monophyly: Species monophyly over a tree

Description

Determines if the species given in sppVector form monophyletic groups on a given tree.

Usage

monophyly(phy, sppVector, pp = NA, singletonsMono = TRUE)

Arguments

phy

A tree of class `phylo'.

sppVector

Species vector. See sppVector

Object of class `prop.part'. Assists in speeding up the function, if it has been called already. Default of NA, calling prop.part internally.

singletonsMono

Logical. Should singletons (i.e. only a single specimen representing that species) be treated as monophyletic? Default of TRUE. Possible values of FALSE and NA.

Value

monophyly returns a logical vector, stating if each species is monophyletic. Values correspond to the species order given by unique(sppVector).

monophylyBoot returns a list with the following elements:

results

A logical vector, stating if each species is monophyletic with a bootstrap support higher than the given threshold.

BSvalues

A numeric vector giving the bootstrap proportions for each node of phy.

Details

monophyly determines if each species is monophyletic. monophylyBoot incorporates a bootstrap test to determine the support for this monophyly. Species with a bootstrap support lower than "thresh" are recorded as FALSE.

Rerooting is done on the longest internal edge in the tree returned by nj(dist.dna(DNAbin)).

Examples

Run this code

# NOT RUN {
#Random trees
set.seed(16)
tr <- ape::rtree(15)
spp <- rep(LETTERS[1:5], rep(3,5))
monophyly(tr, spp)

tr2 <- tr
spp2 <- c(rep(LETTERS[1:4], rep(3,4)), LETTERS[5:7])
monophyly(tr2, spp2)

#Empirical data
# }
# NOT RUN {
data(anoteropsis)
anoTree <- ape::nj(ape::dist.dna(anoteropsis))
anoSpp <- sapply(strsplit(dimnames(anoteropsis)[[1]], split="_"), 
    function(x) paste(x[1], x[2], sep="_"))

monophyly(anoTree, anoSpp)
monophyly(anoTree, anoSpp, singletonsMono=FALSE)
unique(anoSpp)

#To get score for each individual
anoMono <- monophyly(anoTree, anoSpp)
anoMono[match(anoSpp, unique(anoSpp))]

data(woodmouse)
woodTree <- ape::nj(ape::dist.dna(woodmouse))
woodSpp <- c("D", "C", "C", "A", "A", "E", "A", "F", "C", "F", "E", "D", "A", "A", "E")
unique(woodSpp)
monophyly(woodTree, woodSpp)
woodMono <- monophylyBoot(woodTree, woodSpp, woodmouse)
woodMono$results
woodMono$BSvalues

monophylyBoot(woodTree, woodSpp, woodmouse, reroot = FALSE)
monophylyBoot(woodTree, woodSpp, woodmouse, thresh = 0.9, reroot = FALSE)
# }
# NOT RUN {

# }

Run the code above in your browser using DataCamp Workspace