Other packages > Find by keyword >

HACSim  

Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment
View on CRAN: Click here


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", "1.0.7-1")



Attach the package and use:
library("HACSim")
Maintained by
Jarrett D. Phillips
[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 1.0.7-1, https://cran.r-project.org/web/packages/HACSim. Accessed 16 Jul. 2026.
Previous versions and publish date:
1.0.0 (2019-05-09 16:10), 1.0.1 (2019-05-16 01:00), 1.0.2 (2019-06-28 17:30), 1.0.3 (2019-07-26 00:20), 1.0.4 (2019-09-15 01:30), 1.0.5 (2020-01-07 22:50), 1.0.6-1 (2022-06-13 08:50), 1.0.6 (2022-05-26 16:30), (2026-07-09 08:06)
Other packages that cited HACSim R package
View HACSim citation profile
Other R packages that HACSim depends, imports, suggests or enhances
Complete documentation for HACSim
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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
wordnet  
WordNet Interface
An interface to WordNet using the Jawbone Java API to WordNet. WordNet (< ...
Download / Learn more Package Citations See dependency  
schoolmath  
Functions and Datasets for Math Used in School
Contains functions and datasets for math taught in school. A main focus is set to prime-calculation. ...
Download / Learn more Package Citations See dependency  
bbdetection  
Identification of Bull and Bear States of the Market
Implements two algorithms of detecting Bull and Bear markets in stock prices: the algorithm of Pagan ...
Download / Learn more Package Citations See dependency  
stevedata  
Steve's Toy Data for Teaching About a Variety of Methodological, Social, and Political Topics
This is a collection of various kinds of data with broad uses for teaching. My students, and academ ...
Download / Learn more Package Citations See dependency  
tarchetypes  
Archetypes for Targets
Function-oriented Make-like declarative pipelines for Statistics and data science are supported in t ...
Download / Learn more Package Citations See dependency  

27,806

R Packages

239,283

Dependencies

73,837

Author Associations

27,807

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA