ENMTools 1.0.4

I forgot to create GitHub releases for versions 1.0.2 and 1.0.3, but I'm going to try to be good about it from now on. Here are the intervening changes:

ENMTools 1.0.4

Bug Fixes

• Raes and ter Steege-style tests were returning incorrect evaluate objects, although plots and p values were correct
• test.prop = "block" wasn't working correctly

Enhancements

• Suppressing maxent startup messages by default
• Added support for bias layers to modeling functions
• Added check.env function to homogenize raster stacks so NAs propagate across layers

ENMTools 1.0.3

Enhancements

• Brought up to date for new spatstat changes
• Removed ppmlasso until it is brought back on CRAN

ENMTools 1.0.2

Enhancements

• Added a new general-purpose function for making background layers from point data. It can do both circular buffers and buffered convex hulls, and can return points, a polygon, or a raster. Converted the existing background buffer functions to just call this one, and will eventually deprecate the single-application functions.
• Added ability to select which corner you want for "block" validation.
• Added a function called multi.variogram which takes a raster stack, builds a variogram for each layer, and then plots the gamma for each variable as a function of distance, scaled by the maximum gama for that variable. This allows users to get some idea of the level of spatial autocorrelation in each predictor variable.

ENMTools 1.0.1

This is the first post-CRAN update to ENMTools, which fixes a few minor issues and adds some useful new features.

Enhancements

• Added variable importance tests via interface with the vip package
• Added clamping for the predict functions, including plots of where
  clamping is happening
• Added clamping for model construction functions, with a TRUE/FALSE
  switch defaulting to TRUE
• Changed naming conventions for predict functions so that the
  suitability raster is in the $suitability slot, just as with
  modeling functions
• Added progress bars for a lot of tests
• Added “verbose” option for a lot of functions, defaulting to FALSE

Bug fixes

• Added some code to fix a bug with recalibration. Basically
  CalibratR’s call to parallel was tanking on Mac OS, and there’s just
  a little code snippet that needed to be added to the call to make
  that work.
• Fixed interactive.plot generic and moved the function to its own
  file to make it easier to extend
• Temporarily suppressing some warnings coming out of leaflet that
  are being produced by the recent rgdal changes
• Fixed background sampling code to resample when necessary
• Changed enmtools.ranger demo code to actually use ranger instead
  of rf
• Fixed code for calculating p values for some of the hypothesis
  tests, the old code was getting wrong answers when there were
  repeated values

Initial beta release

This is intended to be the first official beta release for ENMTools. The release is being made so that we can provide a doi citation target for upcoming publications.