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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: | 1.0.6-1 |
| 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: | 2022-06-13 |
| DOI: | 10.32614/CRAN.package.HACSim |
| 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 |
| Reference manual: | HACSim.pdf |
| Package source: | HACSim_1.0.6-1.tar.gz |
| Windows binaries: | r-devel: HACSim_1.0.6-1.zip, r-release: HACSim_1.0.6-1.zip, r-oldrel: HACSim_1.0.6-1.zip |
| macOS binaries: | r-release (arm64): HACSim_1.0.6-1.tgz, r-oldrel (arm64): HACSim_1.0.6-1.tgz, r-release (x86_64): HACSim_1.0.6-1.tgz, r-oldrel (x86_64): HACSim_1.0.6-1.tgz |
| Old sources: | HACSim archive |
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