Package ‘CoalescentPhylo’

Overview

CoalescentPhylo is an R package for phylogenetic tree estimation through the method of root distances from allele count data using the coalescent model

Installation

Install the released version of this package from CRAN

install.packages("CoalescentPhylo")

Or install the development version of this package from GitHub

remotes::install_github('ArindamRoyChoudhury/CoalescentPhylo', upgrade="never")

Example

library(CoalescentPhylo)

# Load built-in example dataset (9 taxa x 2000 loci)
data(Human_Allele_Count_Data)

# Inspect dimensions: rows = taxa, columns = loci
dim(Human_Allele_Count_Data)

# Preview first few rows and columns
Human_Allele_Count_Data[1:3, 1:5]

# Estimate phylogenetic tree using the Coalescent Model
tree <- RD(mat_allele_count = Human_Allele_Count_Data, n.cores = NULL)

# Summarize the result
print(tree)

# Plot the labeled phylogenetic tree
plot(tree$labeled_tree)