[Biomod-commits] Biomod-commits Digest, Vol 37, Issue 4
Oscar Javier Ramos
oramos at humboldt.org.co
Fri May 11 14:46:52 CEST 2012
Hi Wilfried,
I’m using R version 2.15.0 (2012-03-30), and I tried on two different
machines: XP and Vista 7 (32-bit and 64-bit respect.). I used the
"install.packages" command.
It would be nice if you send me the previous version (to go on with my own
data while the problem is fixed)
Thanks a lot
Oscar
2012/5/11 <biomod-commits-request at lists.r-forge.r-project.org>
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> Today's Topics:
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> 1. Re: Error in model.frame.default - "invalid type (list) for
> variable" - using BIOMOD (Wilfried Thuiller)
> 2. Re: Weight in ensemble forecasting (Wilfried Thuiller)
> 3. Re: Weight in ensemble forecasting (Wilfried Thuiller)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 11 May 2012 08:01:09 +0200
> From: Wilfried Thuiller <wilfried.thuiller at ujf-grenoble.fr>
> To: Kobus Botha <contactkobus at gmail.com>
> Cc: biomod-commits at r-forge.wu-wien.ac.at
> Subject: Re: [Biomod-commits] Error in model.frame.default - "invalid
> type (list) for variable" - using BIOMOD
> Message-ID: <71427227-71B7-43F8-B9AC-8A64D4017C3E at ujf-grenoble.fr>
> Content-Type: text/plain; charset="iso-8859-1"
>
> OK, I have uncovered the bug. It has to do with an update we did sometime
> ago.
> Will update the package soon with the big fixed.
>
> It works with revision 289 BTW (it has, in theory, nothing to do with the
> environment or the R version).
>
> If is really urgent, just send me a private email (out of the list because
> it rejects large email) and I will send you the previous version of the
> function bugging right now (.Biomod.Models)
>
> Sorry for the inconvenience
>
> Wilfried
>
>
>
>
> Le 11 mai 2012 ? 06:48, Kobus Botha a ?crit :
>
> > Hi guys. See my in-line reply below.
> >
> >
> > On 10/05/2012 4:57 PM, Oscar Javier Ramos wrote:
> >> Hi,
> >>
> >> I'm beginning with BIOMOD.
> >>
> >> Just running the example on the "BIOMOD: Tutorial (February 13, 2012)"
> => data(Sp.Env)",
> >>
> >> I got the following error:
> >>
> >> <snip>
> >>
> >> Error in model.frame.default(formula = eval(parse(text =
> paste("Target[Samp$calibration]", :
> >> invalid type (list) for variable 'Var1'
> >>
> >>
> >
> > Oscar: please confirm the details of your system. Specifically:
> >
> > - Is it 32-bit or 64-bit windows (Vista, 7 or 8) or Linux or OSX?
> > - Which version of R are you running? You can check your version of R
> by typing >R.version.string
> > - Did you install BIOMOD from source or did you use the
> "install.packages" command?
> >
> >
> >
> > On 10 May 2012 23:15, Chris Hassall <chassall at connect.carleton.ca>
> wrote:
> > I have exactly the same problem, both with my own data and with the
> tutorial data. I have not found a solution or any previous mention of this
> problem. I have used BIOMOD successfully before on the same computer. I
> have BIOMOD version 1.1-7.02/r300 and R version 2.15.0 (all up to date).
> >
> > Chris: not sure if this will help, but I have been able to get BIOMOD to
> work with the tutorial data using "R version 2.14.2 (2012-02-29)" on a
> Windows 7 64-bit setup. Perhaps reverting to an older version will work
> for you. However, I am getting a similar error with the exact same version
> of R on Ubuntu 12.04 :\
> >
> > If anyone knows what is causing this error I would also like to know.
> >
> > Cheers,
> > Kobus
> > _______________________________________________
> > 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
> Universit? 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
>
> ERC Starting Grant TEEMBIO project:
> http://www.will.chez-alice.fr/Research.html
> FP6 European EcoChange project: http://www.ecochange-project.eu
>
>
>
>
>
>
>
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> ------------------------------
>
> Message: 2
> Date: Fri, 11 May 2012 08:46:34 +0200
> From: Wilfried Thuiller <wilfried.thuiller at ujf-grenoble.fr>
> To: Kumar Mainali <kpmainali at gmail.com>
> Cc: biomod-commits at r-forge.wu-wien.ac.at
> Subject: Re: [Biomod-commits] Weight in ensemble forecasting
> Message-ID: <501F3543-8CA7-41F3-BADF-7A48E35A0E07 at ujf-grenoble.fr>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Kumar,
>
> > Ensemble.Forecasting. How the software computes ensemble probabilities
> is not clear in the manual. But somewhere I came across the information
> that the weights are based on cross validated evaluation score. Since I do
> not have such score, the function should not work.
