<p class="MsoNormal"><span style lang="EN-US">Hi
Wilfried,<br>
<br>
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.<br>
<br>
It would be nice if you send me the previous version (to go on with my own data
while the problem is fixed)<br>
<br>
Thanks a lot<br>
<br>
Oscar</span></p>
<br><br><div class="gmail_quote">2012/5/11 <span dir="ltr"><<a href="mailto:biomod-commits-request@lists.r-forge.r-project.org" target="_blank">biomod-commits-request@lists.r-forge.r-project.org</a>></span><br>
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Today's Topics:<br>
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1. Re: Error in model.frame.default - "invalid type (list) for<br>
variable" - using BIOMOD (Wilfried Thuiller)<br>
2. Re: Weight in ensemble forecasting (Wilfried Thuiller)<br>
3. Re: Weight in ensemble forecasting (Wilfried Thuiller)<br>
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<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 11 May 2012 08:01:09 +0200<br>
From: Wilfried Thuiller <<a href="mailto:wilfried.thuiller@ujf-grenoble.fr" target="_blank">wilfried.thuiller@ujf-grenoble.fr</a>><br>
To: Kobus Botha <<a href="mailto:contactkobus@gmail.com" target="_blank">contactkobus@gmail.com</a>><br>
Cc: <a href="mailto:biomod-commits@r-forge.wu-wien.ac.at" target="_blank">biomod-commits@r-forge.wu-wien.ac.at</a><br>
Subject: Re: [Biomod-commits] Error in model.frame.default - "invalid<br>
type (list) for variable" - using BIOMOD<br>
Message-ID: <<a href="mailto:71427227-71B7-43F8-B9AC-8A64D4017C3E@ujf-grenoble.fr" target="_blank">71427227-71B7-43F8-B9AC-8A64D4017C3E@ujf-grenoble.fr</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
OK, I have uncovered the bug. It has to do with an update we did sometime ago.<br>
Will update the package soon with the big fixed.<br>
<br>
It works with revision 289 BTW (it has, in theory, nothing to do with the environment or the R version).<br>
<br>
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)<br>
<br>
Sorry for the inconvenience<br>
<br>
Wilfried<br>
<br>
<br>
<br>
<br>
Le 11 mai 2012 ? 06:48, Kobus Botha a ?crit :<br>
<br>
> Hi guys. See my in-line reply below.<br>
><br>
><br>
> On 10/05/2012 4:57 PM, Oscar Javier Ramos wrote:<br>
>> Hi,<br>
>><br>
>> I'm beginning with BIOMOD.<br>
>><br>
>> Just running the example on the "BIOMOD: Tutorial (February 13, 2012)" => data(Sp.Env)",<br>
>><br>
>> I got the following error:<br>
>><br>
>> <snip><br>
>><br>
>> Error in model.frame.default(formula = eval(parse(text = paste("Target[Samp$calibration]", :<br>
>> invalid type (list) for variable 'Var1'<br>
>><br>
>><br>
><br>
> Oscar: please confirm the details of your system. Specifically:<br>
><br>
> - Is it 32-bit or 64-bit windows (Vista, 7 or 8) or Linux or OSX?<br>
> - Which version of R are you running? You can check your version of R by typing >R.version.string<br>
> - Did you install BIOMOD from source or did you use the "install.packages" command?<br>
><br>
><br>
><br>
> On 10 May 2012 23:15, Chris Hassall <<a href="mailto:chassall@connect.carleton.ca" target="_blank">chassall@connect.carleton.ca</a>> wrote:<br>
> 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).<br>
><br>
> 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 :\<br>
><br>
> If anyone knows what is causing this error I would also like to know.<br>
><br>
> Cheers,<br>
> Kobus<br>
> _______________________________________________<br>
> Biomod-commits mailing list<br>
