Package: HACSim 1.0.7-1

Jarrett D. Phillips

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

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.

Authors:Jarrett D. Phillips [aut, cre], Steven H. French [ctb], Navdeep Singh [ctb]

HACSim_1.0.7-1.tar.gz
HACSim_1.0.7-1.zip(r-4.7)HACSim_1.0.7-1.zip(r-4.6)HACSim_1.0.7-1.zip(r-4.5)
HACSim_1.0.7-1.tgz(r-4.6-x86_64)HACSim_1.0.7-1.tgz(r-4.6-arm64)HACSim_1.0.7-1.tgz(r-4.5-x86_64)HACSim_1.0.7-1.tgz(r-4.5-arm64)
HACSim_1.0.7-1.tar.gz(r-4.7-arm64)HACSim_1.0.7-1.tar.gz(r-4.7-x86_64)HACSim_1.0.7-1.tar.gz(r-4.6-arm64)HACSim_1.0.7-1.tar.gz(r-4.6-x86_64)
HACSim_1.0.7-1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
HACSim/json (API)

# Install 'HACSim' in R:
install.packages('HACSim', repos = c('https://jphill01.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jphill01/hacsim.r/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

dna-barcodinghaplotype-accumulation-curvescpp

3.00 score 2 scripts 723 downloads 2 mentions 9 exports 59 dependencies

Last updated from:2472318b95. Checks:8 WARNING, 2 OK, 3 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING146
linux-devel-x86_64WARNING159
source / vignettesOK268
linux-release-arm64WARNING144
linux-release-x86_64WARNING153
macos-release-arm64WARNING158
macos-release-x86_64WARNING277
macos-oldrel-arm64FAIL117
macos-oldrel-x86_64FAIL210
windows-develWARNING119
windows-releaseWARNING152
windows-oldrelFAIL53
wasm-releaseOK108

Exports:accumulateenvrHAC.simHAC.simrepHACClassHACHypotheticalHACReallaunchAppsim.seqs

Dependencies:apebase64encbslibcachemcallrclicommonmarkdata.tabledigestfastmapfontawesomefreshfsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclemagrittrmatrixStatsmemoisemimenlmeotelpegasprocessxpromisespspurrrR.cacheR.methodsS3R.ooR.utilsR6rappdirsRcppRcppArmadillorlangrprojrootrstudioapisassshinyshinycssloadersshinydashboardshinydashboardPlusshinyjsshinymetashinyWidgetssourcetoolsstringistringrstylervctrswaiterwithrxtable