Collapse the tips of a phylogenetic tree based on a temporal threshold

This function collapses, or prune, the tips of a phylogenetic tree based on an inputted temporal threshold.

Usage

prune_tips(tree, time, qtl = FALSE, method = 1)

Arguments

tree

phylo. An ultrametric phylogenetic tree in the "phylo" format.

time

numeric or numeric vector. A numeric value, or vector, containing the temporal threshold(s) in million years for pruning the tree tips. It must be within the interval of the tips ages present in the phylogenetic tree.

qtl

logical. A logical value indicating whether the user wants to use the quantile values of the tip ages to prune the tree. Default is FALSE

method

numerical. A numerical value indicating the method to prune the tips. If "method = 1", the function will prune the tips originating after an inputted temporal threshold. If method = 2, the function will prune the tips originating before a temporal threshold. Default is 1.

Value

The function returns a pruned tree in the "phylo" format if a single temporal threshold was inputted. Otherwise, if a vector of thresholds was inputted, it returns an list of pruned trees.

Details

It uses the tip ages location in relation to an inputted time threshold to prune the phylogenetic tree. Setting "method = 2" makes slices based on the quantile distribution of tip ages available within the phylogenetic tree.

References

See the tutorial on how to use this function on our website.

See also

Other slicing methods: squeeze_root(),squeeze_tips(),squeeze_int(),phylo_pieces()

Author

Matheus Lima de Araujo matheusaraujolima@live.com

Examples

# Generate a random tree
tree <- ape::rcoal(20)

# Pruning the tips originating after 0.3 million years
tree1 <- prune_tips(tree, time = 0.1)

# Plot it
plot(tree1)



# Pruning the tips based on quantiles of tip ages
tree2 <- prune_tips(tree, time = c(0.25, 0.75), qtl = TRUE)
plot(tree2[[1]])

plot(tree2[[2]])