> <a href="mailto:Biomod-commits@lists.r-forge.r-project.org" target="_blank">Biomod-commits@lists.r-forge.r-project.org</a><br>
> <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits" target="_blank">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits</a><br>
<br>
--------------------------<br>
Dr. Wilfried Thuiller<br>
Laboratoire d'Ecologie Alpine, UMR CNRS 5553<br>
Universit? Joseph Fourier<br>
BP53, 38041 Grenoble cedex 9, France<br>
tel: <a href="tel:%2B33%20%280%294%2076%2051%2044%2097" value="+33476514497" target="_blank">+33 (0)4 76 51 44 97</a><br>
fax: <a href="tel:%2B33%20%280%294%2076%2051%2042%2079" value="+33476514279" target="_blank">+33 (0)4 76 51 42 79</a><br>
<br>
Email: <a href="mailto:wilfried.thuiller@ujf-grenoble.fr" target="_blank">wilfried.thuiller@ujf-grenoble.fr</a><br>
Personal website: <a href="http://www.will.chez-alice.fr" target="_blank">http://www.will.chez-alice.fr</a><br>
Team website: <a href="http://www-leca.ujf-grenoble.fr/equipes/emabio.htm" target="_blank">http://www-leca.ujf-grenoble.fr/equipes/emabio.htm</a><br>
<br>
ERC Starting Grant TEEMBIO project: <a href="http://www.will.chez-alice.fr/Research.html" target="_blank">http://www.will.chez-alice.fr/Research.html</a><br>
FP6 European EcoChange project: <a href="http://www.ecochange-project.eu" target="_blank">http://www.ecochange-project.eu</a><br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
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Message: 2<br>
Date: Fri, 11 May 2012 08:46:34 +0200<br>
From: Wilfried Thuiller <<a href="mailto:wilfried.thuiller@ujf-grenoble.fr" target="_blank">wilfried.thuiller@ujf-grenoble.fr</a>><br>
To: Kumar Mainali <<a href="mailto:kpmainali@gmail.com" target="_blank">kpmainali@gmail.com</a>><br>
Cc: <a href="mailto:biomod-commits@r-forge.wu-wien.ac.at" target="_blank">biomod-commits@r-forge.wu-wien.ac.at</a><br>
Subject: Re: [Biomod-commits] Weight in ensemble forecasting<br>
Message-ID: <<a href="mailto:501F3543-8CA7-41F3-BADF-7A48E35A0E07@ujf-grenoble.fr" target="_blank">501F3543-8CA7-41F3-BADF-7A48E35A0E07@ujf-grenoble.fr</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear Kumar,<br>
<br>
> 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.<br>
<br>
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.<br>
This is something we need to modify in the manual, sorry for the confusion it gave you.<br>
<br>
> Instead, it gives me weight:<br>
><br>
> $weights<br>
> ANN CTA GAM GBM GLM MARS FDA RF SRE<br>
> PA1 0 0 0.1729 0.2766 0.108 0 0 0.4425 0<br>
><br>
> Where are these weights coming from? These numbers do not match with any column in Evaluation.results (after rescaling to make the total =1).<br>
> <a href="https://r-forge.r-project.org/scm/viewvc.php/pkg/R/Ensemble.Forecasting.R?view=markup&root=biomod&pathrev=168" target="_blank">https://r-forge.r-project.org/scm/viewvc.php/pkg/R/Ensemble.Forecasting.R?view=markup&root=biomod&pathrev=168</a><br>
<br>
It depends on the weighting scheme you use (i.e. decay). Please look at the "decay" explanation in the help of Ensemble.Forecasting.<br>
If you set decay= 'proportional', you should retrieve easily the weights with the evaluation scores (as they are proportional).<br>
<br>
Hope it helps,<br>
<br>
Wilfried<br>
<br>
<br>
<br>
><br>
> Thanks in advance,<br>
> Kumar<br>
> --<br>
> Section of Integrative Biology<br>
> University of Texas at Austin<br>
> Austin, Texas 78712, USA<br>
> _______________________________________________<br>
