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>. 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.

Version: 1.0.5
Imports: ape (≥ 5.2), graphics (≥ 3.5.1), pegas (≥ 0.11), Rcpp (≥ 1.0.0), stats (≥ 3.5.1), utils (≥ 3.5.1)
LinkingTo: Rcpp, RcppArmadillo
Published: 2020-01-07
Author: Jarrett D. Phillips [aut, cre], Steven H. French [ctb]
Maintainer: Jarrett D. Phillips <phillipsjarrett1 at gmail.com>
License: GPL-3
NeedsCompilation: yes
CRAN checks: HACSim results


Reference manual: HACSim.pdf


Package source: HACSim_1.0.5.tar.gz
Windows binaries: r-devel: HACSim_1.0.5.zip, r-release: HACSim_1.0.5.zip, r-oldrel: HACSim_1.0.5.zip
macOS binaries: r-release (arm64): HACSim_1.0.5.tgz, r-release (x86_64): HACSim_1.0.5.tgz, r-oldrel: HACSim_1.0.5.tgz
Old sources: HACSim archive


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