Version 1.4.1 with minor bug fixes

Hey everybody,
   
Here's a new version that fixes a couple of minor problems with version 1.4.  There was a problem with newlines in the sorted.csv file for the identity test in the previous version, so that all values would appear on a single line.  That should be fixed now, as should a bug that was causing extraneous text to appear after visiting the ENMTools Options page.


ENMTools 1.4.1

Testing new version of ENMTools

Sorry for the long delay between posts/versions; my postdoctoral work took me in a direction that made it very hard to update for a while.  I'm now at The Australian National University for a new postdoc, though, and I'm hoping that I'll have a little more time to keep up with ENM Tools.  On that front, here's an updated version that fixes a few minor problems:

http://www.danwarren.net/enmtools/builds/Test/ENMTools_1.4.zip

This update consists of two main revisions and a bit of code-tidying.  The first revision was to fix the "Resample from raster: exponential" function, which didn't work properly with scores over 1.  The second was to add some code to calculate overlaps and breadths using a different method that is suitable for larger files.  To use this method, just go to the ENMTools options and click the button for "Large file overlap/breadth".

Unfortunately at the moment there's only a perl script version available - Activestate updated the Perl Dev Kit so that it stopped working with Tkx, and I'm waiting to find out how much it's going to cost to upgrade.  If anyone out there has a working copy of Perlapp and can build Windows and OSX version, feel free.  You would have my, and everyone else's, heartfelt thanks.  We'll try to get something worked out soon regardless.

Unfortunately the issue with Mac line endings is still not fixed - I don't know if it's a Tk issue or what, but it's proving more challenging to fix than it should be.  I will keep hacking at it, though, as the line ending issue is a major pain in the ass for everyone, including me.  

If anyone out there has specific requests for the next revision, please let me know!

ENMTools 1.3 is out!

We have a shiny new version of ENMTools ready to go! This version includes some minor bug fixes and adds a few new features. The new features are described in detail in the user manual, but here's a quick rundown:

*Handy tool for eliminating duplicate occurrence points from a .csv file using either exact location or an ASCII grid.
*New feature to make maps of the spatial distribution of residuals from a regression between two environmental variables (Warren and Moskwik, in prep).
*Tool to standardize raster files so that they sum to 1 over the geographic space.
*Tool for calculating range overlap from rasters, applying a user-selected presence/absence threshold.
*New rank-based overlap metric for rasters (RR) that estimates the probability that a pair of rasters agree in the relative ranking of any two patches of habitat (Warren and Seifert 2011).
*Addition of RR metric to hypothesis tests.

The manual has been expanded considerably, including some basic troubleshooting FAQs.

New Functions in ENMTools to Identify Environmental Barriers to Dispersal

We're pleased to announce publication of a paper that uses new functions in ENMTools to identify environmental barriers to dispersal. These new features of ENMTools permit identification of two types of environmental barriers that might be acting to maintain geographic boundaries between populations in nature: (1) steep environmental gradients and (2) ribbons of unsuitable habitat. ENMTools is now able to assess the significance of such boundaries in nature using geographically informed randomization procedures. Although you may have noticed that these 'new' features have been available in the last few releases of ENMTools, they haven't been published on previously, or really been explained in enough detail to make them useful. We hope that this will change with publication of this paper! For more details on how to use these new 'range breaking' methods please see section II.c.iii of the ENMTools manual [pdf document].

Glor, R. E. and D. Warren (Accepted Article) Testing ecological explanations for biogeographic boundaries. Evolution. [doi link]

New version of ENMTools up

We've got a new version of ENMTools. This update fixes a couple of issues and adds one handy little tool. The manual is not completely updated yet, but the program is here:

http://www.danwarren.net/enmtools/builds/Release/ENMTools_1.2.zip

Here's what has changed:

-The problems with the I metric that were mentioned in a previous post/email have been fixed. It should now scale from 0 to 1.

-The breadth metrics have both been changed to standardized niche breadth, scaling from 0, where only one grid cell has a nonzero suitability score, to 1, where all grid cells are equally suitable.

-There's a new tool called "standardize rasters". It basically just takes a bunch of rasters and scales suitability scores so that they sum to 1.

-The model selection functions are now in the main build, but as yet are not documented in the manual. See my previous blog post/mailing for how to use that function. For more details read the Warren and Seifert paper currently in the "accepted" section of Ecological Applications' web page.

Error in I metric (but don't panic!)

Thanks to a manuscript by Dennis Rödder and Jan Engler that is currently in revision for Global Ecology and Biogeography (entitled “Quantitative metrics of overlaps in Grinnellian niches: advances and possible drawbacks”), we have discovered a typographical error in our description of the niche overlap metric I, Eq. (3) of Warren, Glor and Turelli (2008, Evolution 62:2868-2883). Unfortunately, this error also found its way into ENMTools. Fortunately, the error is only a scaling issue. It does not affect the statistical tests presented in our paper or any known test based on ENMTools. Those tests use only relative rankings of overlaps (rather than specific values), and our error does not change relative rankings.

The formula we provided for Hellinger distance, H, is one of several alternatives. In the form we provided, H ranges from 0 to Sqrt(2). The incorrect formula we published is I = 1 – (H/2), which ranges from 1 – (1/Sqrt(2)) to 1 (not 0 to 1 as we stated). The correct formula is 1 – (H^2/2), which ranges from 0 to 1. Denoting our incorrect formula, Iold, and the intended formula, Icorrect,

Icorrect = 1 – 2(1 – Iold)^2.

Because both formulas decrease monotonically from 1 with increasing H, our typo does not alter relative rankings of I values. Hence, it does not affect P values obtained from resampling-based tests of niche identity or similarity, such as those in Warren et al. (2008). If you have manuscripts that use the I metric, there is no need to re-run any analyses based on ranks; and resulting conclusions about niche identity or similarity remain valid.

We will release an updated version of ENMTools shortly that corrects this error. We thank Dennis Rödder and Jan Engler for bringing it to our attention. We apologize for any inconvenience it has caused.

Model selection paper now online

The paper I've been working on with Stephanie Seifert on model selection in Maxent is now available as a preprint from Ecological Applications. The paper demonstrates that AIC and BIC can be useful in setting regularization, and also acts as the first demonstration of the utility of ENMTools' data simulation functions.