Configuring lidR catalog to overwrite raster output (with different extension)?

Question

I have a small issue with configuring the lidR package for parametrizing the extracted raster files with grid_metrics() function.

My question is how to set in the catalog options that:

1. be able to overwrite the results with a second run if I want to run my script several times and I do not want to name each output differently.
2. instead of .tif I would like to get .grd files as output.

My current code (which is working) is the following:

normalizedctg = catalog(workingdirectory)
opt_output_files(normalizedctg) <- paste(workingdirectory,"/clipped/normalized/{XLEFT}_{YBOTTOM}_height",sep="")
height = grid_metrics(normalizedctg, max(Z),res = resolution)

But with a second run on the same code I get the following error:

Error in .getGDALtransient(x, filename = filename, options = options,  : 
  filename exists; use overwrite=TRUE

Answer 1

Your question is related to LAScatalog processing engine tuning. A topic not documented in the official documentation. The only one existing documentation at the time being (june 2019) is a wiki page that provide an example to change the drivers.

In short the drivers used to write objects to files are stored in the LAScatalog object. You can access to them with regular R code. The difficulty is the fact it is not documented.

To save .grd instead of .tif

normalizedctg@output_options$drivers$Raster$extension <- ".grd"
normalizedctg@output_options$drivers$Raster$param$format <- "raster"

To force the overwrite option in raster::writeRaster

normalizedctg@output_options$drivers$Raster$param$overwrite <- TRUE