Package: HACSim
Type: Package
Title: Iterative Extrapolation of Species' Haplotype Accumulation
        Curves for Genetic Diversity Assessment
Version: 1.0.7-1
Date: 2025-09-17
Authors@R: c(person(given = c("Jarrett", "D."),
                        family = "Phillips",
                        role = c("aut", "cre"),
                        email = "phillipsjarrett1@gmail.com"),
                 person(given = c("Steven", "H."),
                        family = "French",
                        role = "ctb"),
                 person(given = "Navdeep",
                        family = "Singh",
                        role = "ctb"))
Maintainer: Jarrett D. Phillips <phillipsjarrett1@gmail.com>
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) <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.
License: GPL-3
URL: <https://github.com/jphill01/HACSim.R>
        <https://github.com/jphill01/HACSim-RShiny-App>
        <https://jphill01.shinyapps.io/HACSim>
NeedsCompilation: yes
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
RoxygenNote: 6.1.1
Packaged: 2025-09-19 17:10:03 UTC; jarrettphillips
Author: Jarrett D. Phillips [aut, cre],
  Steven H. French [ctb],
  Navdeep Singh [ctb]
Repository: CRAN
Date/Publication: 2025-09-19 17:30:02 UTC
Built: R 4.6.0; aarch64-apple-darwin23; 2026-04-26 03:50:53 UTC; unix
Archs: HACSim.so.dSYM
