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),
        shiny (>= 1.7.0), shinydashboard (>= 0.7.2), shinydashboardPlus
        (>= 2.0.3), shinyjs (>= 2.1.0), shinyWidgets (>= 0.7.6),
        shinycssloaders (>= 1.0.0), shinymeta (>= 0.2.0.3), stats (>=
        3.6.1), stringr (>= 1.5.0), utils (>= 3.6.1)
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.1.1
Packaged: 2026-10-09 21:15:11 UTC; root
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev zlib1g-dev
Repository: https://jphill01.r-universe.dev
Date/Publication: 2026-10-09 17:56:33 UTC
RemoteUrl: https://github.com/jphill01/hacsim.r
RemoteRef: HEAD
RemoteSha: 3cc15a361b0e153d0dd15de52de92474d2b846b3
Author: Jarrett D. Phillips [aut, cre],
  Steven H. French [ctb],
  Navdeep Singh [ctb]