PhyloCompare function

Compares sister groups

Calculates the comparison of some statistic between sister groups along a phylogeny

PhyloCompare(tree, node.data, ComparisonFunc = PCAsimilarity, ...)

Arguments

• tree: phylogenetic tree
• node.data: list of node data
• ComparisonFunc: comparison function, default is PCAsimilarity
• ...: Additional arguments passed to ComparisonFunc

Returns

list with a data.frame of calculated comparisons for each node, using labels or numbers from tree; and a list of comparisons for plotting using phytools (see examples)

Note

Phylogeny must be fully resolved

Examples

library(ape)
data(bird.orders)
tree <- bird.orders
mat.list <- RandomMatrix(5, length(tree$tip.label))
names(mat.list) <- tree$tip.label
sample.sizes <- runif(length(tree$tip.label), 15, 20)
phylo.state <- PhyloW(tree, mat.list, sample.sizes)

phylo.comparisons <- PhyloCompare(tree, phylo.state)

# plotting results on a phylogeny:
## Not run:

library(phytools)
plotBranchbyTrait(tree, phylo.comparisons[[2]])
## End(Not run)

Author(s)

Diogo Melo