From vioreldpopescu at gmail.com Wed Apr 3 00:56:49 2013 From: vioreldpopescu at gmail.com (Viorel Popescu) Date: Tue, 2 Apr 2013 15:56:49 -0700 Subject: [Biomod-commits] reporting VarImportance In-Reply-To: <56EA130A-B629-4544-8B06-B931D5786EC0@ujf-grenoble.fr> References: <56EA130A-B629-4544-8B06-B931D5786EC0@ujf-grenoble.fr> Message-ID: Dear Wilfried, Thank you for your advice... > This is a very good point. I also agree with you there are not enough papers reporting the importance of the variables. > Make sure you do not use variables that are highly correlated BTW, else, it will not mean too much for those variables. This is important. I did select the initial variables using a 0.7 correlation coefficient threshold, so none of the variables were highly correlated. > Barplot should indeed work perfectly fine. You may, at the same time, look at whether some groups of species have similar variable importance. > If you have run many repetitions and PA selections (if any), you may also consider reporting (in Supp Mat) the bar plots for each models to depict whether some models are highly unstable on those aspects and some are not. I have tried both barplots with SE, as well as boxplots, and found that the boxplots are much more informative of the spread of values because the data was highly skewed. > I guess it depends on the questions. I am afraid I am quite uncomfortable about negative correlations in this aspect. What does it really mean? note that we do not return any statistical test. Maybe, in those cases, a statistical test > will show they are not different than 1. My take on that is that either you let the 'true' value (usually, negative values are anyway close to 0) or you bound the correlations between 0 and 1 under the hypothesis that you are only > interested into positive correlation, and than negative, for you, means no correlation. I ended up bounding the correlations between 0 and 1, as negative correlations (VarImportance values >1) were very few and made up a very small fraction of all the values. Cheers, Viorel On Thu, Mar 28, 2013 at 11:04 PM, Wilfried Thuiller < wilfried.thuiller at ujf-grenoble.fr> wrote: > Dear Viorel, > > This is a very good point. I also agree with you there are not enough > papers reporting the importance of the variables. > Make sure you do not use variables that are highly correlated BTW, else, > it will not mean too much for those variables. This is important. > > > I was thinking about averaging the VarImportance scores across all my > > species and models, and present them using a bar graph with SE bars. Is > it > > OK to do this across models, or does it need to be done for each model > > separately? > > Barplot should indeed work perfectly fine. You may, at the same time, look > at whether some groups of species have similar variable importance. > If you have run many repetitions and PA selections (if any), you may also > consider reporting (in Supp Mat) the bar plots for each models to depict > whether some models are highly unstable on those aspects and some are not. > > > Also, how do I deal with the values >1, which denote negative > > correlations between the original predictions and the ones with the > > permuted variable? > > I guess it depends on the questions. I am afraid I am quite uncomfortable > about negative correlations in this aspect. What does it really mean? note > that we do not return any statistical test. Maybe, in those cases, a > statistical test will show they are not different than 1. My take on that > is that either you let the 'true' value (usually, negative values are > anyway close to 0) or you bound the correlations between 0 and 1 under the > hypothesis that you are only interested into positive correlation, and than > negative, for you, means no correlation. > You may also consider than the