HACSim: 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. A Shiny app is also available.
| Version: |
1.0.7-1 |
| Imports: |
ape (≥ 5.3), data.table (≥ 1.12.8), graphics (≥ 3.6.1), matrixStats (≥ 0.56.0), pegas (≥ 0.13), Rcpp (≥ 1.0.3), stats (≥ 3.6.1), stringr (≥ 1.5.0), utils (≥ 3.6.1) |
| LinkingTo: |
Rcpp, RcppArmadillo |
| Published: |
2025-09-19 |
| DOI: |
10.32614/CRAN.package.HACSim |
| Author: |
Jarrett D. Phillips [aut, cre],
Steven H. French [ctb],
Navdeep Singh [ctb] |
| Maintainer: |
Jarrett D. Phillips <phillipsjarrett1 at gmail.com> |
| License: |
GPL-3 |
| URL: |
<https://github.com/jphill01/HACSim.R>
<https://github.com/jphill01/HACSim-RShiny-App>
<https://jphill01.shinyapps.io/HACSim> |
| NeedsCompilation: |
yes |
| CRAN checks: |
HACSim results |
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