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In R, I have a raster object for which I would like to set a certain level of transparency. When I visualize it, everything is fine

library(raster)

test <- raster(x = matrix(1:16, 4))

plot(test,
     alpha = 0.25)

but now I would like to write my raster in .tif format through the writeRaster() function. Is it possible to store the level of transparency at the pixel level?

I need this step because, starting from the .tif object, I would like to produce tiles of such raster that will be displayed as basemaps Leaflet inside an online application.

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Generally speaking a tiff (GeoTIFF) file is a means to store data. You are trying to store visualization metadata as a part of that file. While this might be possible, I would think twice before doing so: Usually visualization applications such as leaflet tiles allow you to set the transparency (opacity) value in the application itself (one example: Leaflet - Opacity method for L.tileLayer.wms?).

If you really want to create a transparency (alpha) band for the GeoTIFF file, you can do so with gdal after writing out the raster to GeoTIFF with R as explained in this thread: Adding transparency to Geotiff files.

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