Forum: biomod2 package is now available !
Posted by: damien georges
Content: Dear BIOMOD-users,You were eagerly waiting for it, and we are happy to say that the new version of BIOMOD called biomod2 is now online on R-Forge. Although we kept the same modelling philosophy than the former version (which we will still maintain for a while), we have made crucial changes. biomod2 is now fully object-oriented and made for running on a single species only (see vignette MultiSpeciesModelling for multi-species modelling at once). For advanced BIOMOD users, the new functions might be a bit disturbing at the beginning. Then, you will see that this new version is much more advanced and practical than the former ones. Among the novelties, the addition of MAXENT in the modelling techniques, a large range of evaluation metrics, a more refined definition of ensemble modelling and ensemble forecasting, the possibility to give presence-only data and environmental rasters to biomod2 and let it extract pseudo-absence data directly. We have created several vignettes for you to get use to this new version and a figure explaining the different ways of giving data to BIOMOD. Please bear in mind that R-Forge is a development platform, it means that this new package would experience repeated updating the next couple of weeks (correcting bugs, adding documentation, adding functionalities) so think about updating the package before each new study you will do. Last but not least, all comments are welcome! If you find a bug, if you think some documentation points are unclear, if you think about new functionalities that may be useful, just let us know ASAP. We count on you to help finalizing this new version to a very nice tool. We will then release it to CRAN by the end of July. Please remember to add your code, R-version, OS and BIOMOD-version every time you report a bug or a mistake in the vignette or help files. Hoping you will enjoy this new version of BIOMOD. With our best wishes, Damien & Wilfried |
Latest Newsbiomod2 is now devel on githubdamien georges - 2020-03-02 17:08 -
biomod2 package is now available !damien georges - 2012-07-26 13:56 -
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| RE: Problem when running Maxent in biomod2 setting background [ Reply ] By: damien georges on 2018-12-07 10:42 | [forum:46462] |
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Hi Cecilia, Just to be sure that it is no due to a java configuration issue.. Does a biomod2 run with MAXENT and Pseudo Absences does smooth? Could you send me the output of sessionInfo() ? Best, Damien |
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| Problem when running Maxent in biomod2 setting background [ Reply ] By: Cecilia Passadore on 2018-08-28 17:55 | [forum:46459] |
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Hi, I’m trying to run Maxent in biomod2 setting background data as it was described in the following link (https://rpubs.com/dgeorges/190889). I followed all the steps in the script, and when I run the Maxent with background points (bm.mod.maxent.bg) I get the following error: Model=MAXENT.Phillips Creating Maxent Temp Proj Data..Error in colnames(Back_swd) : object 'Back_swd' not found Also: Warning message: In system("java", intern = TRUE) : 'java' has estatus 1 PLEASE, ANY SUGGESTIONS ON HOW CAN I MAKE IT WORK? I tried running the script in different computers, updated the R version, the java version, and I always get the same error. I also looked for messages talking about the same error, and I tried the solutions that were suggested to them but still the same error. In the following link (i.e. https://r-forge.r-project.org/forum/forum.php?thread_id=31867&forum_id=995&group_id=302) it was suggested to check if the version of biomod2 supports the background_data_dir by typping: BIOMOD_ModelingOptions()@MAXENT.Phillips and I get the following: MAXENT.Phillips = list( path_to_maxent.jar = ‘C:/Users/Cecilia/Documents/SRpaper’, memory_allocated = 512, background_data_dir = 'default', maximumbackground = 'default', maximumiterations = 200, visible = FALSE, linear = TRUE, quadratic = TRUE, product = TRUE, threshold = TRUE, hinge = TRUE, lq2lqptthreshold = 80, l2lqthreshold = 10, hingethreshold = 15, beta_threshold = -1, beta_categorical = -1, beta_lqp = -1, beta_hinge = -1, betamultiplier = 1, defaultprevalence = 0.5) I past below the outcome of the bm.mod.default, although it runs it also says ‘In system("java", intern = TRUE) : 'java' has estatus 1’. > bm.mod.default <- BIOMOD_Modeling( bm.dat, + models = c('MAXENT.Phillips'), + models.options = bm.opt.default, + NbRunEval = 1, + DataSplit = 100, + models.eval.meth = c('TSS','ROC'), + do.full.models = TRUE, + modeling.id = "default") Loading required library... Checking Models arguments... Creating suitable Workdir... ! Weights where automaticly defined for GuloGulo_PA1 to rise a 0.5 prevalence ! -=-=-=-=-=-=-=-=-=-=-=-=-= GuloGulo Modeling Summary -=-=-=-=-=-=-=-=-=-=-=-=-= 5 environmental variables ( bio3 bio4 bio7 bio11 bio12 ) Number of evaluation repetitions : 1 Models selected : MAXENT.Phillips Total number of model runs : 1 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -=-=-=- Run : GuloGulo_PA1 -=-=-=--=-=-=- GuloGulo_PA1_Full Model=MAXENT.Phillips Creating Maxent Temp Proj Data.. Running Maxent... Getting predictions... Removing Maxent Temp Data.. Evaluating Model stuff... -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Done -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Warning message: In system("java", intern = TRUE) : 'java' has status 1 > ## > bm.mod.maxent.bg <- BIOMOD_Modeling( bm.dat, + models = c('MAXENT.Phillips'), + models.options = bm.opt.maxent.bg, + NbRunEval = 1, + DataSplit = 100, + models.eval.meth = c('TSS','ROC'), + do.full.models = TRUE, + modeling.id = "maxent_bg") Loading required library... Checking Models arguments... Creating suitable Workdir... ! Weights where automaticly defined for GuloGulo_PA1 to rise a 0.5 prevalence ! -=-=-=-=-=-=-=-=-=-=-=-=-= GuloGulo Modeling Summary -=-=-=-=-=-=-=-=-=-=-=-=-= 5 environmental variables ( bio3 bio4 bio7 bio11 bio12 ) Number of evaluation repetitions : 1 Models selected : MAXENT.Phillips Total number of model runs : 1 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -=-=-=- Run : GuloGulo_PA1 -=-=-=--=-=-=- GuloGulo_PA1_Full Model=MAXENT.Phillips Creating Maxent Temp Proj Data..Error in colnames(Back_swd) : object 'Back_swd' not found Also: Warning message: In system("java", intern = TRUE) : 'java' has status 1 > get_evaluations(bm.mod.default) , , MAXENT.Phillips, Full, PA1 Testing.data Cutoff Sensitivity Specificity TSS 0.98 565 100 98 ROC 0.99 565 100 98 > get_evaluations(bm.mod.maxent.bg) Error in get_evaluations(bm.mod.maxent.bg) : object 'bm.mod.maxent.bg' not found THANKS FOR ANY ADVISE! Cecilia |
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