PEpoisnorm: Probability functions of trait change under pulsed evolution...

In wu-lab-uva/RasperGade: Reconstructing Ancestral State under Pulsed Evolution in R by Gaussian Decomposition

Probability functions of trait change under pulsed evolution with 1 compound Poisson process

Description

Density function, cumulative distribution function and random generation for the trait change under Pulsed evolution with 1 compound Poisson process

Usage

dPEpoisnorm(x, t, lambda, size, sigma, epsilon = 0, margin = 1e-06)

pPEpoisnorm(
  q,
  t,
  lambda,
  size,
  sigma,
  epsilon = 0,
  margin = 1e-06,
  lower.tail = TRUE
)

rPEpoisnorm(n, t, lambda, size, sigma, epsilon = 0)

Arguments

x	the trait change between two nodes
t	the branch length between two nodes
lambda	the rate at which jumps happen
size	the variance of trait change introduced per jump
sigma	the rate of BM (variance of gradual trait change per unit branch length)
epsilon	the variance of time-independent variation
margin	the total probability mass of the number of jumps not covered, defaults to 1e-6
q	the trait change between two nodes
lower.tail	logical, if TRUE (default), probability of trait change smaller or equal to q is returned. If false, the probability of being greater is returned.
n	the number of random values to return

Value

dPEpoisnorm returns the probability density

pPEpoisnorm returns the cumulative distribution

rPEpoisnorm returns a vector of random numbers following the specified distribution

Examples

# generate some random trait changes under pulsed evolution
dtrait = rPEpoisnorm(n=1e3,t=1,lambda=1,size=1,sigma=1,epsilon=0.1)

# test the empirical distribution against the theoretical one
ks.test(dtrait,pPEpoisnorm,t=1,lambda=1,size=1,sigma=1,epsilon=0.1)

wu-lab-uva/RasperGade documentation built on June 24, 2022, 2:47 p.m.