[Biomod-commits] MaxEnt and BIOMOD

[Charles Novaes de Santana]

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
> _______________________________________________
> Biomod-commits mailing list
> Biomod-commits at lists.r-forge.r-project.org
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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