MIAmaxent (development version)

MIAmaxent 1.4.1

• Patch for fixing CRAN check results: HTML5 standards for docs and oldrel-windows compatibility in vignette

MIAmaxent 1.4.0

• 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

MIAmaxent 1.3.0

• 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

MIAmaxent 1.2.0

• 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

MIAmaxent 1.1.1

• Patch for compatibility with dplyr v1.0

MIAmaxent 1.1.0

• 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.

MIAmaxent 1.0.0

Major changes

• 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

Minor changes

• 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

MIAmaxent 0.4.0

• 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.

MIAmaxent 0.3.7

• 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.

MIAmaxent 0.3.6

• First public release.