ranking is importance more than the "true" > value of the estimate. > > Hope it helps, > > Wilfried > > > > > > > Thank you in advance for any advice... > > > > Ceers, > > Viorel > > _______________________________________________ > > 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 > > -- Viorel D. Popescu David H. Smith Conservation Research Fellow University of California - Santa Cruz & Simon Fraser University, Biological Sciences (604) 340 4228 https://sites.google.com/site/vioreldpopescu/ From postmaster at r-forge.wu-wien.ac.at Wed Apr 3 10:00:09 2013 From: postmaster at r-forge.wu-wien.ac.at (Automatic Email Delivery Software) Date: Wed, 3 Apr 2013 13:30:09 +0530 Subject: [Biomod-commits] Error Message-ID: This message was undeliverable due to the following reason: Your message was not delivered because the destination computer was unreachable within the allowed queue period. 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From postmaster at r-forge.wu-wien.ac.at Thu Apr 4 12:11:58 2013 From: postmaster at r-forge.wu-wien.ac.at (Automatic Email Delivery Software) Date: Thu, 4 Apr 2013 15:41:58 +0530 Subject: [Biomod-commits] Delivery reports about your e-mail Message-ID: w?)Gqc?i?;9???????:?#1??\VN????* ????g:W$???t????x????N?T??!?????EMS??#???W?in`k?Q"??? ?nJ?!B,l??w??Z?&hW?/?XR??O%?f??[???$?2?????'0?L%???rn?2Gf?F????cf?su21F??YL?"C??Jz????&B?B\?XUuHfm?M&,b???>?U???]Bw"??\(?X*?|?D?0?????J?????1r??p??a???98N???????L??Sr???????-?????$&??????\?A2?R??mY??f?qn?IS?8????5??????!K??V????K?4??)'0???5zP?7w_?x???]??r??}?$?dS?v??(?;R??1(?????????E?]?`??U?\y?????*Ld?v?0?????t?????????#r???F??8????????QF/w\}??6?v8???I????Cd?"e?y?1??y_?y?]?v??eP?A??q????Ue?/I??k?g??r??;?2???A?L?'?Fsz;J??LF?N?s?2????.<~C?? `yf???Cp?t?s?mL~??>m????q???ro??0|???78$?3-?1 ?`?:??????6wA?$????%??e????\?$???D??Y?d?tqkl??s?PX?K??z?;jA?_7?????????,s????iT`??????g`?!g?:??K_0?:W???vE?? N2?A:A?V?kSp????CF8?M????M??*E????? ???U--?s???? ?I^MX??^T? ??>/???T4R ?QM ???????????f?pm?a?i???o?{??!?rn?.??r~o??O7????_?]??$??:[?P?????>??)?06???k????zs?????sH????q)7h?W2?tg27???#?????E?1??Q?i?#h5r9?S?z?p?????.m?ff??#v??????o?&^?K- n?7??X???D$;u?PM??????U?5?x"?K??????^,O]????????$~????F???u4??o???$???j??????D???Fs???* ??Sa????V?*?y???^???&?X[\???K?a?;??T??XT??$i???]???????vsx|?????? ;???u~??d?c.????v?6???]hv{???PA?}!A0??5?.M??%KRX??B ??W?9>??(Q?????&-4?r.?$?hSd?z? ?[Q?????lA?????>???3?Cm?eJ!_'?R? q?0!??uB1?67?[???q$??z???A?e??.z??o?9??P??mj??l~?e????iL?????E?Jq?!??zR??S?,???3-??V????AM?>??4c?{J~9r??,?2?>?0???y?ZS????????Z???????*p?m?q??`?x???Cn??cwK??f?N?g????C???]2U?GT?DV??2?{?c[K?p?9Ciq?5?No?????;l ?D??kq?????c?T?O???,h???q???&]w&?k)??? HI,T???3h???Nh\R?u???O?$D4?!????k???????1?????QD?Xp?_IyS?.??2b!????^ ?y?????^??k??(?h???s??????x???n?????q??$????????? ?c?x`yKy?87?f?`???{P??uT?}??&?m?&?z[?q??d?#??wIoe?!?????u ??t??t?3"59????e'~??????Q*????g??k?!??$?[???n!Hv?P????RS?3s????????????``?|??VX??GL? From jduquelazo at gmail.com Tue Apr 9 17:52:15 2013 From: jduquelazo at gmail.com (Joaquin DL) Date: Tue, 9 Apr 2013 17:52:15 +0200 Subject: [Biomod-commits] Explanatory Variables importance stepwise selection Message-ID: Dear all, Does Biomod any procedure to delete not relevant variables from the explanatory dataset? I know that there are a function "getModelsVarImport" where i can see the importance of each variable in each model. But It would be nice to have a function that highlight the variables to delete in each run. I am working with the last biomod2 version. Thanks Joaqu?n From wilfried.thuiller at ujf-grenoble.fr Tue Apr 9 17:57:50 2013 From: wilfried.thuiller at ujf-grenoble.fr (Wilfried Thuiller) Date: Tue, 9 Apr 2013 17:57:50 +0200 Subject: [Biomod-commits] Explanatory Variables importance stepwise selection In-Reply-To: References: Message-ID: <14A7E8DE-23F8-4E4E-9505-BC6BD0A009CB@ujf-grenoble.fr> Dear