get_local_ploidy() throws an error with non-SSR loci

[zkamvar]

This is in reference to https://groups.google.com/d/msgid/poppr/189bdc5d-4979-4245-942f-e7ebd01f7f6f%40googlegroups.com.

Here's the worked example:

Setup (click to expand)

if (!file.exists("trial.txt")){
  download.file("https://groups.google.com/group/poppr/attach/54e0e4c1740bf/trial.txt?part=0.1&authuser=0", destfile = "trial.txt")
}

if (!file.exists("strata.txt")){
  download.file("https://groups.google.com/group/poppr/attach/54e0e4c1740bf/strata.txt?part=0.2&authuser=0", destfile = "strata.txt")
}

suppressPackageStartupMessages(library("poppr"))
file <- read.table("trial.txt", header=T)

tfile <- t(file[,1:ncol(file)])   #transpose table
colnames(tfile) = tfile[1, ]   #markers labels
tfile = tfile[-1, ]

# to change rownames because the transposition don't leave the labels "ID"
g <- tfile
ID <- rownames(g)
rownames(g) <- NULL
fx <- cbind(ID,g)
View(fx)

x <- as.data.frame(fx, header=T) #trasform into a data.frame

locs <- x[, -c(1, 2)] 
colnames(locs) <- gsub("\\-", "_", colnames(locs))
# 
# ind <- as.character(file$lines)     # labels of the individuals
# population <- as.character(file$Pop)    # labels of the populations

id <- read.table("strata.txt", header=T)    # add strata

file_genind <- df2genind(locs, ploidy = 2, ind.names = ID, strata = id, NA.char = "NA", type = "codom", sep = "") # conversion into a genind object

file_amova <- poppr.amova(file_genind, ~rep/year/plot)
#> 
#> Found 238 missing values.
#> 
#> 3 loci contained missing values greater than 5%
#> 
#> Removing 3 loci: JHI_Hv50k_2016_206330, JHI_Hv50k_2016_206596,
#> JHI_Hv50k_2016_20687
#> Warning in get_local_ploidy(x): NAs introduced by coercion
#> Error in if (any(as.numeric(unlist(x@all.names, use.names = FALSE)) == : missing value where TRUE/FALSE needed

Created on 2018-06-12 by the reprex package (v0.2.0).