The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
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 |
Please use the canonical form https://CRAN.R-project.org/package=HACSim to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.