>
> No, it works. This is mostly because so few people have independent
> dataset that by default we wrote that the weights are based on the
> cross-validation results. Indeed, when you have independent dataset, the
> weight are calculate based on the scores on the independent evaluation.
> This is something we need to modify in the manual, sorry for the confusion
> it gave you.
>
> > Instead, it gives me weight:
> >
> > $weights
> > ANN CTA GAM GBM GLM MARS FDA RF SRE
> > PA1 0 0 0.1729 0.2766 0.108 0 0 0.4425 0
> >
> > Where are these weights coming from? These numbers do not match with any
> column in Evaluation.results (after rescaling to make the total =1).
> >
> https://r-forge.r-project.org/scm/viewvc.php/pkg/R/Ensemble.Forecasting.R?view=markup&root=biomod&pathrev=168
>
> It depends on the weighting scheme you use (i.e. decay). Please look at
> the "decay" explanation in the help of Ensemble.Forecasting.
> If you set decay= 'proportional', you should retrieve easily the weights
> with the evaluation scores (as they are proportional).
>
> Hope it helps,
>
> Wilfried
>
>
>
> >
> > Thanks in advance,
> > Kumar
> > --
> > Section of Integrative Biology
> > University of Texas at Austin
> > Austin, Texas 78712, USA
> > _______________________________________________
> > 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
> Universit? 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
>
> ERC Starting Grant TEEMBIO project:
> http://www.will.chez-alice.fr/Research.html
> FP6 European EcoChange project: http://www.ecochange-project.eu
>
>
>
>
>
>
>
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> ------------------------------
>
> Message: 3
> Date: Fri, 11 May 2012 10:03:06 +0200
> From: Wilfried Thuiller <wilfried.thuiller at ujf-grenoble.fr>
> To: Kumar Mainali <kpmainali at gmail.com>
> Cc: "biomod-commits at lists.r-forge.r-project.org"
> <biomod-commits at r-forge.wu-wien.ac.at>
> Subject: Re: [Biomod-commits] Weight in ensemble forecasting
> Message-ID: <A32AA44E-0493-43BC-B365-1A96F4E33E20 at ujf-grenoble.fr>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Our mistake, actually not.
>
> The weights are calculated on the final model (100%) if you do not have
> any repetition (like in your case).
>
> We are changing that.
> Priority will be given to "Independent data". Then, cross-validation, then
> final model.
>
> At the moment, we do not check whether or not independent dataset have
> been used.
>
> We'll keep you updated on the package building but everything should work
> back during the day.
>
> Cheers,
> Wilfried
>
>
>
> Le 11 mai 2012 ? 08:46, Wilfried Thuiller a ?crit :
>
> > Dear Kumar,
> >
> >> Ensemble.Forecasting. How the software computes ensemble probabilities
> is not clear in the manual. But somewhere I came across the information
> that the weights are based on cross validated evaluation score. Since I do
> not have such score, the function should not work.
> >
> > No, it works. This is mostly because so few people have independent
> dataset that by default we wrote that the weights are based on the
> cross-validation results. Indeed, when you have independent dataset, the
> weight are calculate based on the scores on the independent evaluation.
> > This is something we need to modify in the manual, sorry for the
> confusion it gave you.
> >
> >> Instead, it gives me weight:
> >>
> >> $weights
> >> ANN CTA GAM GBM GLM MARS FDA RF SRE
> >> PA1 0 0 0.1729 0.2766 0.108 0 0 0.4425 0
> >>
> >> Where are these weights coming from? These numbers do not match with
> any column in Evaluation.results (after rescaling to make the total =1).
> >>
> https://r-forge.r-project.org/scm/viewvc.php/pkg/R/Ensemble.Forecasting.R?view=markup&root=biomod&pathrev=168
> >
> > It depends on the weighting scheme you use (i.e. decay). Please look at
> the "decay" explanation in the help of Ensemble.Forecasting.
> > If you set decay= 'proportional', you should retrieve easily the weights
> with the evaluation scores (as they are proportional).
> >
> > Hope it helps,
> >
> > Wilfried
> >
> >
> >
> >>
> >> Thanks in advance,
> >> Kumar
> >> --
> >> Section of Integrative Biology
> >> University of Texas at Austin
> >> Austin, Texas 78712, USA
> >> _______________________________________________
> >> 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
> > Universit? 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
> >
> > ERC Starting Grant TEEMBIO project:
> http://www.will.chez-alice.fr/Research.html
> > FP6 European EcoChange project: http://www.ecochange-project.eu
> >
> >
> >
> >
> >
> >
> >
>
> --------------------------
> Dr. Wilfried Thuiller
> Laboratoire d'Ecologie Alpine, UMR CNRS 5553
> Universit? 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
>
> ERC Starting Grant TEEMBIO project:
> http://www.will.chez-alice.fr/Research.html
> FP6 European EcoChange project: http://www.ecochange-project.eu
>
>
>
>
>
>
>
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