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.

35 comments:

  1. Hi Dan, Excited to use this--I can't seem to get the program to run correctly though. It keeps giving me the error "no config file found" and the gui that launches only says "Welcome to ENMTools" with no buttons or anything. I saw in an earlier post that you asked if the person had the config file, and I don't...the only files that came with the download are 1.3_OSX.exe, 1.3.exe, _1.3.pl, the manual and a sample data file. This is on Mac OSX 10.6.8... Thanks for any help

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  2. So you don't even see a menu bar up at the top?

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  3. oops, got it, nevermind. thanks!

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  4. Possibly a question displaying my ignorance (easily done), but I am wanting to run ENMTools on a remote high performance cluster, the easiest method of doing which is via command line/scripts (ie not via the GUI). I can't find any reference to how do-able this is or how to configure ENMTools in this way (setting reps, ribbon widths, output locations etc). Would I be better off just being less lazy and learning to use a remote GUI viewer (which is an option on this system)??
    Cheers!
    Bort

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  5. The easiest option is probably to use the method here:

    http://enmtools.blogspot.com/2009/10/how-to-run-enmtools-tests-on-cluster-or.html

    Basically you use ENMTools to construct your replicates, and then submit those to Maxent on the cluster however you would normally do that. Then you can use ENMTools' scripting interface to get measurements of overlap for the hypothesis tests.

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  6. Thanks Dan, I hadn't conceptualised breaking it down like that, but makes sense, will try.

    ps, how easily could the range/ribbon breaking test be modified to include a sliding window option (ie where alternative breaks are along a lat/long axis, not randomised in orientation)? For me this is particularly of interest where there is a strong latitudinal gradient such that one does not expect a large proportion of the randomisations to be close to similar, the question being are breaks on a similar orientation any better or worse...
    Another modification would be stepwise alteration of the width of the ribbon only, to see if the bounds of the region can be identified.
    There would be problems maintaining sample sizes under these tests I imagine, but if that could be negated... thoughts?

    Cheers!
    Bort

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  7. Robert Anderson and I have been talking about doing something similar to the former idea, but I haven't really considered the latter before. You could do both fairly easily either manually or using the scripting interface. If you decide to give one or both of those a shot, I'd be really interested to see how it works out!

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  8. I have one particular data set that when I run niche identity, it cranks through to the end, puts out files at each step, but the final summary is empty. Other data sets/environ layers work. And, this combo works with maxent alone.
    Any simple fixes? thanks Bob Zink, U MN zinkx003@umn.edu

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  9. Hi Bob! The quickest fix is to just measure the overlaps yourself using the scripting interface. There's a post about how to do this on the second page of the blog, here:

    http://enmtools.blogspot.com/2009/10/how-to-run-enmtools-tests-on-cluster-or.html

    Let me know if you run into any problems. Cheers!

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  10. Hey! Congrats for the new release. I was trying to play around with your sample data and reading instructions (am a newbie myself).

    In order to compute, for instance, niche breath or overlap...do we need to run maxent separately beforehand. I know there is an option for the identity, etc. test in which it runs maxent internally, but the outputs do not give you the asc probabilities or binary maps to perform other tests....or I am not understanding anything?? Thank you in advance!
    Pep
    PS: a quick tutorial with your sample data would be very useful...

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  11. You do need to run Maxent separately in order to calculate breadth and overlap.

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  12. Hi, Dan! Thanks for the tools; they're exactly what I needed and I'm slowly learning how to use them. Quick question about the correlation function, to identify environmental variables that can be eliminated. What is the downside of just leaving all of the variables in?

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  13. Hi Diane! There are several reasons that people prefer models with fewer predictor variables, from simple parsimony to reducing spatial autocorrelation between predictors. In practical terms, some coauthors and I will demonstrate in a forthcoming manuscript that reducing the number of predictor variables tends to produce models that have a less smooth distribution of suitability scores across the landscape, i.e., the difference between suitable and unsuitable areas is greater. Whether that means the model itself is better is an open question, but the phenomenon is pretty unmistakable in our data.

