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.
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
1.0.7-1 |
rolling source/ R- | HACSim_1.0.7-1.tar.gz |
23.7 KiB |
1.0.7-1 |
rolling linux/jammy R-4.5 | HACSim_1.0.7-1.tar.gz |
105.0 KiB |
1.0.7-1 |
rolling linux/noble R-4.5 | HACSim_1.0.7-1.tar.gz |
106.9 KiB |
1.0.7-1 |
latest source/ R- | HACSim_1.0.7-1.tar.gz |
23.7 KiB |
1.0.7-1 |
latest linux/jammy R-4.5 | HACSim_1.0.7-1.tar.gz |
105.0 KiB |
1.0.7-1 |
latest linux/noble R-4.5 | HACSim_1.0.7-1.tar.gz |
106.9 KiB |
1.0.7-1 |
2026-04-23 source/ R- | HACSim_1.0.7-1.tar.gz |
23.7 KiB |
1.0.7-1 |
2026-04-09 windows/windows R-4.5 | HACSim_1.0.7-1.zip |
427.4 KiB |
1.0.6-1 |
2025-04-20 source/ R- | HACSim_1.0.6-1.tar.gz |
4.1 MiB |
Dependencies (latest)
Imports
- ape (>= 5.3)
- data.table (>= 1.12.8)
- graphics (>= 3.6.1)
- matrixStats (>= 0.56.0)
- pegas (>= 0.13)
- Rcpp (>= 1.0.3)
- stats (>= 3.6.1)
- stringr (>= 1.5.0)
- utils (>= 3.6.1)