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HACSim (version 1.0.5)

Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment

Description

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) , Phillips et al. (2019) and Phillips et al. (2020) . Any genomic marker can be targeted to assess likely required specimen sample sizes. The method is well-suited to assess sampling sufficiency for DNA barcoding initiatives.

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Version

Install

install.packages('HACSim')

Monthly Downloads

776

Version

1.0.5

License

GPL-3

Maintainer

Jarrett Phillips

Last Published

January 7th, 2020

Functions in HACSim (1.0.5)

envr

Simulation variable storage environment
accumulate

Internal C++ code
HACReal

Set up an object to simulate haplotype accumulation curves for a real species
HACSim-package

HACSim
HAC.simrep

Run a simulation of haplotype accumulation curves for hypothetical or real species
HAC.sim

Internal R code
HACHypothetical

Set up an object to simulate haplotype accumulation curves for a hypothetical species
HACClass

Internal R code