ENMTools - 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.

Biosphere - Species Distribution Modeling - R
Published by danlwarren almost 4 years ago

ENMTools - 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

Biosphere - Species Distribution Modeling - R
Published by danlwarren over 4 years ago

ENMTools - 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.

Biosphere - Species Distribution Modeling - R
Published by danlwarren almost 6 years ago