Error rename individuals using gl.recode.ind()

[Chiara Duijser]

Hi there,

I want to rename some individuals in my genlight object and have tried this using the following code:

gl.make.recode.ind(gl, out.recode.file="SNP_recode2_ind.csv", outpath=getwd())

gl <- gl.recode.ind(gl, ind.recode="SNP_recode2_ind.csv")

gl$ind.names

 [1] "1"    "2"    "3"    "4"    "5"    "6"    "7"    "8"    "9"    "10"   "11"   "12"   "13"  

[14] "14"   "15"   "16"   "17"   "18"   "18.1" "19"   "19.1" "20"   "20.1" "21"   "21.1" "22"  

[27] "22.1" "23"   "23.1" "24"   "24.1" "25"   "25.1" "26"   "26.1" "33.1" "33.1" "33.1" "33.1"

[40] "33.1" "33.1" "33.1" "33.1" "33.1" "33.1" "33.1" "33.1" "33.1" "33.1" "54.1" "54.1" "54.1"

[53] "54.1" "54.1" "55"   "54.1" "55"   "54.1" "55"   "54.1" "55"   "54.1" "55"   "54.1" "55"  

[66] "54.1" "55"   "54.1" "55"   "54.1" "55"   "54.1" "55"   "54.1" "55"   "55.1" "54.1" "55"  

[79] "55.1" "54.1" "55"   "55.1" "54.1" "55"   "55.1" "54.1" "55"   "55.1" "54.1" "55"   "55.1"

However, if I check the genlight object after this, I see that a lot of numbers are repeated somehow. I checked the “SNP_recode2_ind.csv” file again, but it shows the correct numbers there.

I’ve also tried gl.edit.recode.ind() and the same thing happens that when I change one individual it changes correctly, but once I rename more it repeats some of them. Would anyone know how to solve this? 

I’m using dartR version 2.7.2; 2022-12-06 [1] CRAN (R 4.2.0) and R version 2022.07.2. 

Thanks in advance!

Kind regards,

Chiara