[Biomod-commits] MaxEnt and BIOMOD

Tue Apr 26 06:56:11 CEST 2011

Ok... now I see the "light" :)

Thanks again!!  :)

Charles

On Tue, Apr 26, 2011 at 1:50 AM, Wilfried Thuiller
<wilfried.thuiller at ujf-grenoble.fr> wrote:
> The main problem with Maxent (Maximum Entropy) is that this is a technique
> (like a GLM or Bayesian framework) and not the name of a model.
> The Maxent you are refering to (in FD) is not made to a model species
> distributions but to retrieve abundance distribution within communities
> based on functional traits.
> Shipley, B., D. Vile, et al. (2006). From plant traits to plant communities:
> a statistical mechanistic approach to biodiversity. Science 314, 812-814.
> Cheers,
> Wilfried
>
> Le 25 avr. 2011 à 23:39, Charles Novaes de Santana a écrit :
>
> Thank you very much for your answer, Wilfried!! That are really good
> news!! It is good to know that you are working on it!
>
> Just a comment more: Do you know that there is a package in R (FD)
> that already have an implementation of MaxEnt? Would it be useful to
> implement MaxEnt for BIOMOD?
>
> - http://cran.r-project.org/web/packages/FD/
> - http://cran.r-project.org/web/packages/FD/FD.pdf
>
> Anyway, good luck with your great work!! I hope I can help you with
> this someday in the future (I am still starting to know the world of
> niche modeling... :) )
>
> Charles
>
> On Sat, Apr 23, 2011 at 10:38 AM, Wilfried Thuiller
> <wilfried.thuiller at ujf-grenoble.fr> wrote:
>
> Dear Charles,
>
> First of all, I must say that it is a great pleasure to read all the
>
> interesting discussions we have in this list, we learn a lot with
>
> every message! Thanks, and congratulations!!
>
> Well, sorry if the question I will point here has been done before,
>
> but I really didn't find anything about it in previous messages I
>
> have:
>
> Is it posible to include MaxEnt among the models simulated by BIOMOD?
>
> In my opinion, the great strength of BIOMOD, beyond many other
>
> benefits, is to allow the ensemble of many models in an easy way, and
>
> so to give us more confidence results of our simulations. But I see
>
> that MaxEnt is often used to simulate distribution of species and
>
> sometimes I ask myself why it is not included in BIOMOD (yet). Is it a
>
> "stupid" question? (I really believe that there are NO "stupid"
>
> questions, but... :-))
>
> This is indeed a very interesting question.
>
> The answer is no and yes.
>
> No because Maxent is coded in Java, much more efficient than in R. We'll
>
> have to recode the entire program in C or C++ to fully integrate it in R and
>
> latter in BIOMOD.
>
> However, this is easy to run Maxent using a batch command from R. I have
>
> thought about putting Maxent within BIOMOD that way since a while. I am just
>
> to busy to do it but hope to start looking at that this year.
>
> For curious, find below a short code for running Maxent from R.
>
> You need the ascii data for running it and modify all paths and data for
>
> your own data.
>
> My species is Sp290.csv (Sp290 from SpEnv data in BIOMOD exported in csv
>
> format for Maxent).
>
> The environmental variables are the same than SpEnv, as many ascii files as
>
> variables.
>
> You need maxent.jar in your working directory.
>
> dir.create(path=paste(getwd(), "/MaxEnt.res", sep=""))
>
> MaxEnt.layers <- paste(getwd(), "/europe/ascii/current", sep="")
>
> MaxEnt.out <- paste(getwd(), "/MaxEnt.res", sep="")
>
> MaxEnt.samples <- paste(getwd(), "/europe/point", sep="")
>
> layers <- list.files(MaxEnt.layers)
>
> # run MaxEnt:
>
> system(command=paste("java -jar maxent.jar environmentallayers=",
>
> MaxEnt.layers, " samplesfile=", MaxEnt.samples, "/Sp290.csv", "