> Biomod-commits mailing list<br>
> <a href="mailto:Biomod-commits@lists.r-forge.r-project.org" target="_blank">Biomod-commits@lists.r-forge.r-project.org</a><br>
> <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits" target="_blank">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits</a><br>
<br>
--------------------------<br>
Dr. Wilfried Thuiller<br>
Laboratoire d'Ecologie Alpine, UMR CNRS 5553<br>
Universit? Joseph Fourier<br>
BP53, 38041 Grenoble cedex 9, France<br>
tel: <a href="tel:%2B33%20%280%294%2076%2051%2044%2097" value="+33476514497" target="_blank">+33 (0)4 76 51 44 97</a><br>
fax: <a href="tel:%2B33%20%280%294%2076%2051%2042%2079" value="+33476514279" target="_blank">+33 (0)4 76 51 42 79</a><br>
<br>
Email: <a href="mailto:wilfried.thuiller@ujf-grenoble.fr" target="_blank">wilfried.thuiller@ujf-grenoble.fr</a><br>
Personal website: <a href="http://www.will.chez-alice.fr" target="_blank">http://www.will.chez-alice.fr</a><br>
Team website: <a href="http://www-leca.ujf-grenoble.fr/equipes/emabio.htm" target="_blank">http://www-leca.ujf-grenoble.fr/equipes/emabio.htm</a><br>
<br>
ERC Starting Grant TEEMBIO project: <a href="http://www.will.chez-alice.fr/Research.html" target="_blank">http://www.will.chez-alice.fr/Research.html</a><br>
FP6 European EcoChange project: <a href="http://www.ecochange-project.eu" target="_blank">http://www.ecochange-project.eu</a><br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
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<br>
Message: 3<br>
Date: Fri, 11 May 2012 10:03:06 +0200<br>
From: Wilfried Thuiller <<a href="mailto:wilfried.thuiller@ujf-grenoble.fr" target="_blank">wilfried.thuiller@ujf-grenoble.fr</a>><br>
To: Kumar Mainali <<a href="mailto:kpmainali@gmail.com" target="_blank">kpmainali@gmail.com</a>><br>
Cc: "<a href="mailto:biomod-commits@lists.r-forge.r-project.org" target="_blank">biomod-commits@lists.r-forge.r-project.org</a>"<br>
<<a href="mailto:biomod-commits@r-forge.wu-wien.ac.at" target="_blank">biomod-commits@r-forge.wu-wien.ac.at</a>><br>
Subject: Re: [Biomod-commits] Weight in ensemble forecasting<br>
Message-ID: <<a href="mailto:A32AA44E-0493-43BC-B365-1A96F4E33E20@ujf-grenoble.fr" target="_blank">A32AA44E-0493-43BC-B365-1A96F4E33E20@ujf-grenoble.fr</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Our mistake, actually not.<br>
<br>
The weights are calculated on the final model (100%) if you do not have any repetition (like in your case).<br>
<br>
We are changing that.<br>
Priority will be given to "Independent data". Then, cross-validation, then final model.<br>
<br>
At the moment, we do not check whether or not independent dataset have been used.<br>
<br>
We'll keep you updated on the package building but everything should work back during the day.<br>
<br>
Cheers,<br>
Wilfried<br>
<br>
<br>
<br>
Le 11 mai 2012 ? 08:46, Wilfried Thuiller a ?crit :<br>
<br>
> Dear Kumar,<br>
><br>
>> 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.<br>
><br>
> 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.<br>
> This is something we need to modify in the manual, sorry for the confusion it gave you.<br>
><br>
>> Instead, it gives me weight:<br>
>><br>
>> $weights<br>
>> ANN CTA GAM GBM GLM MARS FDA RF SRE<br>
>> PA1 0 0 0.1729 0.2766 0.108 0 0 0.4425 0<br>
>><br>
>> Where are these weights coming from? These numbers do not match with any column in Evaluation.results (after rescaling to make the total =1).<br>
