modified genind2hierfstat to include conversion pathway for loci when…

[EricArcher]

… alleles are present that are neither nucleotides nor all numeric

I've tested this against examples of all 3 possible types and it seems to work now.

[jgx65]

Thanks a lot Eric. This seems to work in most cases. One situation when it does not is when the number of allelic states differ between loci, i.e., some have less than 10 and are thus encoded with one digit and the others have more than 10, hence encoded as two digits. I'm looking into how to fix it

[thierrygosselin]

In my case I fixed that using

stringi::stri_pad_left(str = ALLELE, width = 3, pad = 0)

where ALLELE is my column of all the alleles

if that can help Thierry

[EricArcher]

Howabout moving the digits assignment higher and calculating it like this (new lines are max.length and digits assignments outside of the do.call loop with the previous digits assignment inside the loop deleted):

    if(length(grep("[[:alpha:]|[:punct:]]", alleles.name)) > 0) {
      # for loci where alleles are not all numeric nor all nucleotides
      dat <- as.matrix(genind2df(dat, sep = "", usepop = FALSE,
oneColPerAll = TRUE))
      dat <- apply(dat, 2, function(a) ifelse(a == "NA", NA, a))
      max.length <- max(sapply(alleles(dat), length))
     digits <- floor(log10(max.length))  
      # cycle through each locus
      do.call(cbind, lapply(seq(ploid, ncol(dat), by = ploid),
function(end) {
        start <- end - ploid + 1
        alleles <- sort(unique(as.vector(dat[, start:end])))
        # match alleles of each genotype with sorted order: index is new
allele
        apply(dat[, start:end, drop = FALSE], 1, function(gntp) {
          if(any(is.na(gntp))) return(NA)
          gntp <- match(gntp, alleles)
          # zero pad numeric alleles and return collapsed genotype
          gntp <- formatC(gntp, digits = digits, flag = "0", mode =
"integer")
          as.integer(paste(gntp, collapse = ""))
        })
      }))
    }

---

Eric Archer, Ph.D. Southwest Fisheries Science Center NMFS, NOAA 8901 La Jolla Shores Drive La Jolla, CA 92037 USA 858-546-7121 (work) 858-546-7003 (FAX)

Marine Mammal Genetics Group: swfsc.noaa.gov/mmtd-mmgenetics ETP Cetacean Assessment Program: swfsc.noaa.gov/mmtd-etp

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  • John C. "Craig" George

On Tue, Mar 1, 2016 at 9:21 AM, Jerome Goudet notifications@github.com wrote:

Thanks a lot Eric. This seems to work in most cases. One situation when it does not is when the number of allelic states differ between loci, i.e., some have less than 10 and are thus encoded with one digit and the others have more than 10, hence encoded as two digits. I'm looking into how to fix it

— Reply to this email directly or view it on GitHub https://github.com/jgx65/hierfstat/pull/15#issuecomment-190821190.

[jgx65]

Yeap, it works, great! (moved the line max.lenght... before the call to genind2df