CRABS (version 1.2.0)

full.plot.regularity.thresholds: Plots the rate functions after filtering them according to a given penalty and predefined thresholds.

Description

Plots the rate functions after filtering them according to a given penalty and predefined thresholds.

Usage

full.plot.regularity.thresholds(
  samples,
  filtering_fractions = c(0.01, 0.05, 0.2, 0.9),
  penalty = "L1",
  rates = c("lambda", "mu")
)

Value

Plots an array of rate trajectories for the chosen rates and thresholds.

Arguments

samples

A list of (congruent) CRABS models

filtering_fractions

A vector of thresholds for filtering, as fractions of the most regular trajectories.

penalty

The choice of penalty, among "L1", "L2" and "L1_derivative" (penalty on derivative shifts).

rates

A vector of rate(s) to be plotted, among "lambda" (speciation), "mu" (extinction), "delta" (net-diversification) and "epsilon" (turnover).

Examples

data("primates_ebd")
set.seed(123)

l <- approxfun(primates_ebd[["time"]], primates_ebd[["lambda"]])
mu <- approxfun(primates_ebd[["time"]], primates_ebd[["mu"]])
times <- primates_ebd[["time"]]

model <- create.model(l, mu, times)

sample.joint.rates <- function(n) {
  sample.basic.models.joint(times = times, 
                            p.delta = model$p.delta,  
                            beta.param = c(0.5,0.3),  
                            lambda0 = l(0.0),  
                            mu0.median = mu(0.0))
}

joint.samples <- sample.congruence.class(model = model, 
                                         num.samples = 100, 
                                         rate.type = "joint", 
                                         sample.joint.rates = sample.joint.rates)

full.plot.regularity.thresholds(joint.samples)