Thursday, October 13, 2016

Nice tutorial on conducting background tests using the Perl version of ENMTools

Here's a really nice tutorial by Daniel Romero on how to do the background test in the standalone version of ENMTools.  He walks you through setting up the program, running the analysis, and how to avoid some of the errors that might crop up when trying to run the software.

Thanks, Daniel!

13 comments:

  1. Hi Dan!
    Thank you for sharing the tutorial. A pleasure to work with ENMTools.
    Best wishes

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  2. Hi, let me ask an offtop question: is there "resampling from a raster" function in R version of ENMTools?

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  3. Not at present, but dismo has a function called randomPoints that can do it. If I recall correctly it doesn't allow sampling with replacement, but you can hack it to do so fairly easily.

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  4. Hi, I'm having problems to run my background test and after a lot tempts, I still didn't figure out what is the problem. The program keeps showing the error "missing some spatial data (ex. Alt)", but I already checked it and I cliped my background's area using the layer of Alt. I really don't know what to do anymore. -.-

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    1. Can you use the background points file it generated and extract the values from your rasters at the background points? That would probably tell you where you're getting nodata values.

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    2. Yes, I can. I'll try it. Thank you. I forgot to tell that all this trouble started when I ran the analysis and all my spreedsheets came showing 100 identical values os d, i and rr. So I tried to redo the background asc and now I have this new problem.

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  5. Hi Dr. Warren and more experienced ENMTools users,
    I am trying to do a background test in the standalone version of ENMTools using a mask for background area. So far I've found your instructions in the user manual and Dr. Romero-Alvarez's video very helpful but I am having a few issues. I am using the up to date version (1.4.4). In my tests it runs all the way through and produces outputs but in the main results csv all the D and I values are 1 which seems unlikely given the distribution of the species in question. Also when I go to set up the analysis I am missing the regularization parameter and remove duplicate options in the GUI. Also I would like to add a bias grid but can't find how to incorporate that into this analysis. Any suggestions would be greatly appreciated.
    Thank you,
    Nick

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    1. Can you find your reps file and run it in Maxent manually?

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  6. Thanks for such a quick response, I really appreciate the help. The rep file would be the Sp1_versus_Sp2_reps.csv correct? Pardon my inexperience but how do I run the actual comparison in Maxent? Do I just treat each rep as it's own species under my preferred parameters for Sp1 and then come back and measure niche overlap for each output paired with the Sp1 in ENMtools?

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    1. I just meant for you to try to run it, to make sure it's working correctly.

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    2. Pardon me, yes, I found it and the reps ran well in Maxent.

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    3. Right on. Well assuming it's producing output rasters, you can use the method outlined here:

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

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