flexsdm 1.4.2

• tune_max: a grid combination whose fits all failed was assigned the previous combination’s model/performance (stale mod); now initialised to NULL and checked with is.null() (#478)
• fit_max: the final refit fallback used the CV loop index in its check and could discard a successful fit; it now uses is.null(mod) and falls back on presences + background (data_2) (#478)
• tune_svm: removed na.omit() on partition performance so all combinations are compared across the same partitions (#478)
• fit_gbm: final model now uses bag.fraction = 0.9, consistent with the CV models; tune_gbm validity guard also uses 0.9 (#478)
• occfilt_geo: moran method no longer collapses to one record (Inf distance) when no Moran’s I falls in the selection window; the closest value is used, and the threshold comparison is now numeric (#479)
• sample_pseudoabs: factor maskval now matches raster category IDs in the kmeans, env_const, env_clust and env_kmeans methods (#479)
• get_absences: NA in the species column no longer creates phantom NA rows (#479)
• calib_area: mcp/bmcp with three or more groups no longer errors (#479)
• part_sband: fixed uninitialised imoran_bands_c assignment (#479)
• CRAN review: every exported function now has a small, fast example that is executed on CRAN (the longer examples remain inside \donttest{}); examples of sdm_directory() and homogenize_na() / extra_eval() no longer leave files in the working directory or alter par()
• sdm_directory: main_dir no longer defaults to a sub-folder of the working directory and must be provided by the user
• Functions no longer call set.seed() with a fixed number (fit_*, occfilt_geo, correct_colinvar, p_extra, …). Results can be reproduced by calling set.seed() before running them; tune_*, sdm_varimp and sdm_uncertainty draw the seeds used by parallel workers from the caller’s random-number stream
• tune_gbm, tune_max, tune_net, tune_raf, tune_svm, sdm_varimp and sdm_uncertainty: no cluster is started when n_cores = 1, the computation runs sequentially in the current session
• occfilt_geo: the warn option is restored when the function exits
• Gaussian process code used by fit_gau() and esm_gau(), fit_max() and tune_max(): print() and cat() calls replaced by message() or warning() (or removed)
• Check time after the last CRAN incoming check (examples took 161 s and tests 104 s on win-builder): the examples executed on CRAN are now tiny toy examples without plotting (the full examples, with their plots, are inside \donttest{}), test files that take more than a fraction of a second are skipped as a whole on CRAN with skip_on_cran() (they run when NOT_CRAN=true), and vignette v04 is now precomputed (source in vignettes/v04_Red_fir_example.Rmd.orig)
• DESCRIPTION: reworded “ensembling” in the Description field

flexsdm 1.4.1

• get_absences: Function to build a presence-absence database from multi-species occurrence data, by @sjevelazco
• occ_reproject: Function to reproject occurrence coordinates to a new coordinate reference system, by @sjevelazco
• minor warnings and package formality were fixed, by @sjevelazco 467
• correct_colinvar: Unicode box-drawing characters in the documentation’s example directory tree were replaced with plain ASCII, fixing a LaTeX error that caused the PDF manual build to fail on CRAN, by @sjevelazco
• Vignette v07_Complete_workflow: two dataset links were missing the https:// scheme (www.doi.org/...), which CRAN flagged as invalid URIs; fixed to https://doi.org/..., by @sjevelazco
• tune_max: fixed a bug where the default hyperparameter grid (used when grid = NULL) tested a regmult step of 0.05 instead of the documented 0.5, producing ~10x more combinations than intended, by @sjevelazco
• Test suite and vignette runtimes were substantially reduced in response to CRAN’s request (test suite ~17 min -> ~3 min; vignette rebuilding ~14 min -> ~2 min, as measured locally) by shrinking hyperparameter grids, dataset sizes, and replicate/fold counts in tests and vignettes, and by gating the most expensive/redundant test cases behind skip_on_cran(), by @sjevelazco
• Further reduced test and vignette runtimes after win-builder’s automated “Overall checktime > 10 min” rejection, by gating most secondary/edge-case assertions in the tune_* and sdm_uncertainty test files behind skip_on_cran() (kept a representative case running on CRAN for each), and by shrinking dataset sizes and search-grid sizes (part_sband, part_sblock, occfilt_env, occfilt_geo) further in the vignettes, by @sjevelazco
• Test and vignette runtimes were cut again after CRAN’s incoming check (tests ~6 min, vignettes ~6 min on win-builder): all but one representative test_that() block per test file (or none for the slowest files) now run only when NOT_CRAN=true, and vignettes v01, v02, v03, v05 and v06 are now precomputed (source in vignettes/*.Rmd.orig, excluded from the build), by @sjevelazco
• Shortened the \donttest{} examples of the slowest functions (sdm_varimp, fit_max, fit_gau, tune_*, esm_gam, fit_gam, occfilt_geo, sdm_summarize, esm_max) by using smaller hyperparameter grids, fewer folds/replicates and subsampled datasets (~10 min -> ~3.5 min locally), by @sjevelazco
• fit_raf: the ntree argument was ignored in the no-partition fit and in the cross-validation fits (hardcoded to 500); it is now used everywhere, reported in #474, by @sjevelazco
• tune_raf: the final model now uses the tuned ntree instead of the randomForest default, #474, by @sjevelazco
• esm_gbm: n_trees and shrinkage were hardcoded and are now forwarded to fit_gbm; esm_net: size and decay are now forwarded to fit_net, #474, by @sjevelazco
• esm_svm: performance_part was labelled esm_gau; now esm_svm. fit_svm and fit_max: partition ids in performance_part were wrong (earlier folds were relabelled), #474, by @sjevelazco
• Removed the DeepWiki badge from README.md, whose URL returned HTTP 429 in CRAN’s URL check, by @sjevelazco
• sdm_eval: fixed a bug in the KAPPA metric calculation, by @sjevelazco
• sample_background and sample_pseudoabs: fixed three bugs in categorical maskval/k-means handling reported in #472: maskval on a factor raster was resolved to its row position in the levels table instead of its actual category ID; the k-means branch of sample_pseudoabs masked and overwrote the environmental raster with the region raster instead of the other way around; and the internal kf() helper could fail with “differing number of rows” when the environmental raster had no NA cells, by @sjevelazco