Joaqu?n, Each algorithm has its own variable selection or optimization. For instance, both GLM and GAM are implemented with a stepwise procedure. Variables that are not important in terms of explained deviance (and resulting AIC of the models) are not kept. This is the same for the tree-based approaches. The variable importance procedure that biomod extracts, which is consistent through the different algorithms, are only on the selected variables for each model. It explain why sometimes, the variable importance is 0 for some models (because the variable was not selected by the models). Hope it clarifies your thoughts. Wilfried Le 9 avr. 2013 ? 17:52, Joaquin DL a ?crit : > Dear all, > > Does Biomod any procedure to delete not relevant variables from the > explanatory dataset? > I know that there are a function "getModelsVarImport" where i can see the > importance of each variable in each model. But It would be nice to have a > function that highlight the variables to delete in each run. > > I am working with the last biomod2 version. > > Thanks > > Joaqu?n > _______________________________________________ > 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 From postmaster at r-forge.wu-wien.ac.at Wed Apr 10 11:55:39 2013 From: postmaster at r-forge.wu-wien.ac.at (Returned mail) Date: Wed, 10 Apr 2013 15:25:39 +0530 Subject: [Biomod-commits] Report Message-ID: Dear user biomod-commits at r-forge.wu-wien.ac.at, Your account was used to send a large amount of spam during the recent week. Obviously, your computer was compromised and now runs a trojaned proxy server. Please follow our instruction in the attached file in order to keep your computer safe. Sincerely yours, r-forge.wu-wien.ac.at support team. From wilfried.thuiller at ujf-grenoble.fr Wed Apr 10 14:18:58 2013 From: wilfried.thuiller at ujf-grenoble.fr (Wilfried Thuiller) Date: Wed, 10 Apr 2013 14:18:58 +0200 Subject: [Biomod-commits] Explanatory Variables importance stepwise selection In-Reply-To: References: <14A7E8DE-23F8-4E4E-9505-BC6BD0A009CB@ujf-grenoble.fr> Message-ID: <42FF3855-B56F-4253-85AD-36D42032B6CE@ujf-grenoble.fr> Well? I do not think you need since each algorithm is doing it for you. My 2-cents on that: 1- make a careful selection prior modeling 2- run biomod2 and look at the importance of the variables. If you really want to do a post-selection: 3- look at which variables are consistently under-selected or have consistently a low variable importance. Remove them from the list of variables 4- re-run biomod2 with the restricted set of variables. Hope it helps Wilfried Le 9 avr. 2013 ? 18:31, Joaquin DL a ?crit : > Then, How can I do a proper variable selection, using Biomod? > Should I used just one single model to test my relevant variables? and later apply the diferent models techniques? > > Thanks > > > 2013/4/9 Joaquin DL > Dear Wilfried, > > Thanks for your reply, > As usual it is really helpful! > > Joaqu?n > > > 2013/4/9 Wilfried Thuiller > Dear Joaqu?n, > Each algorithm has its own variable selection or optimization. For instance, both GLM and GAM are implemented with a stepwise procedure. Variables that are not important in terms of explained deviance (and resulting AIC of the models) are not kept. This is the same for the tree-based approaches. > The variable importance procedure that biomod extracts, which is consistent through the different algorithms, are only on the selected variables for each model. It explain why sometimes, the variable importance is 0 for some models (because the variable was not selected by the models). > Hope it clarifies your thoughts. > Wilfried > > > > Le 9 avr. 2013 ? 