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  "Title": "Iterative Extrapolation of Species' Haplotype Accumulation\nCurves for Genetic Diversity Assessment",
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  "Date": "2025-09-17",
  "Authors@R": "c(person(given = c(\"Jarrett\", \"D.\"),\nfamily = \"Phillips\",\nrole = c(\"aut\", \"cre\"),\nemail = \"phillipsjarrett1@gmail.com\"),\nperson(given = c(\"Steven\", \"H.\"),\nfamily = \"French\",\nrole = \"ctb\"),\nperson(given = \"Navdeep\",\nfamily = \"Singh\",\nrole = \"ctb\"))",
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  "Description": "Performs iterative extrapolation of species' haplotype\naccumulation curves using a nonparametric stochastic (Monte\nCarlo) optimization method for assessment of specimen sampling\ncompleteness based on the approach of Phillips et al. (2015)\n<doi:10.1515/dna-2015-0008>, Phillips et al. (2019)\n<doi:10.1002/ece3.4757> and Phillips et al. (2020) <doi:\n10.7717/peerj-cs.243>. 'HACSim' outputs a number of useful\nsummary statistics of sampling coverage (\"Measures of Sampling\nCloseness\"), including an estimate of the likely required\nsample size (along with desired level confidence intervals)\nnecessary to recover a given number/proportion of observed\nunique species' haplotypes. Any genomic marker can be targeted\nto assess likely required specimen sample sizes for genetic\ndiversity assessment. The method is particularly well-suited to\nassess sampling sufficiency for DNA barcoding initiatives.\nUsers can also simulate their own DNA sequences according to\nvarious models of nucleotide substitution. A Shiny app is also\navailable.",
  "License": "GPL-3",
  "URL": "<https://github.com/jphill01/HACSim.R>\n<https://github.com/jphill01/HACSim-RShiny-App>\n<https://jphill01.shinyapps.io/HACSim>",
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      "page": "HACSim-package",
      "title": "Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment",
      "topics": [
        "HACSim-package"
      ]
    },
    {
      "page": "accumulate",
      "title": "Internal C++ code",
      "topics": [
        "accumulate"
      ]
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      "page": "envr",
      "title": "Simulation variable storage environment",
      "topics": [
        "envr"
      ]
    },
    {
      "page": "HAC.sim",
      "title": "Internal R code",
      "topics": [
        "HAC.sim"
      ]
    },
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      "title": "Run a simulation of haplotype accumulation curves for hypothetical or real species",
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        "HAC.simrep"
      ]
    },
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      "title": "Internal R code",
      "topics": [
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      ]
    },
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      "topics": [
        "HACHypothetical"
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    },
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      "title": "Set up an object to simulate haplotype accumulation curves for a real species",
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        "HACReal"
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      "title": "Simulate DNA sequences according to DNA substitution models",
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