flexsdm 1.4.0

• map_env_dist: C++ function to calculate Euclidean and Mahalanobis distance was implemented, by @sjevelazco 463
• extra_eval: C++ function to calculate Euclidean and Mahalanobis distance was implemented, by @sjevelazco 463
• fit_dom: C++ function to calculate gower distance was optimized, by @sjevelazco 463
• map_env_dist: C++ function to calculate gower distance was optimized, by @sjevelazco 463
• msdm_posteriori: a new argument that assumes unsuitable cells with presences as patches. This is only used in the ‘lq’ approach, by @sjevelazco 461
• sdm_eval: Boyce metric was readapted based on enmSdmX package, by @sjevelazco 457
• msdm_posteriori: now car return semi-binary suitability maps, by @sjevelazco 455
• part_senv: new argument to use or not presences-absences coordinate to perform environmental partition, by @sjevelazco 445

flexsdm 1.3.9

• map_env_dist was improved. Now it is possible to calculate Euclidean and Mahalanobis distances in addition to the Gower distance (Domain algorithm), by @sjevelazco.
• sdm_eval() now calculates three additional performance metrics: the Matthews Correlation Coefficient (MCC). the Continuous Ranked Probability Score (CRPS), and a prevalence-weighted average of TPR and TNR (W_TPR_TNR), by @sjevelazco 445.
• fit_gbm() and tune_gbm() were improved to prevent the argument is of length zero error. This was achieved by adding a safeguard that dynamically adjusts n.minobsinnode based on the size of the training data partition, ensuring it remains valid for the gbm algorithm, by @sjevelazco 445.
• sdm_uncertainty This new function calculates species distribution model uncertainty using a bootstrap procedure, by @sjevelazco #442
• fit_ functions now can handle partition = NULL, by @sjevelazco #442
• A new vignette demonstrating how to model several species and periods of time was added by @mrose048 @sjevelazco @iminoli-dev 438

flexsdm 1.3.8

• fit_, tune_, esm_ and fit_ensemble functions now return a performance table for each partition and replicate (performance_part), by @sjevelazco #432 and 434
• p_pdp was improved to depict exactly training range values when projection data are used, by @sjevelazco #429
• sample_pseudoabs a sample approach was implemented based on environmental K-means, by @sjevelazco #410
• sample_pseudoabs K-means step was improved for the geoenv_const_kmeans approach, by @sjevelazco #410
• p_extra Now can handle binary maps to plot suitability or extrapolation values in the geographical or environmental space, by @sjevelazco 418
• map_env_dist This new function calculates environmental distance between presences and projection data. Only the nearest Gower distance was implemented (Domain algorithm), by @sjevelazco 419
• fit_dom This is a new function to fit and validate the Domain algorithm, by @sjevelazco

flexsdm 1.3.6

• 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 a test protocol was 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

flexsdm 1.3.4-5

• 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

flexsdm 1.3.4

• 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

flexsdm 1.3.4

• 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

flexsdm 1.3.3

• 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

flexsdm 1.3.2

• 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

flexsdm 1.3.1

• 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. #