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.
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.CalibDataBat2 now contains slightly different elevation values (the one reported by field workers as opposed to those extracted from a specific elevation map).
CalibDataBat now contains different values for the column "site_ID".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).terra::extract() and lattice::lpolygon() now re-exported and lattice::panel.points()) no longer is.getprecip() was no longer working.
usethis::use_github_release() to create new releases (fixes #177).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().
NEWS.md rather than in inst/NEWS.Rd and use a markdown syntax.
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.
isomultiscape() was still using raster instead of terra.
PrecipBrickDE was still using raster instead of terra..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().
ISOSCAPE, CALIBFIT & ISOFIND are now also defined as S4 classes, which was necessary to design methods for saveRDS() which are compatible with terra.WORDLIST file which is used by devtools::spell_check() (via spelling::spell_check_package) to check for typos in the documentation.| or & which should have always been || or && (spotted via lintr::lint_package()).1:... which should have always been handled by seq_along or seq_len to avoid NULL issues (spotted via lintr::lint_package()).withr::defer).getprecip() now normalizes 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 provided to path when calling getprecip() in addition to "/wc2.1_30s_prec" -- or the reduced path which only contains the folder provided to 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)GNIPDataALLagg and GNIPDataEUagg was incorrect. (#158)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.
the function calibfit() gains an argument method that allows for selecting one of four calibration methods ("wild", "lab", "desk", "desk_inverse"). This allows for users to use:
Note: the "desk" methods allow for the consideration of a fractionation factor too (i.e. slope = 0). See ?calibfit for details. (#20 & #142)
getelev() has been completely rewritten so as to rely on the package elevatr to download elevation data. You should check ?getelev for learning how to use the new version of the function, but we retained the core principle of the previous function so that old workflow will only require minor adjustments. The new version still saves a *.tif file on the disk, albeit using a different file name to avoid (data) confusion. (#140 & #107)isofind() gains an argument neglect_covPredCalib that allows for the computation of a covariance term that was so far neglected in IsoriX. See ?isofind for details. (#143)prepraster() gains an argument values_to_zero to turn a range of elevation values to zeros (nullify negative elevation values by default). This is particular useful because the new version of get_elev() download an elevation raster that includes bathymetry..invert_reg() to invert regression (used for method "desk_inverse" in calibfit().plot() on an object created with calibfit(), the plotting function now returns the fitted values and CI for users to be able to make alternative plots. (#44)
xlim for the plotting function for calibration fits.line for customizing how to plot the regression line in calibration fits.calibfit() performs more check on extrapolation. (#119)plot() on an object of class ISOFIT, the x-axis for the plot showing the Matérn correlation should have a range more adequate irrespective when autocorrelation is strong over short distances. (#134)?plot() now contains a description of what symbols mean in plots. (#138)plot() on an object created with isofind(), the plotting function now detects sample of size 1 and no longer displays "Group" in the title of the assignment plot even if who = "group". (#120)data.frame as input should also now be compatible when provided with a tibble. (#118)calibfit()long_min, long_max, lat_min & lat_max function prepsources() now have explicit default values and should no longer be missing.
ylim for the plotting function for calibration fits.
CountryBorders and OceanMask have been rebuilt for possibly improving the compatibility with new sp & rgdal.
WorlClim has now changed address, so links have been updated.PrecipBrickDE containing monthly precipitation amounts for Germany.y_title for the plotting function for isoscapes to allow one to simply change the title.xlab and ylab for the plotting function for calibration fits.bla.bla have been renamed so as to match the structure bla_bla.
calibfit() gains an argument ... for more control.rasterLayer has been included for convenience.relevate() is now called prepraster().prepdata() is now called prepsources().elevation.raster has been renamed as raster.xxx.data has been renamed as data.zzz.R.
dontrun and donttest calls have been replaced by comments due to new R CMD check flags.downloadfile() is now exported.predict.HLfit(), the prediction are now being made by chunk of 1000 points instead of 150. This should lead to a tiny gain in performance.isoscape() was performing predictions twice every 150 (or now 1000) locations, this was not influencing the isoscapes produced, but this has now been corrected.prepraster() now produces an raster stored in memory if it is possible. This should prevent bugs that appears when using loaded rasters that were previously saved (the temporary link to the hard drive location is no longer correct in this case)..objective_fn_calib() has been moved within the function calibfit() as it is not used elsewhere.calibfit() as been prepared for a possible activation of a random effect for species ID in the future. But whether it would make sense or not remains to be determined..Fisher_method() now directly computes the exponential of the log pv if only one value is provided. This leads to much faster assignment in the case of a single observation.getprecip() and prepcipitate() were not handling paths manually defined properly.MULTIISOFIT.queryGNIP() has been renamed and is now called prepdata(), this function can also handle other datasets than GNIP.relevate() has been modified to make crop possible around the pacific meridian -180/180 (but several issues remain to handle extra plot layers automatically)..converts_months_to_numbers().IsoriX.options(example_maxtime = XX).
relevate() now allows for a cropping larger than the extent of the weather stations by means of the argument margin_pct.prepcipitate() to prepare the precipitation brick.getprecip() to download monthly precipitation rasters from WorldClim.isomultifit() fitting isoscapes per strata (month, year, or any "split").isomultiscape() building isoscapes averaged across strata.create_aliens() simulating of organism data.queryGNIP() have changed.
isofit() has changed.getelev() was breaking in some cases.GNIPdata has been updated and now contains data for 2014.downloadfile() to download non standard elevation raster or any other file.getelev() can perform MD5 sum checks if the package tools is installed.getelev() can display additional information during download if verbose > 1.animalID in the assignment dataset can now handle names with spaces.set_ll_warn from the sp package has been moved to .onLoad() (instead of .onAttach()) and the original state is now restored while unloading IsoriX.
getelev() lost its address argument as downloadfile() should now be used to download non-standard elevation rasters.*.Rd files for documentation are now generated with Roxygen2.queryGNIP() is now provided with a single month argument specifying the months to select.