R/var.sites.R

In fmichonneau/starbeastPPS: A posterior predictive check for the multispecies coalescent model implemented in *BEAST

var.sites <- function(phydat) {
    mat <- as.character(phydat)
    dims <- dim(mat)
    mat <- mat[rowSums(mat == "-" | mat == "?") != dims[2], ]
    uniqEle <- function(vec) {
        uni <- sum(!duplicated(vec))
        uni
    }
    out <- apply(mat, MARGIN = 2, uniqEle)
    var.s <- length(out[out > 1])
    var.s
}