[adegenet-forum] pairwise.fst in the basic tutorial

[Vojtěch Zeisek]

Hello,
You need to run library(hierfstat) first. I see it in that package (version 
0.04-22). For me
library(adegenet)
data(nancycats)
library(hierfstat)
pairwise.fst(nancycats)
works well.
HTH,
V.

Dne středa 25. března 2020 17:17:15 CET, Tyler Smith napsal(a):
> Hello,
> The basic tutorial includes instructions to use the function
> `pairwise.fst`, which I believe was once part of the package
> `hierfstat`. That function no longer exists, and the closest
> match in `hierfstat` is `pairwise.neifst`. That function won't
> work on a `genind` object:
> ```
> > data(nancycats)
> > pairwise.fst(nancycats)
> Error in pairwise.fst(nancycats) : could not find function "pairwise.fst"
> > pairwise.neifst(nancycats)
> Error in names(y) <- nm[!nas] :
>   'names' attribute [11] must be the same length as the vector [1]
> In addition: Warning message:
> In is.na(x) : is.na() applied to non-(list or vector) of type 'S4'
> ```
> Is there a way to calculate pairwise Fst for genind objects now?
> Thanks,
> Tyler
-- 
Vojtěch Zeisek
https://trapa.cz/en/

Department of Botany, Faculty of Science
Charles University, Prague, Czech Republic
https://www.natur.cuni.cz/biology/botany/
https://lab-allience.natur.cuni.cz/
https://botany.natur.cuni.cz/brassiploidy/

Institute of Botany, Czech Academy of Sciences
Průhonice, Czech Republic
https://www.ibot.cas.cz/en/
Computing cluster
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