substitue raster values duplicate error

Question

I have a raster (seg) whose values I want to substitute, and am getting an error from function subs from the raster package that I don't understand at all.

I get the following error

Error in .local(x, y, ...) : duplicate "by" values not allowed

Even though I have no duplicates in my data frame.

The error show up with both of the following commands, which makes no sense to me.

seg <- subs(seg, tabulated, by="seg", which="class")
seg <- subs(seg, tabulated[which(!duplicated(tabulated$seg)),], by="seg", which="class")

From what i could find out from subs, it checks duplicates through the following commands

tt <- table(tabulated$seg)
tt <- tt[ which(tt > 1) ]
if (length(tt) > 0) {
  stop('duplicate "by" values not allowed')
}

When I run those commands myself I find that tt has a length of 0...

I am not sure how to share the specifics, so I copied the structure of the two objects. The dataframe has 5784018 rows, which corresponds to the number of unique values of the raster seg.

I am not sure what I am missing.

The structure of my raster is the following

Formal class 'RasterLayer' [package "raster"] with 12 slots
  ..@ file    :Formal class '.RasterFile' [package "raster"] with 13 slots
  .. .. ..@ name        : chr "/media/olivier/olivier_ext/gedata_current/jde_coffee/data/ES/Classifs/test/es3_seg2.tif"
  .. .. ..@ datanotation: chr "INT4S"
  .. .. ..@ byteorder   : chr "little"
  .. .. ..@ nodatavalue : num -Inf
  .. .. ..@ NAchanged   : logi FALSE
  .. .. ..@ nbands      : int 1
  .. .. ..@ bandorder   : chr "BIL"
  .. .. ..@ offset      : int 0
  .. .. ..@ toptobottom : logi TRUE
  .. .. ..@ blockrows   : int 1
  .. .. ..@ blockcols   : int 11497
  .. .. ..@ driver      : chr "gdal"
  .. .. ..@ open        : logi FALSE
  ..@ data    :Formal class '.SingleLayerData' [package "raster"] with 13 slots
  .. .. ..@ values    : logi(0) 
  .. .. ..@ offset    : num 0
  .. .. ..@ gain      : num 1
  .. .. ..@ inmemory  : logi FALSE
  .. .. ..@ fromdisk  : logi TRUE
  .. .. ..@ isfactor  : logi FALSE
  .. .. ..@ attributes: list()
  .. .. ..@ haveminmax: logi TRUE
  .. .. ..@ min       : num -2.15e+09
  .. .. ..@ max       : num 2.15e+09
  .. .. ..@ band      : int 1
  .. .. ..@ unit      : chr ""
  .. .. ..@ names     : chr "es3_seg2"
  ..@ legend  :Formal class '.RasterLegend' [package "raster"] with 5 slots
  .. .. ..@ type      : chr(0) 
  .. .. ..@ values    : logi(0) 
  .. .. ..@ color     : logi(0) 
  .. .. ..@ names     : logi(0) 
  .. .. ..@ colortable: logi(0) 
  ..@ title   : chr(0) 
  ..@ extent  :Formal class 'Extent' [package "raster"] with 4 slots
  .. .. ..@ xmin: num 268734
  .. .. ..@ xmax: num 337716
  .. .. ..@ ymin: num 7714422
  .. .. ..@ ymax: num 7828590
  ..@ rotated : logi FALSE
  ..@ rotation:Formal class '.Rotation' [package "raster"] with 2 slots
  .. .. ..@ geotrans: num(0) 
  .. .. ..@ transfun:function ()  
  ..@ ncols   : int 11497
  ..@ nrows   : int 19028
  ..@ crs     :Formal class 'CRS' [package "sp"] with 1 slot
  .. .. ..@ projargs: chr "+proj=utm +zone=24 +south +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0"
  ..@ history : list()
  ..@ z       : list()

And the structure of the data frame is

'data.frame':   5784018 obs. of  3 variables:
 $ class: int  2 6 6 2 2 6 11 7 7 7 ...
 $ seg  : int  1 3 6 8 10 15 18 21 22 24 ...
 $ freq : int  2504 375 31 4 102 109 3 6 7 7 ...

Answer 1

Update: The bug that causes this problem was fixed in version 2.8-2 of the raster package.

In version 2.8-1 of the raster package (and earlier ones also) raster::subs has a bug that causes it to fail when the by argument is not the first column.

As a workaround, you could probably get it to work by putting the seg column first:

seg = seg[, c("seg", "class", "freq")]

Answer 2

I found a solution, which doesn't make much sense, except if there is some metadata in the dataframe information?

Anyway, the solution is to transform the dataframe into a matrix and back into a dataframe, as follows.

seg <- subs(seg, as.data.frame(as.matrix(tabulated[,c("seg","class")])), by="seg", which="class")