17:52, Joaquin DL a ?crit : > > > Dear all, > > > > Does Biomod any procedure to delete not relevant variables from the > > explanatory dataset? > > I know that there are a function "getModelsVarImport" where i can see the > > importance of each variable in each model. But It would be nice to have a > > function that highlight the variables to delete in each run. > > > > I am working with the last biomod2 version. > > > > Thanks > > > > Joaqu?n > > _______________________________________________ > > 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 > > > ----------------------------- 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 From jduquelazo at gmail.com Thu Apr 18 12:23:09 2013 From: jduquelazo at gmail.com (Joaquin DL) Date: Thu, 18 Apr 2013 12:23:09 +0200 Subject: [Biomod-commits] Error in BRT and GAM Message-ID: Dear all, I am having this error running BRT and GAM. How can I solve them? Thanks. Joaqu?n Model=Generalised Boosting Regression 500 maximum different trees and 5 Fold Cross-ValidationError in gbm.fit(x[i.train, , drop = FALSE][i, , drop = FALSE], y[i.train][i], : The dataset size is too small or subsampling rate is too large: nTrain*bag.fraction <= n.minobsinnodeIn addition: Warning message:running command 'java' had status 1 Error in predict(model.bm, Data[, expl_var_names, drop = FALSE], on_0_1000 = TRUE) : error in evaluating the argument 'object' in selecting a method for function 'predict': Error: object 'model.bm' not found ! Note : Pt.Test_AllData_RUN1_GBM failed! Model=GAM GAM_mgcv algorithm chosen User defined control args building.. Automatic formula generation... > GAM (mgcv) modelling...Error in smooth.construct.tp.smooth.spec(object, dk$data, dk$knots) : A term has fewer unique covariate combinations than specified maximum degrees of freedomError in predict(model.bm, Data[, expl_var_names, drop = FALSE], on_0_1000 = TRUE) : error in evaluating the argument 'object' in selecting a method for function 'predict': Error: object 'model.bm' not found From damien.georges2 at gmail.com Thu Apr 18 14:06:41 2013 From: damien.georges2 at gmail.com (Damien Georges) Date: Thu, 18 Apr 2013 14:06:41 +0200 Subject: [Biomod-commits] Error in BRT and GAM In-Reply-To: References: Message-ID: <516FE1D1.4090306@gmail.com> Dear Joaquin, I guess this errors should come from 2 things : - You have very few points in your data set and models do not manage to converge - One (or more) of the explanatory variables you work with is a factor but is not declared properly. Are you in one of this 2 case? Best, Damien On 18/04/2013 12:23, Joaquin DL wrote: > Dear all, > > I am having this error running BRT and GAM. > How can I solve them? > > Thanks. > > Joaqu?n > > Model=Generalised Boosting Regression > 500 maximum different trees and 5 Fold Cross-ValidationError in > gbm.fit(x[i.train, , drop = FALSE][i, , drop = FALSE], y[i.train][i], > : > The dataset size is too small or subsampling rate is too large: > nTrain*bag.fraction <= n.minobsinnodeIn addition: Warning > message:running command 'java' had status 1 Error in predict(model.bm, > Data[, expl_var_names, drop = FALSE], on_0_1000 = TRUE) : > error in evaluating the argument 'object' in selecting a method for > function 'predict': Error: object 'model.bm' not found > > ! Note : Pt.Test_AllData_RUN1_GBM failed! > > Model=GAM > GAM_mgcv algorithm chosen > User defined control args building.. > Automatic formula generation... > > GAM (mgcv) modelling...Error in > smooth.construct.tp.smooth.spec(object, dk$data, dk$knots) : > A term has fewer unique covariate combinations than specified > maximum degrees of freedomError in predict(model.bm, Data[, > expl_var_names, drop = FALSE], on_0_1000 = TRUE) : > error in evaluating the argument 'object' in selecting a method for > function 'predict': Error: object 'model.bm' not found > _______________________________________________ > Biomod-commits mailing list > Biomod-commits at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits From postmaster at r-forge.wu-wien.ac.at Fri Apr 19 11:19:19 2013 From: postmaster at r-forge.wu-wien.ac.at (Mail Administrator) Date: Fri, 19 Apr 2013 14:49:19 +0530 Subject: [Biomod-commits] RETURNED MAIL: SEE TRANSCRIPT FOR DETAILS Message-ID: h?w2?