change order of populations in gl.fst.pop

[Sandra Erdmann]

Hi dartR Team,

I've been trying to do this for a while in many different ways, but without success. Is there any way that I can rearrange my populations when applying the function gl.fst.pop? I see that it works through the pairwise comparisons a bit randomly(!?), but I would like to manually sort them in geographical order. Of course, I can manipulate this after running the function, but that takes time when you have 15 populations... Does it make sense to sort the genlight object before using it to run that function or does the ordering occur when the function runs? If it makes sense to do beforehand, how does it work???

This might be more of a R wrangling issue, but I appreciate to get any tips how to do this.

Thanks,

Sunny

[Jose Luis Mijangos]

Hi Sunny,

You can try:

library(dartR.base)
t1 <- bandicoot.gl
popNames(t1)
t2 <- gl.sort(t1,
        sort.by = "pop",
        order.by = c("NSW" ,"QLD","SA" , "VIC" ,"WA" ) )
fst <- gl.fst.pop(t2)

Cheers,

Luis 

[Sandra Erdmann]

Hi Luis,

Thank you so much! I've applied it to my dataset and it worked. So simple at the end. Hope this helps others, too.

Thanks,

Sunny

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