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: Error when building TSS binaries with biomod2 [ Reply ] By: Mirza Cengic on 2018-06-14 15:25 | [forum:46078] |
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Dear Kostas, this error message comes when biomod tries to call raster::calc() function. However, in one of the recent ggplot2 version, there was briefly function with the same name (that was renamed to stat() in order not to cause these issues). In biomod calc function is not referred to by its namespace -- raster::calc, so since ggplot is attached by biomod by default, this would cause this error... In short, to solve this issue update you can try installing the most recent ggplot2 version where function calc() doesn't exist anymore. Try running devtools::install_github("tidyverse/ggplot2") and that should solve the issue (it did for me). Cheers, Mirza |
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| Error when building TSS binaries with biomod2 [ Reply ] By: Kostas Kougioumoutzis on 2018-04-03 08:49 | [forum:45812] |
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Hi everyone, I am using biomod2 3.3.7 and I was not facing any problems when I used the 'binary.meth' arguments in BIOMOD_Projection up until yesterday (02-Apr-2018). Now, when I try to project any model, I get the following error: Building TSS binariesError in calc(data, function(x) { : unused argument (function(x) { x >= threshold }) Any ideas? I've only loaded biomod2 and I haven't change a single line of my previously perfectly working code - I just rerun the models. Your help will be greatly appreciated! |
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