AugmentMultiplePhyloPD: Augment Multiple Phylogenetic Trees with Parameter Diversity

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

Augment Multiple Phylogenetic Trees with Parameter Diversity

Description

This function simulates and augments phylogenetic data across multiple trees using parameter sampling and the augmentPD function.

Usage

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

Arguments

phylo	A phylogenetic tree object.
n_trees	Number of trees to simulate.
mu_interval	Interval for sampling mu parameter.
lambda_interval	Interval for sampling lambda parameter.
betaN_interval	Interval for sampling betaN parameter.
betaP_interval	Interval for sampling betaP parameter.
max_lin	Maximum number of lineages (default 1e+6).
max_tries	Maximum number of tries for augmentation (default 1).

Value

A list containing the generated trees, parameters, rejection reasons, timings, and log-likelihood estimations.

Examples

# Example usage
result <- AugmentMultiplePhyloPD(my_phylo, 10, c(0.1, 0.5), c(0.2, 0.6),
                                 c(0.3, 0.7), c(0.4, 0.8))

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