treats (version 1.0)

drop.things: Drop things from a treats object

Description

Remove fossils or living species or non-bifurcating nodes (singles) from treats objects or phylo objects.

Usage

drop.things(treats, what)
drop.fossils(treats)
drop.livings(treats)
drop.singles(treats)

Value

This function outputs either a "phylo" object if no traits where generated or a treats object that is a list of at least two elements: $tree, a "phylo" object and $data, a "matrix" of the trait values.

Arguments

treats

treats data.

what

what to drop. Can be "fossils", "livings" or "singles" (non-bifurcating nodes).

Author

Thomas Guillerme

Details

NOTE that dropping living or fossils species DOES NOT drop associated internal nodes and edge lengths. To drop both fossil/living taxa AND internal nodes, you can use for example: drop.things(drop.things(my_data, what = "fossils"), what = "singles").

See Also

treats plot.treats

Examples

## A random tree with fossils and traits and internal nodes every 0.5 times
set.seed(3)
my_data <- treats(stop.rule = list(max.taxa = 20),
                bd.params = list(speciation = 1, extinction = 1/3),
                traits    = make.traits(), save.steps = 0.5)

## A tree with 20 tips and 54 nodes
my_data$tree
## And a dataset with 74 rows
dim(my_data$data)

## Removing the fossil species
drop.things(my_data, what = "fossils")$tree
dim(drop.fossils(my_data)$data)

## Removing the living species
drop.things(my_data, what = "livings")$tree
dim(drop.livings(my_data)$data)

## Removing the internal nodes
drop.things(my_data, what = "singles")$tree
dim(drop.singles(my_data)$data)

## Removing the internal nodes AND the fossils
drop.singles(drop.fossils(my_data))