From jenny.williams at kew.org Wed Aug 14 16:26:33 2013 From: jenny.williams at kew.org (Jenny Williams) Date: Wed, 14 Aug 2013 15:26:33 +0100 Subject: [Biomod-commits] (no subject) Message-ID: I am still trying to get my head around biomod2. I have run through the tutorial a few times, which works really well in a linear format. But, I want to see the models and assess them at every part of the process. So, I need to: 1: be able to re-access all the files from /.BIOMOD_DATA/ once R is closed and all the file links are lost. e.g myBiomodModelOut 2: call the summary parameters for the models e.g GLM, I can see the files but not sure how to access them. e.g >myGLMs <- BIOMOD_LoadModels(myBiomodModelOut, models='GLM') #just produces a list >summary(myGLMs[1]) Length Class Mode 1 character character #summary(GLM) doesn't work, but is the output that I am looking to find. 3. find the split datasets used for each of the iterations BIOMOD_Modeling options; NbRunEval for DataSplit Any help or pointers in the right direction would be greatly appreciated. FYI the vignette does not seem to work: http://127.0.0.1:15505/library/biomod2/doc/index.html ****************** Jenny Williams Spatial Information Scientist, GIS Unit Herbarium, Library, Art & Archives Directorate Royal Botanic Gardens, Kew Richmond, TW9 3AB, UK Tel: +44 (0)208 332 5277 email: jenny.williams at kew.org ****************** Film: The Forgotten Home of Coffee - Beyond the Gardens Stories: Coffee Expedition - Ethiopia Kew in Harapan Rainforest Sumatra Articles: Seeing the wood for the trees How Kew's GIS team and South East Asia botanists are working to help conserve and restore a rainforest in Sumatra. Download a pdf of this article here. ________________________________ The Royal Botanic Gardens, Kew is a non-departmental public body with exempt charitable status, whose principal place of business is at Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom. The information contained in this email and any attachments is intended solely for the addressee(s) and may contain confidential or legally privileged information. If you have received this message in error, please return it immediately and permanently delete it. Do not use, copy or disclose the information contained in this email or in any attachment. Any views expressed in this email do not necessarily reflect the opinions of RBG Kew. Any files attached to this email have been inspected with virus detection software by RBG Kew before transmission, however you should carry out your own virus checks before opening any attachments. RBG Kew accepts no liability for any loss or damage which may be caused by software viruses. From javiernori at gmail.com Fri Aug 23 19:23:35 2013 From: javiernori at gmail.com (Javier Nori) Date: Fri, 23 Aug 2013 14:23:35 -0300 Subject: [Biomod-commits] (no subject) Message-ID: Dear all! I am new with Biomod. I'm trying to perform an ensemble between results of five algorithms ('MARS','GAM','GBM', 'MAXENT', 'GLM', 'FDA'), using Pres-PAbs data. I have not problems to generate and project the results of the individual models. However probably i'am making a mistake in the emsemble of them or in the projection' script because I cannot generate the rasters of the ensemble. In addition, I cannot obtain the values of the evaluation index of the ensemble (*Error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ?getModelsEvaluations? for signature ?"BIOMOD.EnsembleModeling.out"?*) Could anyone help me please? Thanks in advance!! below I attached the scripts for projection and ensemble ** Ensemble myBiomodEM <- BIOMOD_EnsembleModeling( modeling.output = myBiomodModelOut, chosen.models = 'all', em.by='all', eval.metric = c('ROC'), eval.metric.quality.threshold = c(0.8), prob.mean = T, prob.cv = T, prob.ci = T, prob.ci.alpha = 0.05, prob.median = T, committee.averaging = T, prob.mean.weight = T, prob.mean.weight.decay = 'proportional' ) Projection myBiomodProj <- BIOMOD_Projection( modeling.output = myBiomodModelOut, new.env = myExpl, proj.name = 'current', selected.models = 'all', binary.meth = 'TSS', filtered.meth ='TSS', cmpress = 'gzip', clamping.mask = T, output.format = '.img') -- *************************************************************************** Javier Nori Centro de Zoolog?a Aplicada - F.C.E.F.y.N. Universidad Nacional de C?rdoba From raquel.garcia at mncn.csic.es Wed Aug 28 20:13:43 2013 From: raquel.garcia at mncn.csic.es (Raquel A. Garcia) Date: Wed, 28 Aug 2013 20:13:43 +0200 Subject: [Biomod-commits] evaluation of ensemble models Message-ID: <20130828201343.Horde.pq9-jag66Bn2Jk_lHPhsAw7@webmail.csic.es> Hi, I have a question about the ensemble function in biomod2 version 2.1.15 - how are the evaluation scores obtained? thanks, Raquel ................ Raquel A. Garcia Integrative Biology and Global Change Group | www.ibiochange.mncn.csic.es Center for Macroecology, Evolution and Climate | www.macroecology.ku.dk