Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment
Internal C++ code
Simulation variable storage environment
Internal R code
Run a simulation of haplotype accumulation curves for hypothetical or ...
Internal R code
Set up an object to simulate haplotype accumulation curves for a hypot...
Set up an object to simulate haplotype accumulation curves for a real ...
tools:::Rd_package_title("HACSim")
Simulate DNA sequences according to DNA substitution models
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. A Shiny app is also available.