Function to simulate continuous trait value histories on a phylogeny.

Usage

simulate_traits(
  phy,
  rate_model = c("continuous", "discrete"),
  temp_trend_rates = 0,
  rate_change,
  rates = NULL,
  anc = c(`1` = 0),
  internal = FALSE,
  nsim = 1,
  pos_strat = c("none", "log", "add_const"),
  temp_trend_mean = 0
)

Arguments

phy: A phylogenetic tree (phylo object) on which to simulate traits
rate_model: The type of rate model for how rates of evolution evolve on the phylogeny: "continuous" for continuous Brownian motion evolution of rates, or "discrete" for evolution of rate "classes" across the phylogeny, using an mk model.
temp_trend_rates: What temporal trend in rates should there be? A positive number for an increase, and negative number for a decrease with the magnitude controlling the strength of linear change. This trend is added to rates simulated under the rate_model.
rate_change: If rate_model is "continuous", this should be a single positive number controlling how fast rates change continuously along the tree. If rate_model is "discrete", this should be a transition matrix for the rate classes. Or, if rate_model is "discrete", and this can be a length 2 numeric vector specifying
rates: Only used if rate_model is "discrete", in which case this should be a named vector whose values are the rates in each rate class, and whose names are the rate class states (e.g. c("1" = 3, "2" = 10)). See sim.history, for more detail on how the discrete model works. Or, if an unnamed numeric vector of length two, a mean and standard deviation parameterizing a normal distribution from which to draw rates for each rate class. If NULL, rates will be drawn from a normals distribution with mean = 0 and sd = 1.
anc: Value of the trait at the root ancestor. For rate_model = "discrete", can be a length 1 named vector where the name is the ancestral state, and the value is the trait starting value. For rate_model = "continuous", any names are ignored, but should be length 2, where the first element is the ancestral trait value and the second element is the ancestral rate of evolution.
internal: Logical value. If TRUE return trait states at internal nodes.
nsim: Number of simulation to run.
pos_strat: ?
temp_trend_mean: A temporal trend in rates.

Value

A vector or matrix (for nsim > 1) containing simulated trait values for each tip if internal = FALSE, or for each node if internal = TRUE