simulate_rate {evolvability}

Simulating evolutionary rate model

Description

simulate_rate Simulates three different evolutionary rates models. In the two first, 'predictor_BM' and 'predictor_gBM', the evolution of y follows a Brownian motion with variance linear in x, while the evolution of x either follows a Brownian motion or a geometric Brownian motion, respectively. In the third model, 'recent_evol', the residuals of the macroevolutionary predictions of y have variance linear in x.

Usage

simulate_rate(
  tree,
  startv_x = NULL,
  sigma_x = NULL,
  a,
  b,
  sigma_y = NULL,
  x = NULL,
  model = "predictor_BM"
)

Arguments

tree

A phylo object. Must be ultrametric and scaled to unit length.

startv_x

The starting value for x (usually 0 for 'predictor_BM' and 'recent_evol', and 1 for 'predictor_gBM').

sigma_x

The evolutionary rate of x.

a

A parameter of the evolutionary rate of y.

b

A parameter of the evolutionary rate of y.

sigma_y

The evolutionary rate for the macroevolution of y (Brownian motion process) used in the 'recent_evolution' model.

x

Optional fixed values of x (only for the 'recent_evol' model), must equal number of tips in the phylogeny, must correspond to the order of the tip labels.

model

Either a Brownian motion model of x 'predictor_BM', geometric Brownian motion model of x 'predictor_gBM', or 'recent_evol'.

Details

See the vignette 'Analyzing rates of evolution' for an explanation of the evolutionary models. The data of the tips can be analyzed with the function rate_gls. Note that a large part of parameter space will cause negative roots in the rates of y (i.e. negative a+bx). In these cases the rates are set to 0. A warning message is given if the number of such instances is larger than 0.1%. For model 1 and 2, it is possible to set ‘a=’scaleme'', if this chosen then 'a' will be given the lowest possible value constrained by a+bx>0.

Value

An object of class 'simulate_rate', which is a list with the following components:

tips				A data frame of x and y values for the tips.
percent_negative_roots				The percent of iterations with negative roots in the rates of y (not given for model = 'recent_evol').
compl_dynamics				A list with the output of the complete dynamics (not given for model = 'recent_evol').

Author(s)

Geir H. Bolstad

Examples

# Also see the vignette 'Analyzing rates of evolution'.
## Not run: 
# Generating a tree with 50 species
set.seed(102)
tree <- ape::rtree(n = 50)
tree <- ape::chronopl(tree, lambda = 1, age.min = 1)

### model = 'predictor_BM' ###
sim_data <- simulate_rate(tree, startv_x = 0, sigma_x = 0.25, a = 1, b = 1, 
model = "predictor_BM")
head(sim_data$tips)
par(mfrow = c(1, 3))
plot(sim_data)
plot(sim_data, response = "y")
plot(sim_data, response = "x")
par(mfrow = c(1, 1))

### model = 'predictor_gBM' ###
sim_data <- simulate_rate(tree, startv_x = 1, sigma_x = 1, a = 1, b = 0.1, 
model = "predictor_gBM")
head(sim_data$tips)
par(mfrow = c(1, 3))
plot(sim_data)
plot(sim_data, response = "y")
plot(sim_data, response = "x")
par(mfrow = c(1, 1))

### model = 'recent_evol' ###
sim_data <- simulate_rate(tree,
  startv_x = 0, sigma_x = 1, a = 1, b = 1, sigma_y = 1,
  model = "recent_evol"
)
head(sim_data$tips)

## End(Not run)