MIAmaxent (development version)

Added vignette on variable selection and model evaluation, using NCEAS benchmark data

MIAmaxent 1.3.1

Allow raster’s Raster*-classes to be passed to projectModel(), for backward compatibility

Handling of NA values in forward stepwise selection (whether cause by unstable parameter estimates, or zero deviance explained)
Bug fix when DV selection yields Chisq <= 0 (e.g. when identical DVs included)
Added ‘filename’ argument to projectModel() to write raster predictions to file
Changed name of calculateFTVA() to calculateRVA(), for consistency with source publication
Package overview documented as per “Documenting packages” in R-exts
Migrated dependency from raster to terra

Enhancement: added ‘retest’ argument to selection functions
Internal utility: shortcut function for deriving stricter selectDVforEV from lenient selectDVforEV
Added calculateFTVA() function for variable contribution
Added ‘duplicates’ argument to readData() to handle cells with multiple occurrence coordinates more explicitly

Added ellipsis to plotFOP() for easier customization of graphic
Feature request: added ‘densitythreshold’ argument to plotFOP()
Predictions NA when a transformation returns NaN.
Minor documentation edits to readData and testAUC
Simplification of F-statistic calculation; may cause rounding differences with respect to previous versions.

Model fitting implemented as infinitely-weighted logistic regression, so that all computation can be done natively in R (maxent.jar no longer required).
Implements choice of algorithm: “maxent” for maximum entropy or “LR” for standard logistic regression (binomial GLM).
No files written to system unless write = TRUE
Choice of Chi-squared or F-test in nested model comparison
More consistency in arguments across top-level functions
Selection trail tables simplified and clarified

increased flexibility in graphics arguments passed to plotting functions
quiet option added to top-level functions performing selection
readData() automatically removes duplicates when two or more presences/absences fall in the same cell
readData() discards presence locations with missing EV data
formula argument to selectEV() function, to specify starting point for selection
plotFOP() smoother changed to loess from exponentially weighted moving average
plotFOP() plots data density behind FOP values
plotFOP() returns plot data invisibly
plotResp() and plotResp2() take identical arguments, the first of which is a model object
projectModel() takes data in data.frame or raster classes, and plots output spatially in the case of the latter
trainmax argument removed from selectDVforEV() and selectEV()
testAUC() plotting optional

Model ranking within selection rounds based on p-value and then F-statistic (tiebreaker), rather than simply F-statistic
Directories specified by ‘dir’ argument are created if they do not already exist.
Existing results in directories specified by ‘dir’ argument are overwritten, if desired.
Fixed bug in selectEV that occurred when the last round of model selection before interaction terms did not result in a significant variable.
Unnecessary dependency on Hmisc removed.

Removed version minimums for dependencies which are default packages, to allow r-oldrel binary.
Changed names of toy data used in examples for better organization.

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