Slices a temporal interval within a phylogenetic tree

This function slices a temporal interval located within an ultrametric phylogenetic tree.

Usage

squeeze_int(tree, from, to, invert = FALSE, criterion = "my", dropNodes = FALSE)

Arguments

tree

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

from

numeric. A temporal threshold value that determines the time at which the interval should start.

to

numeric. A temporal threshold value that determines the time at which the interval should end.

invert

logical. A logical value indicating if the desired slice must be executed inside (invert = FALSE) or outside (invert = TRUE) the defined interval. Using the argument as TRUE will return a list containing a root and tip slices. Default is FALSE.

criterion

character string. The method for cutting the tree. It can be either "my" (million years) or "PD" (accumulated phylogenetic diversity). Default is "my".

dropNodes

logical. A logical value indicating whether the nodes that were sliced (void nodes, presenting no branch length) should be preserved in the node matrix. Default is FALSE.

Value

The function returns an time-slice interval of a phylogenetic tree in the "phylo" format.

Details

Slicing approach

To return a given phylogenetic interval, this function simultaneously applies simultaneously the same logic as squeeze_tips() and squeeze_root(). If "invert = TRUE", then the temporal interval set will be excluded from the phylogeny, returning a list containing a tip and a root slices.

References

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

See also

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

Author

Matheus Lima de Araujo matheusaraujolima@live.com

Examples

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

# Slice an interval from 0.5 to 0.2 million years
tree <- squeeze_int(tree, from = 0.5, to = 0.2)

# Plot it
plot(tree)