Friday, February 12, 2010

ENMTools application note now available

The application note for ENMTools is now available in the Early View section of Ecography's website. Due to the limits of space, the note really only discusses the measurement of overlap and the identity and background tests (i.e., the tests that were presented in Warren et al. 2008). Papers that present the rangebreaking tests and niche breadth measurements are on the way, and should be out fairly soon.

I'm going to be putting out an update of ENMTools shortly which will add a couple of interesting features and fix a few minor issues.


  1. Thanks for the awesome tool... I was just wondering if you have put out the paper describing the niche breadth tool yet, and if not if you would mind expanding on it. I understand that it is from Levins (1966) and have been looking through the literature trying to understand the calculation B = 1/(sigma(p{sub}i^2))^-1 as it relates to, and is given in, ENM tools. Currently I am under the impression the p{sub}i is representative of the proportionate suitability of habitat i and that large B1 (not exactly sure what a large value is) are reflective of generalist (high resource use) individuals... is this correct? I am currently working on modeling an invasive species in hawaii and have an inverse concentration (B1) of 29862 and an Uncertainty (B2) of 38617.

  2. Sorry, this is an issue I've been meaning to fix. Really the breadth measurements mean a lot more when they're standardized for the availability of habitat (i.e., number of grid cells). I've been doing this by hand myself, but keep meaning to add it to ENMTools. Standardized breadth measurements range from 0 (one grid cell has a suitability of one, all other cells are zero), to 1, where all grid cells are equally suitable. In order to calculate the standardized scores, you need the number of grid cells present in your study area (discounting nodata cells). From that you can calculate the minimum and maximum possible B scores. You can then calculate standardized scores using (B-Bmin)/(Bmax-Bmin).

    The unstandardized scores are considerably harder to interpret. I'm going to be putting out a new version of ENMTools soon, I will try to remember to fix this issue in that release. I'm running behind on getting the new release out, but I'm going to try to do it within the next few days.

    In response to your other questions: P{sub}i is proportional to the suitability of habitat - it's suitability standardized over the geographic space (i.e., so that all suitability scores sum to 1). There are two papers that have used the breadth metric. One is the Warren and Seifert paper currently in the "accepted" section at Ecological Applications. The other is a paper by Mandle et al. (I am part of the et al.) that is currently in revision for PLoS One. If you'd like a copy of either, email me and I will send them to you.

  3. I am posting a new version now with standardized breadth metrics.