sim_traits_ontrees: Simulate traits on trees with various evolutionary models.

Description Usage Arguments Value Examples

View source: R/sim_traits_ontrees.r

Description

Use any of Brownian Motion, Orntsein-Uhlenbeck, or Early-Burst. The function uses functions already created for evolving traits on trees from the packages: ape, phytools, and geiger.

Usage

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  sim_traits_ontrees(trees, model = c("bm", "ou", "eb"),
    a = 10, bounds = c(0, 100), alpha = 1, sigma = 1,
    theta = 1, alpha_eb = -0.8, sigma_eb = 3)

Arguments

trees

A list of phylogenetic trees.

model

The model to be used to evolve traiats on a phylogenetic tree. One of "bm","ou", or "eb" for Brownian Motion, Orntsein-Uhlenbeck, and Early-Burst, respectively. "bm" uses the fastBM function from phytools. "ou" uses the rTraitCont function from ape. "eb" transforms a tree using exponentialchangeTree function from geiger, then evolves traits with rTraitCont function from ape.

a

If model = "bm", a value for ancestral state at the root node.

bounds

If model = "bm", a vector with the lower and upper bounds (respectively) for bounded Brownian simulation - by default simulation is unbounded.

alpha

If model = "ou", a value for the Ornstein-Uhlenbeck model of trait evolution. From ape documentation: "a numeric vector giving the strength of the selective constraint for each branch (can be a single value)."

sigma

If model = "ou", is the single value of the standard-deviation of the random component for each branch (can be a single value).

theta

If model = "ou", a numeric vector giving the optimum for each branch (can be a single value)

alpha_eb

If model = "eb", is the exponent of the relationship between rate and time in the exponentialchange model.

sigma_eb

If model = "eb", the single value of the standard-deviation of the random component for each branch (can be a single value). This sigma means the same as for the OU model, but this allows to specify it separately.

Value

A list of named vectors of traits matching the tips of the input trees.

Examples

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## Not run: 
sim_traits_ontrees(trees = trees_colless_plants_bal, model = "bm")
sim_traits_ontrees(trees = trees_colless_plants_bal, model = "ou", alpha=1.5, sigma=2)
sim_traits_ontrees(trees = trees_colless_plants_bal, model = "eb", alpha_eb=-0.9, sigma_eb=3)

## End(Not run)

sckott/treeshape documentation built on May 26, 2017, 3:50 a.m.