[adegenet-forum] NA.REPLACE

[Jombart, Thibaut]

Hi there,

yes, na.replace has been removed in adegenet 2.0.0.

Instead, you can use:
tab(x, NA.method="mean")

where 'x' is your genind. If you want frequencies, you will need to add 'freq=TRUE'. See ?tab, and the basics tutorial for more info on data handling:
https://github.com/thibautjombart/adegenet/wiki/Tutorials

Cheers
Thibaut

________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Raman Lawal [plxral at nottingham.ac.uk]
Sent: 15 July 2015 15:08
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] NA.REPLACE

I have tried to prepare all necessary files but wanted to remove the NA using the na.replace option of the ade4 as seen in command below. When I ran test<- na.replace(genind_ABCDEFGH,"mean", quiet=FALSE), I get “Error: could not find function "na.replace". I am not certainly sure what I was doing wrong. Could you please advise me on what to do.

library(adegenet)

datan<- as.numeric(data4)

pop<-data4 at phdata$pop

genind_ABCDEFGH<-as.genind(datan,pop)

rm(data4)
rm(datan)
#rm(pop)
library(ade4)
## Replacing NAs
test<- na.replace(genind_ABCDEFGH,"mean", quiet=FALSE)

 LAWAL

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