Nothing
## package: megaptera
## author: Christoph Heibl (at gmx.net)
## last update: 2014-04-24
check.Clades <- function(phy, tax){
tax <- tax[, names(tax) != "synonyms"]
tax <- tax[tax$spec %in% phy$tip.label,]
mp <- function(rank, phy, tax){
obj <- NULL
for ( i in unique(tax[, rank]) ){
taxSet <- tax$spec[tax[, rank] == i]
s <- noi(phy, taxSet)
phySet <- descendants(phy, s, labels = TRUE)
id <- phySet %in% taxSet
if ( all(id) ) {
mp <- TRUE
frac <- 0
} else {
mp <- FALSE
frac <- length(id[!id])/length(id)
}
obj <- rbind(obj, c(i, s, mp, frac))
}
cbind(rank, obj)
}
ranks <- names(tax)[names(tax) != "spec"]
obj <- lapply(ranks, mp, phy = phy, tax = tax)
obj <- do.call(rbind, obj)
obj <- data.frame(obj, stringsAsFactors = FALSE)
names(obj) <- c("rank", "taxon", "node", "mp", "prop")
obj$mp <- as.logical(obj$mp)
obj$prop <- as.numeric(obj$prop)
obj
}
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