Dear Zhian, Many thanks for all the help.
You helped me earlier also in another problem. Really appreciate your help and support. Best wishes, Rav > On 22 Jan 2017, at 15:09, Zhian Kamvar <[email protected]> wrote: > > Hi, > > You've got the right idea with make.unique, but you're trying to use repool > on only one population at a time. > > First and foremost: don't use row.names(x$tab) or nrow(x$tab), use > indNames(x) and nInd(x), respectively. > > > Your procedure needs to be done in three steps: > > 1. sample the individuals > 2. rename the individuals > 3. repool the populations > > Taking the example you gave, this should work: > > MySamp8 <- lapply(obj, function(x) x[sample(nInd(x), 8, replace= TRUE)]) > MySamp8 <- lapply(MySamp8, function(x){ indNames(x) <- > make.unique(indNames(x)); return(x)}) > repool(MySamp8) > > > Here it is using a custom function: > > sample_genind_with_replacement <- function(x, n = 8){ > y <- x[sample(nInd(x), n, replace = TRUE)] > indNames(y) <- make.unique(indNames(y)) > return(y) > } > MySamp8 <- lapply(obj, sample_genind_with_replacement, n = 8) > repool(MySamp8) > > > Best, > Zhian > >> On Jan 19, 2017, at 07:50 , Bhuller, Ravneet >> <[email protected]> wrote: >> >> Dear Members, >> >> I am working with a genind object which is subset into populations. I want >> to sample 8 individuals randomly with replacement per population and repool >> them in a way that each population has unique individual names. >> >> I am doing the following steps: >> >> obj<- seppop(niger.data.genind) >> >> MySamp8 <- lapply(obj, function(x) x[sample(1:nrow(x$tab), 8, replace= >> TRUE)]) >> >> new_samp8<- lapply(MySamp8, function(x) >> repool(MySamp8[make.unique(row.names(x$tab))])) >> >> But I am getting the following error: >> >> Error in repool(MySamp8[make.unique(row.names(x$tab))]): x is does not >> contain only valid genind objects. >> >> Please if any one can guide me how can I get valid genind objects to repool >> them in a way that each population has unique individual names. >> >> Many thanks for your time, >> >> Rav >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-genetics mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-genetics > _______________________________________________ R-sig-genetics mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