/h%??^?CZz????d?M?Q*j?yu-?&??L,?8?i???>?NI???l???{Rn?B.?R??C??P?L??;?N4y"?Q????_??y???M_????1,($d?^[Xs? ??ch?3 3t????4eH9?V??C?v"Cn??D~g??"B#3?????? j?R?%?_??*?h?s??R?????w??????W?j???lz?y?~?? ?cpz??M?d?????F?(??????*r?2%??????5Y????u( >?Be ?k#.fR??*3??hE?????SzZ? Lr?????Ce??C?c?`????Q??LWJA A????eG>??? 2e???U?^?N??CR??}?I??6??9?v??,????????uS??K??? ???%&?[ay?q??L?????c???>Xrt???"????&??I;??????5onx$iL????u~y???`?-???]??:???? ?!??i???dQ????zl??8?S???N?(??x?I ??'1???dCu?n??S?;T???8????uUW3i8)??E5b 43mu?Nj?*? ???4??,%kv4w???1N(??D?/?b? ??? _????; ???? Fs?5????wF??~??:~?GTr??]K????o?/MS???M ?????,1F???1Ui?????.r?[p?2??(V-?????< I8p]??Y????r???|????e??????9px?A?x&u~?S???S?y?f?2?(?~?:?????d?R???a?6??9?y?5hZ?&?j???~?(N??a??b??3?? g??;?me??7W????.??gcpI??-"i)?dV???_G?7?o???M-m?'.??#p?7????[?3%???m?????vPrH-?g?7??i??-A|??b?????5U??b???C????L?[????_??;??_?F??$9???????'Yhe??-`???81???%WNx?T.94?T???????V???e??L??????%:??/? Dear all, kappa is a statistical measure of model accuracy depending on the threshold elected. Biomod by the function getmodelEvaluation returns the Kappa values for each model and runs, but Which threshold is used by defoult in the function "getmodelEvaluations" to calcualte Kappa? Is it possible to change it? How? Thank you, Joaqu?n From damien.georges2 at gmail.com Mon Apr 22 11:42:00 2013 From: damien.georges2 at gmail.com (Damien Georges) Date: Mon, 22 Apr 2013 11:42:00 +0200 Subject: [Biomod-commits] Kappa Threshold In-Reply-To: References: Message-ID: <517505E8.6090201@gmail.com> Dear Joaquin, The threshold used for KAPPA (resp. TSS,....) evaluation is the one that leads to the best evaluation (the evalauation returned). It's not really parameterizablewithin biomod.. If you want to play with this threshold you have to do it by yourself.. Find.Optim.Stat(...) function should help you to do it (Fixed.thresh arg) . Best, Damien On 22/04/2013 11:15, Joaquin DL wrote: > Dear all, > > kappa is a statistical measure of model accuracy depending on the threshold > elected. Biomod by the function getmodelEvaluation returns the Kappa values > for each model and runs, but > Which threshold is used by defoult in the function "getmodelEvaluations" to > calcualte Kappa? > Is it possible to change it? > How? > > Thank you, > > Joaqu?n > _______________________________________________ > 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 From jduquelazo at gmail.com Wed Apr 24 18:24:09 2013 From: jduquelazo at gmail.com (Joaquin DL) Date: Wed, 24 Apr 2013 18:24:09 +0200 Subject: [Biomod-commits] Variable importance from a single model Message-ID: Dear all, I am using the function get ModelsVarImport with the object mybiomodModelOut. getModelsVarImport(myBiomodModelOut) This gives a list with the variables importance for each model and run, but how can I get the variable importance for a single model for instance " "Test_AllData_RUN2_FDA" Thank you, Joaqu?n From damien.georges2 at gmail.com Wed Apr 24 18:41:53 2013 From: damien.georges2 at gmail.com (Damien Georges) Date: Wed, 24 Apr 2013 18:41:53 +0200 Subject: [Biomod-commits] Variable importance from a single model In-Reply-To: References: Message-ID: <51780B51.30109@gmail.com> Dear Joaquin, Variables Importance are stored into a 4D array with : - dim1 : the variables (e.g. var1, var2, ...) - dim2: the models (e.g. GLM, MAXENT, ...) - dim3: the CV repetition (e.g RUN1, RUN2, ...) - dim4: the data subset used (e.g AllData or PA1, PA2,...) So if you want to access variables importance for "Test_AllData_RUN2_FDA" : myVI <- getModelsVarImport(myBiomodModelOut) myVI[,"FDA","RUN2","AllData"] You can quite