P2C2M_GMYC.pboot: Run P2C2M.GMYC - parametric bootstrap

In emanuelmfonseca/P2C2M.GMYC: Model violations under the Generalized Mixed Yule Coalescent (GMYC)

Description

Identifying model violations under the Generalized Mixed Yule Coalescent (GMYC) model using parametric bootstrap.

Usage

  P2C2M_GMYC.pboot(tree.input, tree.format, seq, nsim = NULL,
     nboot = NULL, perc.treshold = NULL)

Arguments

tree.input	A file name which contains an ultrametric phylogenetic tree.
tree.format	A character string specifying the format of the phylogenetic tree. Two choices are possible: "nexus" or "newick".
seq	A file name which contains a sequential FASTA alignment.
nsim	Number of simulated trees, Default: 100 trees.
nboot	The size of the null distribution, Default: 100.
perc.treshold	Percentage of the number of species recovered by the empirical dataset used to set the threshold to calculate the p-value, Default: 0.1 (10%).

Details

This function take a ultrametric phylogenetic tree and a sequential FASTA alignment and test for model violation of the GMYC model using a parametric bootstrap framework.

Value

A list containing the p-value, the threshold used to calculate the p-value, and the null distribution.

Examples

## Lygodactylus dataset

P2C2M_GMYC.Pboot(tree.input=system.file("extdata", "Lygodactylus.tre", package="P2C2M.GMYC"),
                 tree.format="nexus",
                 seq=system.file("extdata", "Lygodactylus.fas", package="P2C2M.GMYC"))
  

emanuelmfonseca/P2C2M.GMYC documentation built on Aug. 30, 2020, 5:20 a.m.