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: 1.0.6
Imports: ape (≥ 5.3), data.table (≥ 1.12.8), graphics (≥ 3.6.1), matrixStats (≥ 0.56.0), pegas (≥ 0.13), Rcpp (≥ 1.0.3), shiny (≥ 1.6.0), stats (≥ 3.6.1), utils (≥ 3.6.1)
LinkingTo: Rcpp, RcppArmadillo
Published: 2022-05-26
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

Documentation:

Reference manual: HACSim.pdf

Downloads:

Package source: HACSim_1.0.6.tar.gz
Windows binaries: r-devel: HACSim_1.0.6.zip, r-release: HACSim_1.0.5.zip, r-oldrel: HACSim_1.0.5.zip
macOS binaries: r-release (arm64): HACSim_1.0.6.tgz, r-oldrel (arm64): HACSim_1.0.6.tgz, r-release (x86_64): HACSim_1.0.5.tgz, r-oldrel (x86_64): HACSim_1.0.5.tgz
Old sources: HACSim archive

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