NEWS

enmSdmX 2025-02-19

Added responseCurves() for easy plotting of model response curves.
Bug fix: predictEnmSdm() no longer fails for GLMs when newdata has more columns than necessary.
Bug fix: trainMaxEnt() now removes over-parameterized models (thank you, ML!).
Bug fix: trainNS() correctly records the scale statistics when argument scale = TRUE.
Bug fix: trainByCrossValid() no longer crashes when trying to train MaxEnt models (thank you, ML!).

trainGAM() does not include interaction terms if interaction is NULL, and does not fail when interactions are included and the number of predictors is >2 (thank you, P.T.!).

Clarified mis-leading help in several functions, including all the trainXYZ() functions (thank you, PT!).

Replaced dependency on MuMIn with one one AICcmodavg for calculation of AICc. Received warning that MuMIn was going to be archived on CRAN.

Added function trainESM() for ensembles of small models.
Added several UTM coordinate reference systems accessible through getCRS().
Fixed bug in predictEnmSdm() for predicting kernel density models from the ks package.

Backwards incompatible: trainRF() uses ranger package for random forests (changed from randomForest package)
Backwards incompatible: geoFold() uses complete clustering method by default (changed from single)
New feature: trainGLM() and trainNS() can automatically scale predictors
New feature: Reworked trainGLM() to handle cases with large numbers of predictors
New feature: Added geoFoldContrast() for assigning geo-folds to background or absence sites
Better functionality: trainRF() now indicates if the response is binary using a binary argument (vs. family, which falsely implied more functionality than RFs have)

Better functionality: Expanded capacity of .calcWeights() (a hidden function) to handle different values for family

new feature: Added help page for troubleshooting running functions that support parallel operation
Bug fix: predictEnmSdm() when using a BRT model and predicting to a SpatRaster (thank you, Nikki C!)

New feature: Users can select clustering method in geoThin() and geoFold() (thank you, Pascal T!)
Bug fix: Example in customCRS() when GADM server is down
Bug fix:geoThin() which returned input if it was a data.frame*
Bug fix:geoThin() which returned a data.frame lacking coordinates if input was a data.frame (thank you, Pascal T!)

trainGLM(), trainNS(), and predictEnmSdm() now have options to automatically center and scale predictors. If a GLM or NS model created using trainGLM() or trainSN() is provided to predictEnmSdm(), it will automatically scale the predictors properly.

New feature: getCRS() (no arguments) now displays shiny table of all available CRSs
Bug fix: Fixed issue in nearestGeogPoints() when polygon lay under centroid
Bug fix: Fixed bug with "table" call of getCRS()

Removed dependency on dismo, replaced where possible by predicts; copied gbm.step() and predict() method for MaxEnt to enmSdmX as a momentary fix; would love a professional solution!
Added European Datum 1950 (ED50) to coordinate reference systems table
Added ability to export intermediate values for plotting in evalContBoyce()
Fixed spelling errors in crss data table (coordinate reference system names)

New feature: summarizeByCrossValid() now summarizes natural spline (NS) models
Bug fix: Bug experienced by some users using predictEnmSdm() and predictMaxNet() (Thank you, Nikki!)
Bug fix: trainByCrossValid() using improper call to evalContBoyce()
Bug fix: extract() bug in some examples