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HACSim
View on CRAN: Click
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Download and install HACSim package within the R console
Install from CRAN:
install.packages("HACSim")
Install from Github:
library("remotes")
install_github("cran/HACSim")
Install by package version:
library("remotes")
install_version("HACSim", "1.0.6-1")
Attach the package and use:
library("HACSim")
Maintained by
Jarrett D. Phillips
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-05-09
Latest Update: 2022-06-13
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) , Phillips et al. (2019) and Phillips et al. (2020) . '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.
How to cite:
Jarrett D. Phillips (2019). HACSim: Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment. R package version 1.0.6-1, https://cran.r-project.org/web/packages/HACSim
Previous versions and publish date:
Other packages that cited HACSim R package
View HACSim citation profile
Other R packages that HACSim depends,
imports, suggests or enhances
Functions, R codes and Examples using
the HACSim R package
Some associated functions: HAC.sim . HAC.simrep . HACClass . HACHypothetical . HACReal . HACSim-package . accumulate . envr . launchApp . sim.seqs .
Some associated R codes: HACject.R . HAC.sim.R . HAC.simrep.R . RcppExports.R . launchApp.R . sim.seqs.R . zzz.R . Full HACSim package functions and examples
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