Improves performance on R working with raster files

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I´m trying this code to look for NA and negative pixel values and replace it for 0. But it´s too slow. Any tip for improve the performance of it?

"all.files" is a list of address of the images. "r1" is the stack of Landsat images and "e" is the extents of some region of interest.

for (i in 1:length(all.files)){ r1
 
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