IsoriX 0.9.3

New features

• a new global option title_delta_notation is available to modify the delta notation for all plotted isoscapes. The can be use, for example, to fix some issues with the display of the delta character, or for using another stable isotope than deuterium. See ?options_IsoriX for details.
• new datasets CalibDataBatRev, CalibDataBat2Rev, AssignDataRev and AssignData2Rev which are revised version of CalibDataBat, CalibDataBat2, AssignDataandAssignData2` (respectively). The bat fur isotope values were corrected to align with the current delta values for keratin reference materials (Soto et al. 2017, https://doi.org/10.1002/rcm.7893) ensuring comparability between formerly and more recently normalized datasets of delta values for deuterium.

Breaking changes

• the dataset CalibDataBat2 now contains slightly different elevation values (the one reported by field workers as opposed to those extracted from a specific elevation map).
• the dataset CalibDataBat now contains different values for the column "site_ID".

Major changes

• the functions prepsources(), calibfit() and isofind() emit warnings if some locations share the same location IDs or if several locations IDs correspond to a unique location. This should help users to spot issues in their data (fixes #133).

Minor changes

• the functions terra::extract() and lattice::lpolygon() now re-exported and lattice::panel.points()) no longer is.

Small fixes

• the URL for WorldClim data was outdated so getprecip() was no longer working.
• some internal code had arguments misspelt. It was working as a result of R's ability to do partial matching, but this was not good practice. It is now fixed (fixes #181).
• some links in the documentation were incomplete and flagged is some online CRAN checks ("Found the following Rd file(s) with Rd \link{} targets missing package"). This should now be fixed.
• function names should now be consistently displayed as computer code in the documentation.

Internal (geeky) changes

• the project is now being setup so that the development using VScode is possible.
• the format of the NEWS file has been changed to allow for using usethis::use_github_release() to create new releases (fixes #177).
• the description of datasets now relies on the markdown syntax.

IsoriX 0.9.2

• 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.

CRAN release version 0.9.1

Several spatial packages previously used by IsoriX are likely to retire sometimes in October 2023. The maintainers of those packages have recommended developers to instead rely on alternative packages which have been recently developed and which supersedes the old packages. As a consequence, we had to recode a lot of IsoriX for it to continue to work. For the most part, these changes are internal and should not impact much users, but it is possible that old workflows used to create plots will have to be adapted for the code to keep working. Moreover, IsoriX is not the only package that had to be overhault, other packages used by IsoriX are also being adapted, which means that the programming landscape is dynamic and bugs caused by incompatibility between packages are likely to surface. We will do our best to react quickly, but please let us know as soon as something goes wrong by dropping issues on the GitHub repository for IsoriX (https://github.com/courtiol/IsoriX/issues). All this change can be perceived as annoying, but it is also for the best: it will allow us to add new features more easily in IsoriX in the future and it also makes it easier for users to convert IsoriX outputs so as to manipulate them using packages such as sf and ggplot2.

Major change

• IsoriX no longer relies on the package raster. It instead now uses terra for handling rasters (#90 #161).
• IsoriX no longer relies on the package sp. Plotting functionalities from sp have now been replaced by direct calls to lattice. For now, we had to implement methods and generics calling lattice in IsoriX, but those should ultimately be handled within rasterVis and lattice. See the file interim_avoid_sp.R for details.

Minor change

• getprecip() now normalises the input file and returns the path where the precipitation rasters are stored.
• prepcipitate() can now handle as input for path = either the full path to the files returned by getprecip() -- which contains the folder inputed in path when calling getprecip() in addition to "/wc2.1_30s_prec" -- or the reduced path which only contains the folder inputed in path when calling getprecip().
• getprecip() now changes the timeout R options temporarily so as to avoid the download to fail because the default timeout setting is too short (#148).
• the documentation for the datasets GNIPDataALLagg and GNIPDataEUagg was incorrect (#158).
• one message about possible extrapolation during calibration was erroneous and is now removed (#159).

Geeky change

• OceanMask and CountryBorders are no longer stored as RDA files in /data, but as RDS files in /extata since objects created with terra cannot be saved as RDA files. These files are automatically loaded when the package is attached.
• elevatr moved from Imports to Suggests (#157).

CRAN release version 0.9.0

v0.9.0

Small edits and cashing info

CRAN release version 0.8.3

v0.8.3

Bump version number

CRAN release version 0.8.2

v0.8.2

Merge remote-tracking branch 'origin/master'

CRAN release version 0.5

This is the version that we have just submitted to CRAN!!

First CRAN release

This is the first official release of IsoriX!