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: Screening variables for correlation [ Reply ] By: damien georges on 2018-01-17 13:57 | [forum:45580] |
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Dear Nikhail, Maybe you should try to sample only X points of the rasters and compute correalation on this subset of point (with extract() function for instance). Of course you should then repeat the sampling process to check that the correlations you find between your variable is independant from the sampling points chosen. Hope tat helps , Damien |
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| Screening variables for correlation [ Reply ] By: Nikhail Arumoogum on 2018-01-17 12:37 | [forum:45579] |
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Dear All, This might be a message best suited for another forum, but in trying to screen my bioclimatic predictor variables for collinearity in the rasterVis package i keep getting an error message that a vector cannot be allocated to an object of 6.1 Gb. After trying to screen just 6 of the variables I get a similar message saying a vector cannot be allocated to an object of 1.9Gb. The same message is given to me when I try and do a VIF analysis on these variables in the usdm package. Could someone please help me get around this issue, given computation issues, simply removing variables of little importance after modelling is not a really feasible option. I need to carefully select my variables beforehand. Thanks, Nikhail |
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