generatePhyloPD: Generate Phylogenetic trees under PD model

In franciscorichter/emphasis: Evolutionary Modeling on Phylogenetic Applications with Simulations and Importance Sampling

Generate Phylogenetic trees under PD model

Description

This function simulates phylogenetic trees based on given parameters.

This function simulates phylogenetic trees based on given parameters.

Usage

generatePhyloPD(
  n_trees,
  mu_interval,
  lambda_interval,
  betaN_interval,
  betaP_interval,
  max_lin = 1e+06,
  max_tries = 1
)

generatePhyloPD(
  n_trees,
  mu_interval,
  lambda_interval,
  betaN_interval,
  betaP_interval,
  max_lin = 1e+06,
  max_tries = 1
)

Arguments

n_trees	Number of trees to simulate.
mu_interval	Interval for mu parameter.
lambda_interval	Interval for lambda parameter.
betaN_interval	Interval for betaN parameter.
betaP_interval	Interval for betaP parameter.
max_lin	Maximum number of lineages.
max_tries	Maximum number of tries for simulation.

Value

A list containing the simulated trees and parameters.

A list containing the simulated trees and parameters.

Examples

generatePhyloPD(n_trees <- 10000,
               mu_interval <- c(0, 0.5),
               lambda_interval <- c(0.5, 3),
               betaN_interval <- c(-0.02, 0.02) ,
               betaP_interval <- c(-0.02, 0.02) )
               
generatePhyloPD(n_trees = 10, 
               mu_interval = c(0.1, 0.5), 
               lambda_interval = c(0.1, 0.5),
               betaN_interval = c(0.1, 0.5), 
               betaP_interval = c(0.1, 0.5),
               max_lin = 1e6,
               max_tries = 1)

franciscorichter/emphasis documentation built on Feb. 19, 2024, 7:36 p.m.