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IsoriX 0.9.2

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@courtiol courtiol released this 14 Nov 10:12
v0.9.2
0143f47

  • main release goal

    • This release restores some key features that had been lost after dropping the direct dependencies raster and sp in v0.9.1.:
      • the possibility to save and reload objects created by IsoriX (now via saveRDS() and readRDS()). (#172)
      • the possibility to plot oceans and other masks containing "holes" (thanks to changes in lattice and rasterVis). (#169, #170)

  • breaking changes

    As compared to IsoriX versions < 0.9.1, the following changes may break existing code:

    • code for plots:

      layer(sp.polygons(CountryBorders, col = "white")) +
layer(sp.polygons(OceanMask, col = "white", fill = "lightgreen"))

      now needs to be replaced by:

      layer(lpolygon(CountryBorders, border = "white")) +
layer(lpolygon(OceanMask, border = "white", col = "lightgrey"))

      Notice both the change in the function used to plot polygons and the change in the arguments used to control the colour of the borders and the colour of the fill.
      Similarly, the function sp.points() should be replaced by lpoints() and so on.

    • saving and reloading objects save() & load() can no longer be used, one must instead use saveRDS() & readRDS().

  • new features

    • the NEWS (contained in this file) are now stored in NEWS.md rather than in inst/NEWS.Rd and use a markdown syntax.
    • it is now possible to have missing values in predictors used to build isoscapes and in the isoscapes themselves.

  • major changes

    • plotting methods for polygons, lines and points have been removed from IsoriX and are now handled by lattice and rasterVis.

    • new S3 and S4 methods saveRDS() for objects of the class ISOSCAPE, CALIBFIT & ISOFIND (see ?serialize for details).

    • new S3 and S4 method readRDS() which should be able to read objects created in IsoriX, as well as objects created with terra and objects created otherwise.

      In case of issues reading RDS files not created by IsoriX, try using base::readRDS() with the namespace base:: mentioned explicitly and please let us know of this issue.

  • minor changes

    • the bookdown is now listed in DESCRIPTION.
    • some old URLs have been updated.

  • bug fixes

    • the function isomultiscape() was still using raster instead of terra.
    • the object PrecipBrickDE was still using raster instead of terra.

  • internal (geeky) changes

    • new function .safe_and_quiet_predictions() which turns wraps around spaMM::predict.HLfit(), turns warnings into messages, allows not to display the same messages many times, and outputs NAs when spaMM::predict.HLfit() fails. For testing, options_IsoriX(spaMM_debug = TRUE) may be used to restore the original behaviour of spaMM::predict.HLfit().
    • the classes ISOSCAPE, CALIBFIT & ISOFIND are now also defined as S4 classes, which was necessary to design methods for saveRDS() which are compatible with terra.
    • the package now contains a WORDLIST file which is used by devtools::spell_check() (via spelling::spell_check_package) to check for typos in the documentation.
    • fixed various | or & which should have always been || or && (spotted via lintr::lint_package()).
    • fixed various sequences of the form 1:... which should have always been handled by seq_along or seq_len to avoid NULL issues (spotted via lintr::lint_package()).
    • package withr now suggested; we use it to automatically delete a file created during testing (using withr::defer).
    • instead of one Rproj file used to handle both the package and the bookdown development, we now rely on 2 Rproj files, which solves some limitations encountered with usethis.
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