rdiversity (version 1.2.1)

chainsaw: Function to cut phylogeny from present day species to a specified depth.

Description

Function to cut phylogeny from present day species to a specified depth.

Usage

chainsaw(partition, ps, depth)

Arguments

partition

proportional abundance of types in the subcommunity as a fraction of the metacommunity as a whole (in the phylogenetic case, this corresponds to the proportional abundance of present day species)

ps

phy_struct() output

depth

proportion of total tree height to be conserved (taken as a proportion from the heighest tip). Describes how far back we go in the tree, with 0 marking the date of the most recent tip, and 1 marking the most recent common ancestor. Numbers greater than 1 extend the root of the tree

Value

Returns an object of class phy_struct containing a new structural matrix ('@structure') and the original phylogenetic parameters ('@parameters').

Examples

# NOT RUN {
tree <- ape::rtree(n = 5)
tree$tip.label <- paste0("sp", seq_along(tree$tip.label))
partition <- cbind(a = c(1,1,1,0,0), b = c(0,1,0,1,1))
row.names(partition) <- tree$tip.label
partition <- partition / sum(partition)
ps <- phy_struct(tree, partition)

a <- chainsaw(partition, ps, depth = 0.9)
b <- chainsaw(partition, ps, depth = 2)
z <- chainsaw(partition, ps, depth = 0)
m <- chainsaw(partition, ps, depth = 1)

# }