>> <a href="https://r-forge.r-project.org/scm/viewvc.php/pkg/R/Ensemble.Forecasting.R?view=markup&root=biomod&pathrev=168" target="_blank">https://r-forge.r-project.org/scm/viewvc.php/pkg/R/Ensemble.Forecasting.R?view=markup&root=biomod&pathrev=168</a><br>
><br>
> It depends on the weighting scheme you use (i.e. decay). Please look at the "decay" explanation in the help of Ensemble.Forecasting.<br>
> If you set decay= 'proportional', you should retrieve easily the weights with the evaluation scores (as they are proportional).<br>
><br>
> Hope it helps,<br>
><br>
> Wilfried<br>
><br>
><br>
><br>
>><br>
>> Thanks in advance,<br>
>> Kumar<br>
>> --<br>
>> Section of Integrative Biology<br>
>> University of Texas at Austin<br>
>> Austin, Texas 78712, USA<br>
>> _______________________________________________<br>
>> Biomod-commits mailing list<br>
>> <a href="mailto:Biomod-commits@lists.r-forge.r-project.org" target="_blank">Biomod-commits@lists.r-forge.r-project.org</a><br>
>> <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits" target="_blank">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits</a><br>
><br>
> --------------------------<br>
> Dr. Wilfried Thuiller<br>
> Laboratoire d'Ecologie Alpine, UMR CNRS 5553<br>
> Universit? Joseph Fourier<br>
> BP53, 38041 Grenoble cedex 9, France<br>
> tel: <a href="tel:%2B33%20%280%294%2076%2051%2044%2097" value="+33476514497" target="_blank">+33 (0)4 76 51 44 97</a><br>
> fax: <a href="tel:%2B33%20%280%294%2076%2051%2042%2079" value="+33476514279" target="_blank">+33 (0)4 76 51 42 79</a><br>
><br>
> Email: <a href="mailto:wilfried.thuiller@ujf-grenoble.fr" target="_blank">wilfried.thuiller@ujf-grenoble.fr</a><br>
> Personal website: <a href="http://www.will.chez-alice.fr" target="_blank">http://www.will.chez-alice.fr</a><br>
> Team website: <a href="http://www-leca.ujf-grenoble.fr/equipes/emabio.htm" target="_blank">http://www-leca.ujf-grenoble.fr/equipes/emabio.htm</a><br>
><br>
> ERC Starting Grant TEEMBIO project: <a href="http://www.will.chez-alice.fr/Research.html" target="_blank">http://www.will.chez-alice.fr/Research.html</a><br>
> FP6 European EcoChange project: <a href="http://www.ecochange-project.eu" target="_blank">http://www.ecochange-project.eu</a><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
<br>
--------------------------<br>
Dr. Wilfried Thuiller<br>
Laboratoire d'Ecologie Alpine, UMR CNRS 5553<br>
Universit? Joseph Fourier<br>
BP53, 38041 Grenoble cedex 9, France<br>
tel: <a href="tel:%2B33%20%280%294%2076%2051%2044%2097" value="+33476514497" target="_blank">+33 (0)4 76 51 44 97</a><br>
fax: <a href="tel:%2B33%20%280%294%2076%2051%2042%2079" value="+33476514279" target="_blank">+33 (0)4 76 51 42 79</a><br>
<br>
Email: <a href="mailto:wilfried.thuiller@ujf-grenoble.fr" target="_blank">wilfried.thuiller@ujf-grenoble.fr</a><br>
Personal website: <a href="http://www.will.chez-alice.fr" target="_blank">http://www.will.chez-alice.fr</a><br>
Team website: <a href="http://www-leca.ujf-grenoble.fr/equipes/emabio.htm" target="_blank">http://www-leca.ujf-grenoble.fr/equipes/emabio.htm</a><br>
<br>
ERC Starting Grant TEEMBIO project: <a href="http://www.will.chez-alice.fr/Research.html" target="_blank">http://www.will.chez-alice.fr/Research.html</a><br>
FP6 European EcoChange project: <a href="http://www.ecochange-project.eu" target="_blank">http://www.ecochange-project.eu</a><br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
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</blockquote></div><br>