HACSim

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.

Last 30 days

This package has been downloaded 637 times in the last 30 days. More downloads than an obscure whitepaper, but not enough to bring down any servers. A solid effort! The following heatmap shows the distribution of downloads per day. Yesterday, it was downloaded 62 times.

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Last 365 days

This package has been downloaded 9,429 times in the last 365 days. A solid achievement! Enough downloads to get noticed at department meetings. The day with the most downloads was Sep 11, 2024 with 85 downloads.

The following line graph shows the downloads per day. You can hover over the graph to see the exact number of downloads per day.