Changelog • flexsdm

flexsdm 1.3.x

sample_pseudoabs it was implemented a sample approach based on environmental K-means #410
sample_pseudoabs K-means step was improved for the geo_env_km_const approach #410
p_extra Now can handle binary maps to plot suitability or extrapolation values in the geographical or environmental space 418
map_env_dist This new function calculates environmental distance between presences and projection data. Only the nearest Gower distace was implemented (Domain algorithm) 419
fit_dom This is a new function to fit and validate Domain algorithm

occfilt_geo adapted to test different values for the three methods by @sjevelazco in 386
occfilt_env now can filter with several bins by @sjevelazco in 388
occfilt_select was created and test protocol written by @sjevelazco in 389
occfit_select included in vignette and website by @sjevelazco in 390
mean change in sdm_predict to handle 0 weight value for weighted mean by @sjevelazco in 391
documentation of occfilt_select was improved by @sjevelazco in 392
It is possible to tune ntree hyperparameter of random forest algorithm by @sjevelazco in 393
correct_colinvar can be used with species points by @sjevelazco in 394
Update pkg_citation.md by @mrose048 in 396
sdm_varimp was added and tested by @mrose048 and @sjevelazco in 399
min change in warning message calib_area by @sjevelazco in 400

min change in interp function by @sjevelazco in 362
min change in occfilt_geo by @sjevelazco in 364
Rlof was removed from dependencies by @sjevelazco in 365
min change in occfilt_geo by @sjevelazco in 370
new argument in occfilt_geo by @sjevelazco in 371
esm_ functions were improved by @sjevelazco in 373 & 373
geographically constraint cell of env_var argument in correct_colinvar by @sjevelazco in 374
new argument in correct_colinvar by @sjevelazco in 375
calib_area was sped up by @sjevelazco in 377
correct_colivar was fixed and improved, FA method by @sjevelazco in 383
occfilt_geo ‘defined’ method was fixed by @sjevelazco in 384

it is possible to restrict the cell used to perform collinearity reduction analysis to a geographical area smaller than the full extent of environmental variables in correct_clinvar()
esm_ family function was improved and debugged
occfilt_geo has a new argument “rep” to control number o repetition to filter occurrences

rgeos was removed from dependencies #356
New vignette about how use different tools to explore model extrapolation and truncate models was added #352
Univariate and combinatorial extrapolation metric added to extra_eval.
Minor bugs were fixed to project PCA for other time periods #351
Best grid raster names was changed to .part in part_sblock and part_sband
Improvements in correct_colinvar to speed up function when using maxcell argument
Improvements in correct_colinvar to project PCA for other time periods

Improvements in correct_colinvar It is now possible to sample rasters to reduce machine memory and speed up the process
Improvements in sdm_predict It is possible predict model in chunks to reduce machine memory
p_extra, p_pdp, and p_bpdp were fixed
New function p_bpdp Bivariate Partial Dependent Plot
New function data_bpdp Calculate data to construct bivariate partial dependence plots
Improvements in p_dpd Calculate data to construct partial dependence plots

New function p_extra Graphical exploration of extrapolation or suitability pattern in the environmental and geographical space
New function p_pdp Partial Dependent Plot
New function data_pdp Calculate data to construct partial dependence plots

New argument “crs” added to function msdm_posteriori
New argument “sp_name” in sample_background and sample_pseudoabs
raster, flexclust, ape, and sp were removed from dependencies
Functions using CRS data have improved codes
It is possible use a numeric value to specify threshold in msdm_posteriori
extra_eval can use tibble or SpatRaster object in env_calib argument
extra_truncate has a new argument to define values used for model truncation and documentation was improved. #