Create mask for each layer of time-series raster in R

Question

I'm trying to create a mask using each layer of my stacked Pixel Reliability QA rasters in R. I'm trying to exclude pixels with values greater than 1. I will use them to mask my vegetation index time-series layers. I tried for one layer and it worked with this code:

rely_ts <- load("Rely/MOD13Q1_MYD13Q1_Rely_1_2019_169_2019_RData.RData")
rely_ts <- get(rely_ts)
test_pix <- raster(rely_ts, layer=4)
test_pix[test_pix>1] <- NA
plot(test_pix, main="Pixel Reliability < 1")

Being new in coding with R, I am still struggling to do loops. I tried this code below but no go:

pix <- load("Rely/MOD13Q1_MYD13Q1_Rely_1_2019_169_2019_RData.RData")
pix <- get(pix)
for (aPix in pix){
  aPix[aPix>1] <- NA
  plot(aPix)
}

I get this error and I don't know what to do with it:

Error in for (aPix in pix) { : invalid for() loop sequence

RData files are accessible HERE for testing.

UPDATE:

I followed @Spacedman's advise as I understood it. I was able to create and write my masks, however it doesn't follow the filename that I want... the filenames created are "1.tif" to "22.tif". Here's my code:

pix <- load("Rely/MOD13Q1_MYD13Q1_Rely_1_2019_169_2019_RData.RData")
px.mask <- get(pix)

for(i in 1:nlayers(px.mask)){
  px.mask[[i]][px.mask[[i]]>1] <- NA
  #plot(px.mask[[i]])
  fname <- gsub("MYD|MOD|13Q1_Rely_2019_", " ", 1:nlayers(px.mask))
  writeRaster(px.mask, file = paste0(fname), 
              bylayer=TRUE, format="GTiff")
}

Answer 1

You are trying to loop over the single object pix, where pix is:

> pix
class      : RasterStack 
dimensions : 668, 1105, 738140, 22  (nrow, ncol, ncell, nlayers)
[etc]

but R is a bit fussy about what you can loop over. For example you get the same error if you try and loop over a function:

> for(f in sqrt){f}
Error in for (f in sqrt) { : invalid for() loop sequence

If you want to loop over all layers of a raster stack then loop over the layer indexes:

> s = stack(list(raster(matrix(1:12,3,4)),raster(matrix(1:12,3,4))))
> for(i in 1:nlayers(s)){plot(s[[i]])}