Error in predict when working with Random Forest and specify a categorial variable as a predictor

[consbiol-unibern]

Error in predict when working with Random Forest and specify a categorial variable as a predictor

[sgvignali]

Thanks for reporting the error, I will check it today or tomorrow.

[sgvignali]

The error happens because the function "predict" in the randomForest package expects to have a factor for the "biome" variable, but in the raster object "biome" is a numeric variable.

To avoid this error you can pass an additional argument to the predict function. The predict function for raster dataset implemented in SDMtune uses the predict function implemented in the raster package https://rdrr.io/cran/raster/man/predict.html. You can use the factors argument to pass the levels of the "biome" factor. Here is the code:

f <- list(biome = levels(data@data$biome))
map <- predict(default_model, data = predictors, factors = f)

Note that the factors argument is a named list. You have to match the name with the name of the raster layer, in this case biome.
Be aware that you might have to handle cases in which there are more levels in the raster layer compared to the training dataset (google it and you will find some examples).

[ManuelSpinola]

It works. Thank you very much Sergio. El mar., 26 may. 2020 a las 1:20, Sergio Vignali (<[email protected]>) escribió:

…

The error happens because the function "predict" in the *randomForest* package expects to have a factor for the "biome" variable, but in the raster object "biome" is a numeric variable. To avoid this error you can pass an additional argument to the predict function. The predict function for raster dataset implemented in *SDMtune* uses the predict function implemented in the *raster* package https://rdrr.io/cran/raster/man/predict.html. You can use the *factors* argument to pass the levels of the "biome" factor. Here is the code: f <- list(biome = ***@***.***$biome)) map <- predict(default_model, data = predictors, factors = f) Note that the *factors* argument is a named list. You have to match the name with the name of the raster layer, in this case *biome*. Be aware that you might have to handle cases in which there are more levels in the raster layer compared to the training dataset (google it and you will find some examples). — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFI3FB3GNTZCO4ZTLXUBRBLRTNUVRANCNFSM4NIUWEUA> .

-- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA [email protected] <[email protected]> [email protected] Teléfono: (506) 8706 - 4662 Personal website: Lobito de río <https://sites.google.com/site/lobitoderio/> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>