>
> outputdirectory=", MaxEnt.out, "  maximumiterations=100 redoifexists autorun
>
> nowarnings notooltips", sep=""))
>
> # NOT RUN
>
> system(command=paste("java -mx4000m -jar maxent.jar environmentallayers=",
>
> MaxEnt.layers, " samplesfile=", MaxEnt.samples, "/Sp290.csv", "
>
> outputdirectory=", MaxEnt.out, " 'applythresholdrule=equal training
>
> sensitivity and specificity' maximumiterations=100 redoifexists autorun
>
> nowarnings notooltips", sep=""))
>
> list.files(MaxEnt.out)
>
> #Import the predictions on the presence points
>
> Pred.Maxent.Sp290.sample <- read.csv(paste(getwd(),
>
> "/MaxEnt.res/Sp290_samplePredictions.csv", sep=""))
>
> #Plot the results from Maxent
>
> library(BIOMOD)
>
> par(mfrow=c(1,2))
>
> level.plot(Sp.Env$Sp290, XY=Sp.Env[,2:3], color.gradient = "grey",
>
> cex=0.3,show.scale=F, title="Original data")
>
> level.plot(Pred.Maxent.Sp290.sample$Logistic.prediction,
>
> XY=Pred.Maxent.Sp290.sample[,1:2], color.gradient = "grey",
>
> cex=0.3,show.scale=F, title="Maxent")
>
> points(Sp.Env[Sp.Env$Sp290<1,2], Sp.Env[Sp.Env$Sp290<1,3], cex=0.3,
>
> pch=2,col="grey93")
>
> You see, this is not that difficult. I just need to see how to fully
>
> implement this in the existing structure of BIOMOD, the most difficult part
>
> obviously.
>
> Cheers,
>
> Wilfried
>
>
>
>
> Thanks for the attention,
>
> Best regards,
>
> Charles
>
> --
>
> Um axé! :)
>
> --
>
> Charles Novaes de Santana
>
> PhD student - Global Change
>
> Laboratorio Internacional de Cambio Global
>
> Department of Global Change Research
>
> Instituto Mediterráneo de Estudios Avanzados(CSIC/UIB)
>
> Calle Miquel Marques 21, 07006
>
> Esporles - Islas Baleares - España
>
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>
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>
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>
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>
> --------------------------
>
> Dr. Wilfried Thuiller
>
> Laboratoire d'Ecologie Alpine, UMR CNRS 5553
>
> Université Joseph Fourier
>
> BP53, 38041 Grenoble cedex 9, France
>
> tel: +33 (0)4 76 51 44 97
>
> fax: +33 (0)4 76 51 42 79
>
> Email: wilfried.thuiller at ujf-grenoble.fr
>
> Personal website: http://www.will.chez-alice.fr
>
> Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm
>
> FP6 European MACIS project: http://www.macis-project.net
>
> FP6 European EcoChange project: http://www.ecochange-project.eu
>
>
>
>
>
>
>
>
>
> --
> Um axé! :)
>
> --
> Charles Novaes de Santana
> PhD student - Global Change
> Laboratorio Internacional de Cambio Global
> Department of Global Change Research
> Instituto Mediterráneo de Estudios Avanzados(CSIC/UIB)
> Calle Miquel Marques 21, 07006
> Esporles - Islas Baleares - España
> _______________________________________________
> Biomod-commits mailing list
> Biomod-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits
>
> --------------------------
> Dr. Wilfried Thuiller
> Laboratoire d'Ecologie Alpine, UMR CNRS 5553
> Université Joseph Fourier
> BP53, 38041 Grenoble cedex 9, France
> tel: +33 (0)4 76 51 44 97
> fax: +33 (0)4 76 51 42 79
> Email: wilfried.thuiller at ujf-grenoble.fr
> Personal website: http://www.will.chez-alice.fr
> Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm
>
> FP6 European MACIS project: http://www.macis-project.net
> FP6 European EcoChange project: http://www.ecochange-project.eu
>
>
>
>
>
>

-- 
Um axé! :)

--
Charles Novaes de Santana
PhD student - Global Change
Laboratorio Internacional de Cambio Global
Department of Global Change Research
Instituto Mediterráneo de Estudios Avanzados(CSIC/UIB)
Calle Miquel Marques 21, 07006
Esporles - Islas Baleares - España