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  14. Hi Dan,

    I'm new to both Maxent and ENMTools so there's probably an easy explanation for this.
    I was trying to use ENMTools to compare 5 different models I did in Maxent. However, because I've used cross-validation with 5 replicates I don't get a lambdas file for the average of the replicate runs but a single lambdas file for each run. My idea was to compare the average runs of different models but because there are no lambdas files it seems that I won't be able to do this. Do you have any suggestions?

    Thanks in advance,

    David

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  15. Yes, in fact! I have an unreleased version of ENMTools that does model averaging, so you could feed it all of your lambda files from your replicates and get an averaged model over all reps. Would that work?

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  16. Hi Dan,

    Thanks for your prompt reply! That sounds great! I think it will do just what I need. Where can I get this new version?

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  17. Just send me an email at dan dot l dot warren at gmail, and I'll send you a copy with some instructions. Cheers!

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  18. I am trying to install ENMTools on windows. i get the message saying "no config file found", but it opens and has top menu bar. but with all the options. and there is no ocnfig file in .zip thanks for any help!

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  19. That just means you need to go set up the ENMTools and Maxent options and hit "save options".

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  20. sorry without all the options!!

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  21. ok thank you for prompt reply!! yes it works!

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  22. Hello,
    I wonder if the ENMTools can be deployed in cluster?

    thank you

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  23. There is a way to do a lot of the tests on a cluster, it's here:

    http://enmtools.blogspot.com/2009/10/how-to-run-enmtools-tests-on-cluster-or.html

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  24. Hi Dan,

    I'm trying to use the trim duplicate occurrences tool using a .csv file containing all my species occurrences and a grid file however, the resulting .csv file ends up with only one point. I know something's wrong because I should have at least 250 points. Any idea on what I might be doing wrong?

    Many thanks,

    David

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  25. Hi David, could you send me your input files at dan.l.warren@gmail.com? Thanks!

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  26. Hi Dan,

    I´ve been using Maxent in the last couple of months but i'm new to ENMTools. I want to estimate AICs for model selection but i've encoutered the same problem that David Abecasis presented. I've used 10 fold cross-validation and i need an average lambdas value. Hope you can help me with this.

    Cheers!

    Hugo

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  27. This comment has been removed by the author.

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  28. Hi Hugo,

    The problem in David's case was very simple - ENMTools looks at column headers to figure out which column is lat and which is long. In his case they weren't named that, so the script got confused. Is that true in your case as well? If not, could you send me your .csv file?

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  29. Hello, I have a problem. I'm trying to use the trim duplicate occurrences tool using a .csv file and a grid file however, I can´t open the files and appear this message

    Can't locate utf8.pm in @INC (@INC contains:) at ENMTools_3-17-2011.pl line 1811.
    BEGIN failed--compilation aborted.

    What does it means?

    Thanks a lot

    Yolanda

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  30. Hi Yolanda, could you send me your .csv file

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  31. Hi, this happened to me. The folder where I had the files had a "ñ", so that was causing the computer to freak out. I changed the name of the folder to a less hispanic one and that solved it.

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    Replies
    1. Thanks!!! =)the problem was the name of the folder

      Delete
  32. Hi Dan! I am new to ENMtools so probably me doing something completely wrong! I am trying to use the trim duplicate occurrences tool for grid cells, I've been told I'm using a csv file, but I can't seem to get it to run. Not sure if it's because I've got my settings wrong or because I'm not sure what I'm meant to enter as the folder after pressing go. I get the message: Error: Can't open!
    Thanks,
    Helen

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  33. Hi. I have a problem using the trim duplicate occurrences tool for grid cells. I used a csv file with the longitude and latitud and then the asc file, but it doesn't work. Should I change/add something to the csv file or to the asc file? Thanks

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