subscript out of bounds in gl.filter.ld

[Claudia Escobar]

Hi all,

I was running gl.filter.ld after gl.report.ld.map
In the report, I noticed that if ind.limit = 3, it returns an error, so I chose 4.

When I tried to run gl.filter.ld, I've got the error:
Error in ld_tmp_pop[[i]] : subscript out of bounds

I suspected it could be the ind.limit = 4, so changed it to 5 and gave it a try and it didn't work either: it returned the same error after a long time running.

The report and filter functions I used were:
LD_map <- gl.report.ld.map(
  gl, maf = 0.01, ld.stat = "R.squared", ind.limit = 5, stat.keep = "AvgPIC",
  ld.threshold.pops = 0.2, plot.display = TRUE, bins = 50,
)

gl <- gl.filter.ld(
  gl,
  ld.report = LD_map,
  threshold = 0.2,
  pop.limit = 8,
)

Maybe this is useful:
table(pop(gl), useNA="always")
   AN   BD   BF   CN   FM   FP   MB   MS   RE   RN   SB   SC   TO   WP   WW   YA
   3    5    4    6    3    6    4    6    6    4    5    4    6    6    6    6
<NA>
   0