rubias - Bayesian Inference from the Conditional Genetic Stock Identification Model

Implements Bayesian inference for the conditional genetic stock identification model. It allows inference of mixed fisheries and also simulation of mixtures to predict accuracy. A full description of the underlying methods is available in a recently published article in the Canadian Journal of Fisheries and Aquatic Sciences: <doi:10.1139/cjfas-2018-0016>.

Last updated 1 years ago

noaa-omics-softwarecpp

5.90 score 3 stars 89 scripts 229 downloads

CKMRpop - Forward-in-Time Simulation and Tallying of Pairwise Relationships

Provides an R wrapper around the program 'spip' (<https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1471-8286.2005.00884.x>), a C program for the simulation of pedigrees within age-structured populations with user-specified life histories. Also includes a variety of functions to parse 'spip' output to compile information about related pairs amongst simulated, sampled individuals, to assess the feasibility and potential accuracy of close-kin mark-recapture (CKMR). Full documentation and vignettes are mirrored at <https://eriqande.github.io/CKMRpop/index.html> and can be read online there.

Last updated 1 years ago

noaa-omics-softwarecpp

5.38 score 4 stars 24 scripts 807 downloads

whoa - Evaluation of Genotyping Error in Genotype-by-Sequencing Data

This is a small, lightweight package that lets users investigate the distribution of genotypes in genotype-by-sequencing (GBS) data where they expect (by and large) Hardy-Weinberg equilibrium, in order to assess rates of genotyping errors and the dependence of those rates on read depth. It implements a Markov chain Monte Carlo (MCMC) sampler using 'Rcpp' to compute a Bayesian estimate of what we call the heterozygote miscall rate for restriction-associated digest (RAD) sequencing data and other types of reduced representation GBS data. It also provides functions to generate plots of expected and observed genotype frequencies. Some background on these topics can be found in a recent paper "Recent advances in conservation and population genomics data analysis" by Hendricks et al. (2018) <doi:10.1111/eva.12659>, and another paper describing the MCMC approach is in preparation with Gordon Luikart and Thierry Gosselin.

Last updated 4 years ago

cpp

5.16 score 6 stars 24 scripts 643 downloads

gscramble - Simulating Admixed Genotypes Without Replacement

A genomic simulation approach for creating biologically informed individual genotypes from empirical data that 1) samples alleles from populations without replacement, 2) segregates alleles based on species-specific recombination rates. 'gscramble' is a flexible simulation approach that allows users to create pedigrees of varying complexity in order to simulate admixed genotypes. Furthermore, it allows users to track haplotype blocks from the source populations through the pedigrees.

Last updated 12 months ago

noaa-omics-software

4.83 score 15 scripts 647 downloads

gaiah - Genetic and Isotopic Assignment Accounting for Habitat Suitability

Tools for using genetic markers, stable isotope data, and habitat suitability data to calculate posterior probabilities of breeding origin of migrating birds.

Last updated 2 years ago

2.74 score 1 stars 11 scripts 256 downloads