Tuesday, August 4, 2015

Tutorials on Maxent and ENMTools

A few months ago, I gave a workshop at James Cook University in Townsville, Australia.  We covered some basic concepts for niche modeling and ecological biogeography, and then ran through some sample exercises in Maxent, ENMTools, and ecospat.

First, here's a tutorial on basic ideas and procedures for niche modeling:



Then a very brief foray into the different assumptions that need to be made when using niche models for different purposes in ecological biogeography:






The main event is a two hour demo of ENMTools.  We're having problems with the audio right now, but we'll try to get it uploaded shortly.



For those of you who want to play along at home, the demo data is here:

http://www.danwarren.net/enmtools/Demos.zip

I really want to thank JCU for having me out, and in particular Megan Higgie and Conrad Hoskin for their hospitality.

Tuesday, September 3, 2013

Fixed error in resampling in ENMTools 1.4.3

I've fixed a bug in 1.4.3 that kept the "resample from raster" command from printing results to the output file.  It was a very silly error; basically I had disabled printing for debugging and forgot to turn it back on!

Anyway, it's fixed now and should be working fine.  While I was at it, I fixed it so that the resample command now uses the output directory set in the ENMTools Options tab, instead of printing to the directory where the layers you're resampling from are located.  The new version is here:

http://www.danwarren.net/enmtools/builds/ENMTools_1.4.3.zip

Saturday, July 6, 2013

ENMTools 1.4.3

While trying to iron out the weirdness of Perl with Mac line endings in .csv files (unsuccessfully), I added some bits of code that seem to have caused the model selection functions in ENMTools to stop working on some input files.  Here's a fixed version.

Sunday, June 16, 2013

Version 1.4.2, adding sampling without replacement to "Resample From Raster" function

By request, I have added a radio button for sampling with or without replacement to the "resample from raster" function.  This function was initially intended for simulating data for methodological studies, but can also be used to sample random points for conducting significance tests for AUC values a la Raes and ter Steege 2007 (using the "constant" setting).  The initial setup was to always resample with replacement.  This isn't ideal for the Raes and ter Steege test, but was unlikely to have any real impact except on models built over very small geographic regions and/or those with very coarse resolution (i.e., study areas with a very small number of grid cells).

I'll post a detailed tutorial eventually, once I get a spare moment to breathe.  Long story short: if you have N data points and want to do X replicates, you load up a raster file that has data in grid cells for your study area and nodata values outside the study area.  This can even be the .asc file for your model itself.  Use the resample from raster tool, constant sampling function, to sample N data points for X replicates.  Then build a single model for each of those replicates using the same study area, model construction settings, and environmental predictors as in your model for your empirical data.  Collect all of the AUC train and test scores from those replicate models, and use those as the null distribution against which to compare your empirical values for AUC train and test.  Guidance on how to do that is here:

Species In Space

The new version is here:

ENMTools 1.4.2

Perl version only, see my previous kvetching about Active State if you want to know why.

Thanks to Marie-France Ostrowski for the suggestion and Renee Catullo for testing it.

Sunday, April 7, 2013

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

Monday, November 12, 2012

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:


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!

Monday, March 21, 2011

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.