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MIAmaxent (development version)

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.