jphill01/HACSim.R: Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment

Performs iterative extrapolation of species' haplotype accumulation curves using a nonparametric stochastic (Monte Carlo) optimization method for assessment of specimen sampling completeness based on the approach of Phillips et al. (2015) <doi:10.1515/dna-2015-0008>, Phillips et al. (2019) <doi:10.1002/ece3.4757> and Phillips et al. (2020) <doi: 10.7717/peerj-cs.243>. HACSim outputs a number of useful summary statistics of sampling coverage ("Measures of Sampling Closeness"), including an estimate of the likely required sample size (along with desired level confidence intervals) necessary to recover a given number/proportion of observed unique species' haplotypes. Any genomic marker can be targeted to assess likely required specimen sample sizes for genetic diversity assessment. The method is particularly well-suited to assess sampling sufficiency for DNA barcoding initiatives. Users can also simulate their own DNA sequences according to various models of nucleotide substitution.

Getting started

Package details

AuthorJarrett D. Phillips [aut, cre], Steven H. French [ctb]
MaintainerJarrett D. Phillips <phillipsjarrett1@gmail.com>
LicenseGPL-3
Version1.0.6
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("jphill01/HACSim.R")
jphill01/HACSim.R documentation built on Sept. 2, 2020, 10:34 a.m.