R/gap.matrix.R

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

gap.matrix <- function(partition, data) {
    nseq <- length(data$alignments[[partition]])
    nbp <- length(data$alignments[[partition]][[1]])
    gap.mat <- matrix(nrow = nseq, ncol = nbp)
    rownames(gap.mat) <- names(data$alignments[[partition]])
    for (i in 1:nseq) {
        gap.mat[i, ] <- !(data$alignments[[partition]][[i]] == "A" | data$alignments[[partition]][[i]] == 
            "a" | data$alignments[[partition]][[i]] == "C" | data$alignments[[partition]][[i]] == 
            "c" | data$alignments[[partition]][[i]] == "G" | data$alignments[[partition]][[i]] == 
            "g" | data$alignments[[partition]][[i]] == "T" | data$alignments[[partition]][[i]] == 
            "t")
    }
    return(gap.mat)
}