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The problem comes when I try to put the values back into raster format to plot. Here is the code:

Rstack <- Rstack[[name]]              # match names in raster stack to same order as model 
data_vals <- values(Rstack)           # convert raster to values
map_rftree <- predict(rf_tree1000, newdata = data_vals, missing = NA)    # make predictions
map_rftree_trans <- exp(map_rftree)   # back transform values
r <- Rstack[[3]]                      # use any raster from data set as template for predictions 
values(r) <- map_rftree_trans         # assign the predicted values to it

I get this error.

Error in setValues(x, value) : 
  length(values) is not equal to ncell(x), or to 1

I check and see lengths are not equal but I am not sure how to fix this.

> length(r)
[1] 90632698
> length(map_rftree_trans)
[1] 22023903

1 Answer 1

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The raster package allows to predict using a RandomForest model directrly over the RasterStack containing the predictors.

Suppose the rf_model variable contains your fitted model (classification model) and raster_stack is the RasterStack containing your predictors.

First, define the names of the RasterStack's layers. Make sure they are the same names as when you trained your model.

names(raster_stack)<-c("x1","x2", "x3", "x4", "x5", "...")

Then you can predict the value or the probability using as follows:

N = 3
r_pred <- raster::predict(model=rf_model, object=raster_stack)
r_prob <- raster::predict(model=rf_model, object=raster_stack, type="prob", index=1:N)

where N is the number of classes to classify.

Finally plot the results:

plot(r_pred)
plot(r_prob)
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  • This is a regressive RF model, not classification so N is infinite?
    – BHope
    Apr 1 at 21:21
  • In this case you can't use the probability, only the prediction. Try to use only: names(raster_stack)<-c("x1","x2", "x3", "x4", "x5", "...") r_pred <- raster::predict(model=rf_model, object=raster_stack)
    – sermomon
    Apr 1 at 21:39
  • This worked perfectly but my predicted values are log-transformed and I don't know how to back-transform them.
    – BHope
    Apr 1 at 22:40
  • 1
    Well, you could simply back-transform the resulting raster eg., back.transform <- function(y) exp(y + 0.5 * stats::var(y, na.rm=TRUE)) then raster::calc(x, back.transform) Apr 26 at 15:27

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