R Observatory: Metrics for HACSim version 1.0.7-1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HACSim

1.0.7-1

Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment

0packages depend

8.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Jarrett D. PhillipsFirst published 2019-05-099 releasesCRAN page ↗

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.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("HACSim", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-hacsim

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-HACSim

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-HACSim

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.0 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

9

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 83%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 11%

Downloads

8.7K

CRAN downloads in the past year

Rank #5,127 · ~24/day · ~725/mo

Releases R versions

Daily download trend is not available in this view yet.

20930 days

1.5K90 days

8.7K1 year

Compare downloads with other packages →

Also on400 r2u14 autocran

Repository

GitHub ↗ jphill01/hacsim.r

0Stars

4Forks

2Open issues

0Open PRs

0Releases

1,223Commits

2Contributors

dna-barcodinghaplotype-accumulation-curvesr

License GPL-3.0 · 1,223 commits · Last activity 2025-09-18

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/jphill01/hacsim.r on 2026-08-09.

Continuous integration (1)

Travis CI

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (9)

ape data.tablegraphicsmatrixStats pegas Rcppstatsstringrutils

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Jarrett D. Phillips

Author, Maintainer

Authors (1)

Jarrett D. Phillips

Author, Maintainer

Contributors (2)

Steven H. French

Contributor

Navdeep Singh

Contributor · added in 1.0.6

Listed in earlier versions (2)

French

no longer listed · 1.0.7-1

Phillips

no longer listed · 1.0.7-1

Package Timeline

9 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.7-1Latest
2025-09-19 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.6-1
2022-06-13 · diff ↗
1.0.6
2022-05-26 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.0.5
2020-01-07 · diff ↗
1.0.4
2019-09-15 · diff ↗
1.0.3
2019-07-26 · diff ↗
1.0.2
2019-06-28 · diff ↗
1.0.1
2019-05-16 · diff ↗
1.0.0
2019-05-09

Show 1 earlier events

R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-05-09
Total releases: 9 / 7 yrs
License: GPL-3 OSI
Download size: 24 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("HACSim")

Format

Phillips, J. D., French, S. H., & Singh, N. (2025). HACSim: Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment (Version 1.0.7-1) [Computer software]. https://doi.org/10.32614/CRAN.package.HACSim

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for HACSim version 1.0.7-1 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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