Dear all,
I am new in ENMTools and feel confused about identity test.
After perform identity test, how to make a identity test plot like the one in user manual ver1.3 page 17.
I now know the null distribution data is in the "sorted csv" file.
But, I do not know how (where) to find the value of red arrow.
Can somebody explain me how to make a identity test plot like the one in user manual?
Best regards,
Sandy
Sandy!
As for how to plot it, you can do that in Excel, R, or pretty much anywhere. The observed value (red arrow) is just the overlap measured between the ENMs for your two species built using the real data. You can get that from using the overlap function in ENMTools. For a conceptual overview of what you're doing and why, check out this blog post:
http://www.speciesinspace.com/species-in-space/monte-carlo-methods-nonparametric-tests-and-you
(it has replied by Dan)
Sincerely,
Mahmoud
For true calculated niche overlap, use this menu:
http://www.image-share.com/upload/2788/161.jpg
For histogram drawing of you two mentioned species' niche range, create an excel sheet like this:
http://www.image-share.com/upload/2788/162.jpg
Yong! are you still need someone to answer this question. I can helo you in that one for sure!
Hi Abdallah,
Apologies to no respond your question, but I'm also trying to run the Identity test in ENMTools, but I have an error that I can't solve (Can't open /Users/ricardo/Dropbox/Rstat/PhD/Results/Overlap/Identitymac/Cephalorhynchus eutropia_rep0.asc! at ENMTools_1.4.4.pl line 5302.while executing
"::perl::CODE(0x7fef7c44cb60)" invoked from within ".b5 invoke "
invoked from within".b5 instate {pressed !disabled} { .b5 state !pressed; .b5 invoke } "
(command bound to event)
Could you explain me how to run the Identity test please?? It could be useful to run the test successfully.
Thank you very much in advance
Ricardo
Richardo,
You must change your ENMtools settings as similar as the tutorial (ENMtools option > show Maxent GUI & Large file overlap/breath = yes).
Also, define the environmental layer path exactly.
Hope this help.
Hi Mahmoud,
Sorry to bother you, but I just couldn't open the URL that you have given (http://www.speciesinspace.com/species-in-space/monte-carlo-methods-nonparametric-tests-and-you).
I didn't konw how to use the ENMStools_1.4.4.pl in windows, so I did the identity test using ENMSTools pacakge in R, and got 6 pictures (First figure ) that I don't know how to explain, Because they just look quite different with the histogram drawing of two species' niche range (Second figure). The raster.overlap values of two species GLM models are D = 0.460, I = 0.7443, Rank.cor = 0.6519.
So could you please explain that for me? Thanks a lot.
Yulong !
Sorry indeed for delay. I find your question today after a long time! Maybe the RG notification arrived in my spam box. You can have "one-sample t-test" to finding significant difference when you have measurement of niche overlap between ENMTools built from real occurrence points for a pair of species. Then, you should have a comparison between real niche (a constant value) and generated number from your replicated run test.
In attached excel sheet, I had a run with only 20 replicate for two species with two constant for I and D. Now. I can run the statistical test for each of I and D separably. Actually, not have any idea about ranked correlation. May you pleases kindly send me the R script here?
P.S: it seems the website is out of order at this moment. But you can give the text via cached address in google:
https://tinyurl.com/ENMTools
Mr Shi yong,
Could you please send me a model about sorted .cvs conducted in the identity test in ENMtools? I try many times but not succeed.
Best wishes！
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