Package: HACSim 1.0.6

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_1.0.6.tar.gz
HACSim_1.0.6.zip(r-4.5)HACSim_1.0.6.zip(r-4.4)HACSim_1.0.6.zip(r-4.3)
HACSim_1.0.6.tgz(r-4.4-x86_64)HACSim_1.0.6.tgz(r-4.4-arm64)HACSim_1.0.6.tgz(r-4.3-x86_64)HACSim_1.0.6.tgz(r-4.3-arm64)
HACSim_1.0.6.tar.gz(r-4.5-noble)HACSim_1.0.6.tar.gz(r-4.4-noble)
HACSim_1.0.6.tgz(r-4.4-emscripten)HACSim_1.0.6.tgz(r-4.3-emscripten)
HACSim.pdf |HACSim.html✨
HACSim/json (API)

Peer review:

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

On CRAN:

dna-barcodinghaplotype-accumulation-curves

9 exports 1.40 score 37 dependencies 2 mentions 5 scripts 1.2k downloads

Last updated 7 months agofrom:2a525ad40c. Checks:OK: 1 WARNING: 8. Indexed: yes.

Exports:accumulateenvrHAC.simHAC.simrepHACClassHACHypotheticalHACReallaunchAppsim.seqs

Dependencies:apebase64encbslibcachemclicommonmarkcrayondata.tabledigestfastmapfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclemagrittrmatrixStatsmemoisemimenlmepegaspromisesR6rappdirsRcppRcppArmadillorlangsassshinysourcetoolswithrxtable