Does anyone know how to get the "basic.stats" (hierfstat), "wc" (hierfstat), and/or other hierfstat commands to work on a genind object that has NA in the @pop section? I can convert the genind to hierfstat, but the other commands are not happy with the NA:
Error in 1:sum(data[, 1] == i) : NA/NaN argument
I would like to keep the original data file intact, because it contains other information and categories where the "NA" samples are included and I would like to work from the one reference file as much as possible. There are just some samples that are from single representatives of populations and so I do not want them to be used/shown in other data (I map the samples later too and don't want these on there).
In short: I have a fasta data file (PvMtFas) made into a genind object (PvMtGen) and added @pop from another file (PvMtData) which contains some NA in the column I am using (and contains loads of other data I use). These NA appear to be stopping me from using the basic.stats and wc commands from hierfstat. Any easy solutions?
PvMtFas <- read.FASTA ('~/Documents/PvMtFasta.fasta')
PvMtGen <- DNAbin2genind(PvMtFas, pop=NULL, exp.char=c("a","t","g","c"), polyThres=1/100)
PvMtData <- read.csv ('~/Documents/PvMtData.csv')
PvMtGen$pop = PvMtData$GeoCatLV29 #PvMtData$GeoCatLV29 contains NA for some sequences
PvMtHier <- genind2hierfstat(PvMtGen) #this works fine
basic.stats(PvMtGen) #this doesn't
wc(PvMtGen) #this doesn't
Any suggestions are welcome! I looked into using "na.exclude" but that didn't work (obviously, because I am not sure how to target the @pop within a genind object and I would want the whole 'row' gone, not just the @pop NA's but also the samples it refers to).
