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Projecting model to landscape
7 messages · AdrianR, Tim Meehan, Nicole K.S. Barker +2 more
Hi, Li. I am far from certain, but I believe this might be a good place to look: http://cran.r-project.org/web/packages/spatstat/index.html http://www.spatstat.org/ Regards, Adrian Rasmussen Li Wen-2 wrote
Dear list member I have fitted a Random Forest model for species distribution, and want to use it to project the model to a defined landscape (i.e. forecasting for all grids in an area) . The landscape has all the environment covariates (rasters) and cover a large region (over 1000*1000 grids). I wonder if there is package in R to do this. Thank you for your help in advance. Cheers Li [[alternative HTML version deleted]]
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Thanks, Nicole I want to compare a few methods as in Elith et al 2006 Ecography 29: 129-51. So, what I am after is a generic method to do "spatial projection" with fitted statistical models, could be GAM, GLM, or MARS, etc. Maybe using prediction.model is the only way to this at the moment. Cheers, Li -----Original Message----- From: r-sig-ecology-bounces at r-project.org [mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Nicole K.S. Barker Sent: Wednesday, 6 March 2013 5:00 AM To: Li Wen Cc: r-sig-ecology at r-project.org Subject: Re: [R-sig-eco] Projecting model to landscape If you extract the information from your rasters into a dataframe (one column per raster), can you use the predict.randomForest function in the randomForest package? If yes, you can then input your predictions back into a raster of the same dimensions as the environmental variables. I don't have any experience with random forest model, but that's what I do with my Boosted Regression Tree predictions. Nicole K.S. Barker Ph.D Student / ?tudiante au Doctorat Laval University / Universit? Laval Ducks Unlimited Canada / Canards Illimit?s Canada LinkedIn: www.linkedin.com/in/nksbarker Phone: 647-470-3207
On Tue, Mar 5, 2013 at 5:21 AM, Li Wen <li01.wen at gmail.com> wrote:
Dear list member
I have fitted a Random Forest model for species distribution, and want to
use it to project the model to a defined landscape (i.e. forecasting for
all
grids in an area) . The landscape has all the environment covariates
(rasters) and cover a large region (over 1000*1000 grids). I wonder if
there
is package in R to do this. Thank you for your help in advance.
Cheers
Li
[[alternative HTML version deleted]]
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You may want to consider the Biomod <http://www.will.chez-alice.fr/Software.html> package ( Thuiller 2009 <http://www.will.chez-alice.fr/pdf/ThuillerEcography2009.PDF> ). This sounds like what you are looking for, assuming you are working with presence/absence data. Biomod does not accommodate abundance data. It can generate pseudo-absences if you have presence-only data. Biomod is an ensemble forecasting package that can output multiple kinds of models including random forests, ANN, GLM, GAM, classification trees, etc. It will make predictions for all grid cells in your raster layers based on any single model or using an ensemble consensus approach. It provides parameters that can be used to compare models and assess variable importance. Hope this helps. Good luck! -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/Projecting-model-to-landscape-tp7577935p7577941.html Sent from the r-sig-ecology mailing list archive at Nabble.com.
Thanks, Doug It seems that Biomod is the one I am after. Thanks again. Li -----Original Message----- From: r-sig-ecology-bounces at r-project.org [mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of doug.leasure Sent: Wednesday, 6 March 2013 9:30 AM To: r-sig-ecology at r-project.org Subject: Re: [R-sig-eco] Projecting model to landscape You may want to consider the Biomod <http://www.will.chez-alice.fr/Software.html> package ( Thuiller 2009 <http://www.will.chez-alice.fr/pdf/ThuillerEcography2009.PDF> ). This sounds like what you are looking for, assuming you are working with presence/absence data. Biomod does not accommodate abundance data. It can generate pseudo-absences if you have presence-only data. Biomod is an ensemble forecasting package that can output multiple kinds of models including random forests, ANN, GLM, GAM, classification trees, etc. It will make predictions for all grid cells in your raster layers based on any single model or using an ensemble consensus approach. It provides parameters that can be used to compare models and assess variable importance. Hope this helps. Good luck! -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/Projecting-model-to-landscape-tp7577935p7577941.html Sent from the r-sig-ecology mailing list archive at Nabble.com. _______________________________________________ R-sig-ecology mailing list R-sig-ecology at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- This email is intended for the addressee(s) named and may contain confidential and/or privileged information. If you are not the intended recipient, please notify the sender and then delete it immediately. Any views expressed in this email are those of the individual sender except where the sender expressly and with authority states them to be the views of the Office of Environment and Heritage, NSW Department of Premier and Cabinet. PLEASE CONSIDER THE ENVIRONMENT BEFORE PRINTING THIS EMAIL