Predict xgboost model onto raster stack yields error

Question

I am using an xgboost model to predict onto a raster stack. I have successfully used the same approach with CART, xgb and Random Forest models:

library(raster)

# create a RasterStack or RasterBrick with with a set of predictor layers
logo <- brick(system.file("external/rlogo.grd", package="raster"))
names(logo)

# known presence and absence points
p <- matrix(c(48, 48, 48, 53, 50, 46, 54, 70, 84, 85, 74, 84, 95, 85,
              66, 42, 26, 4, 19, 17, 7, 14, 26, 29, 39, 45, 51, 56, 46, 38, 31,
              22, 34, 60, 70, 73, 63, 46, 43, 28), ncol=2)
a <- matrix(c(22, 33, 64, 85, 92, 94, 59, 27, 30, 64, 60, 33, 31, 9,
              99, 67, 15, 5, 4, 30, 8, 37, 42, 27, 19, 69, 60, 73, 3, 5, 21,
              37, 52, 70, 74, 9, 13, 4, 17, 47), ncol=2)

# extract values for points
xy <- rbind(cbind(1, p), cbind(0, a))
v <- data.frame(cbind(pa=xy[,1], extract(logo, xy[,2:3])))

xgb <- xgboost(data = data.matrix(subset(v, select = -c(pa))), label = v$pa, 
               nrounds = 5)

raster::predict(model = xgb, logo)

But with xgboost I get the following error:

Error in xgb.DMatrix(newdata, missing = missing) : xgb.DMatrix does not support construction from list

please include a minimal, reproducible, self-contained example. For example, adapt the example from `raster::predict`. — Robert Hijmans, Apr 21 '22 at 05:31
@RobertHijmans I have updated the question by including a minimal, reproducible, self-contained example. I am also facing the same problem. Can you please help me out? — UseR10085, Nov 05 '22 at 16:44

Robert Hijmans · Accepted Answer · 2022-11-05T19:17:06.263

The problem is that predict.xgb.Booster does not accept a data.frame for argument newdata (see ?predict.xgb.Booster). That is unexpected (all common predict.* methods take a data.frame), but we can work around it. I show how to do that below, using the "terra" package instead of the obsolete "raster" package (but the solution is exactly the same for either package).

The example data

library(terra)
library(xgboost)    
logo <- rast(system.file("ex/logo.tif", package="terra"))   
p <- matrix(c(48, 48, 48, 53, 50, 46, 54, 70, 84, 85, 74, 84, 95, 85,
              66, 42, 26, 4, 19, 17, 7, 14, 26, 29, 39, 45, 51, 56, 46, 38, 31,
              22, 34, 60, 70, 73, 63, 46, 43, 28), ncol=2)
a <- matrix(c(22, 33, 64, 85, 92, 94, 59, 27, 30, 64, 60, 33, 31, 9,
              99, 67, 15, 5, 4, 30, 8, 37, 42, 27, 19, 69, 60, 73, 3, 5, 21,
              37, 52, 70, 74, 9, 13, 4, 17, 47), ncol=2)    
xy <- rbind(cbind(1, p), cbind(0, a))
v <- extract(logo, xy[,2:3])
xgb <- xgboost(data = data.matrix(v), label=xy[,1], nrounds = 5)

The work-around is to write a prediction function that first coerces the data.frame with "new data" to a matrix. We can use that function with predict<SpatRaster>

xgbpred <- function(model, data, ...) {
    predict(model, newdata=as.matrix(data), ...)
}

p <- predict(logo, model=xgb, fun=xgbpred)
plot(p)

Predict xgboost model onto raster stack yields error

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