treats (version 1.0)

make.traits: make.traits

Description

Making traits objects for treats

Usage

make.traits(
  process = BM.process,
  n = NULL,
  start = NULL,
  process.args = NULL,
  trait.names = NULL,
  add = NULL,
  update = NULL,
  test = TRUE,
  background
)

Value

This function outputs a treats object that is a named list of elements handled internally by the treats function.

Arguments

process

The trait process(es) (default is BM.process).

n

Optional, the number of traits per process (default is 1).

start

Optional, the starting values for each traits (default is 0).

process.args

Optional, a named list of optional arguments for the trait process.

trait.names

Optional, the name(s) of the process(s).

add

Optional, another previous "treats" traits object to which to add the trait.

update

Optional, another previous "treats" traits object to update (see details).

test

Logical, whether to test if the traits object will work with treats (TRUE - default).

background

Optional, another "treats" "traits" object to simulate background trait evolution (see details).

Author

Thomas Guillerme

Details

When using update, the provided arguments (to make.traits) will be the ones updated in the "traits" object. If the "traits" object contains multiple processes, you can specify which ones should be affected with the trait.names argument. Note that you cannot update the traits.names or the number of traits per processes (n) not use the add argument when updating a "traits" object.

If a background "traits" object is given, this object is then applied to all living edges at the same in the background while the main "traits" is computed.

More details about the "treats" "traits" objects is explained in the treats manual: http://tguillerme.github.io/treats.

See Also

treats trait.process

Examples

## A simple Brownian motion trait (default)
make.traits()

## Two independent Brownian motion traits
make.traits(n = 2)

## Two different traits with different process
## (Brownian motion and Ornstein-Uhlenbeck)
make.traits(process = list(BM.process, OU.process))

## A multidimensional Brownian motion trait with correlation
## and different starting points
my_correlations <- matrix(1/3, ncol = 3, nrow = 3)
(my_traits <- make.traits(n = 3, start = c(0, 1, 3),
                          process.args = list(Sigma = my_correlations)))

## Adding a Ornstein-Uhlenbeck trait to the previous trait object
make.traits(process = OU.process, trait.names = "OU_trait",
            add = my_traits)