 
+^.*\.Rproj$
+^\.Rproj\.user$
+^cran-comments\.md$

IsoriX/DESCRIPTION

@@ -1,5 +1,5 @@
 Package: IsoriX
-Version: 0.9.1.9999
+Version: 0.9.2
 Encoding: UTF-8
 Title: Isoscape Computation and Inference of Spatial Origins using Mixed Models
 Authors@R: c(
@@ -41,10 +41,11 @@ Suggests:
     rgl,
     spelling,
     testthat,
-    webshot2
+    webshot2,
+    withr
 LazyData: true
-URL: https://github.com/courtiol/IsoriX/
-BugReports: https://github.com/courtiol/IsoriX/issues/
+URL: https://github.com/courtiol/IsoriX, https://bookdown.org/content/782
+BugReports: https://github.com/courtiol/IsoriX/issues
 RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Language: en-GB

IsoriX_project.Rproj → IsoriX/IsoriX.Rproj

@@ -1,8 +1,8 @@
 Version: 1.0
 
-RestoreWorkspace: No
-SaveWorkspace: No
-AlwaysSaveHistory: No
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
 UseSpacesForTab: Yes
@@ -14,7 +14,5 @@ LaTeX: pdfLaTeX
 
 BuildType: Package
 PackageUseDevtools: Yes
-PackagePath: IsoriX
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace

IsoriX/NAMESPACE

@@ -10,12 +10,17 @@ S3method(print,CALIBFIT)
 S3method(print,ISOFIND)
 S3method(print,ISOFIT)
 S3method(print,ISOSCAPE)
+S3method(readRDS,character)
+S3method(saveRDS,CALIBFIT)
+S3method(saveRDS,ISOFIND)
+S3method(saveRDS,ISOSCAPE)
 S3method(summary,CALIBFIT)
 S3method(summary,ISOFIND)
 S3method(summary,ISOFIT)
 S3method(summary,ISOSCAPE)
 export("crs<-")
 export("ext<-")
+export()
 export(RdBuTheme)
 export(calibfit)
 export(cellSize)
@@ -45,9 +50,15 @@ export(prepcipitate)
 export(prepraster)
 export(prepsources)
 export(rast)
+export(saveRDS_IsoriX)
 export(shift)
 export(values)
 export(xyplot)
+exportClasses(CALIBFIT)
+exportClasses(ISOFIND)
+exportClasses(ISOSCAPE)
+exportMethods(readRDS)
+exportMethods(saveRDS)
 importFrom(grid,gpar)
 importFrom(grid,grid.text)
 importFrom(lattice,panel.points)
@@ -65,5 +76,7 @@ importFrom(terra,plot)
 importFrom(terra,points)
 importFrom(terra,polys)
 importFrom(terra,rast)
+importFrom(terra,readRDS)
+importFrom(terra,saveRDS)
 importFrom(terra,shift)
 importFrom(terra,values)