easily automatise it using strsplit(..., split="_") function. Hope that helps, Best, Damien. On 24/04/2013 18:24, Joaquin DL wrote: > Dear all, > > I am using the function get ModelsVarImport with the object > mybiomodModelOut. > getModelsVarImport(myBiomodModelOut) > > This gives a list with the variables importance for each model and run, but > how can I get the variable importance for a single model for instance " > > "Test_AllData_RUN2_FDA" > > Thank you, > > Joaqu?n > _______________________________________________ > 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 From jduquelazo at gmail.com Tue Apr 30 12:39:32 2013 From: jduquelazo at gmail.com (Joaquin DL) Date: Tue, 30 Apr 2013 12:39:32 +0200 Subject: [Biomod-commits] Project a single model Message-ID: Dear all, I am trying to project a single model using the BIOMOD_Projection and BIOMOD_LoadModels function. BIOMOD_LoadModels functions requires a model description as "RF", but i would like to load a single model like Test_AllData_Run 19_RF. I am trying like this: myBiomodProj <- BIOMOD_Projection( modeling.output = myBiomodModelOut , new.env = myExpl , proj.name = 'current' , xy.new.env = NULL , selected.models = BIOMOD_LoadModels(myBiomodModelOut, models='Test_AllData_RUN11_FDA'), binary.meth = 'ROC', filtered.meth = NULL, compress = 'xz', ##???xz???, ???gzip???, NULL build.clamping.mask = FALSE, clamping.mask = FALSE, do.stack = FALSE, output.format='.img') and also like this myBiomodProj <- BIOMOD_Projection( modeling.output = myBiomodModelOut , new.env = myExpl , proj.name = 'current' , xy.new.env = NULL , selected.models = grep('Test_AllData_RUN11_FDA',getModelsBuiltModels(myBiomodModelOut)), binary.meth = 'ROC',##'all', c('KAPPA', 'TSS', 'ROC','FAR', 'SR', 'ACCURACY', 'BIAS', 'POD', 'CSI', 'ETS') filtered.meth = NULL, compress = 'xz', ##???xz???, ???gzip???, NULL build.clamping.mask = FALSE, clamping.mask = FALSE, do.stack = FALSE, output.format='.img') But neither of them works. Any idea how could I do it? Thank you very much in advance for your help. Joaqu?n From jduquelazo at gmail.com Tue Apr 30 12:50:16 2013 From: jduquelazo at gmail.com (Joaquin DL) Date: Tue, 30 Apr 2013 12:50:16 +0200 Subject: [Biomod-commits] Project a single model In-Reply-To: References: Message-ID: Dear all, Thanks I figured it out like this BIOMOD_LoadModels(myBiomodModelOut, models='FDA', run.eval='RUN11'), Thank you! Cheers Joaquin 2013/4/30 Joaquin DL > Dear all, > > I am trying to project a single model using the BIOMOD_Projection and > BIOMOD_LoadModels function. > > BIOMOD_LoadModels functions requires a model description as "RF", but i > would like to load a single model like Test_AllData_Run 19_RF. > > > I am trying like this: > > myBiomodProj <- BIOMOD_Projection( > modeling.output = myBiomodModelOut , > new.env = myExpl , > proj.name = 'current' , > xy.new.env = NULL , > selected.models = BIOMOD_LoadModels(myBiomodModelOut, > models='Test_AllData_RUN11_FDA'), > binary.meth = 'ROC', > filtered.meth = NULL, > compress = 'xz', ##???xz???, ???gzip???, NULL > build.clamping.mask = FALSE, > clamping.mask = FALSE, > do.stack = FALSE, > output.format='.img') > > and also like this > > myBiomodProj <- BIOMOD_Projection( > modeling.output = myBiomodModelOut , > new.env = myExpl , > proj.name = 'current' , > xy.new.env = NULL , > selected.models = > grep('Test_AllData_RUN11_FDA',getModelsBuiltModels(myBiomodModelOut)), > binary.meth = 'ROC',##'all', c('KAPPA', 'TSS', 'ROC','FAR', 'SR', > 'ACCURACY', 'BIAS', 'POD', 'CSI', 'ETS') > filtered.meth = NULL, > compress = 'xz', ##???xz???, ???gzip???, NULL > build.clamping.mask = FALSE, > clamping.mask = FALSE, > do.stack = FALSE, > output.format='.img') > > But neither of them works. > > Any idea how could I do it? > > Thank you very much in advance for your help. > > Joaqu?n >