a_freq_list | Convert data frame of allele frequencies to nested lists |

alewife | Microsat data from alewife herring reference populations |

allelic_list | Create genotype lists for each locus |

assess_pb_bias_correction | Test the effects of the parametric bootstrap bias correction... |

assess_reference_loo | Simulate mixtures and estimate reporting group and collection... |

assess_reference_mc | Partition a reference dataset and estimate reporting group... |

avg_coll2correctRU | Get the average within-RU assignment rate for each collection |

bias_comparison | Test the effects of bias corrections on a reference dataset... |

blueback | Microsat data from blueback herring reference populations. |

bootstrap_rho | Perform a parametric bootstrapping correction on an estimated... |

check_refmix | A helper function to check that the input data frame is OK |

chinook | SNP data from chinook reference populations |

chinook_all | SNP data from Chinook reference and mixtures mixed together |

chinook_mix | SNP data from Chinook salmon taken in May/August 2015 from... |

count_missing_data | for each individual count the number or loci missing and... |

dirch_from_allocations | Given a vector of different categories in 1...n and a prior,... |

dirch_from_counts | Given a vector of counts for different categories in 1...n... |

geno_logL | Calculate a matrix of genotype log-likelihoods for a genetic... |

geno_logL_ssq | Calculate a matrix of sum-of-squares of genotype... |

gprob_sim_gc | Simulate genotype log-likelihoods from a population by gene... |

gprob_sim_gc_missing | Simulate genotypes by gene copy, with missing data from... |

gprob_sim_ind | Simulate genotype log-likelihoods from a population by... |

gsi_em_1 | EM algorithm from the simplest GSI model for pi and the... |

gsi_mcmc_1 | MCMC from the simplest GSI model for pi and the individual... |

gsi_mcmc_2 | MCMC from a hierarchical GSI model for rho, pi, and the... |

gsi_mcmc_bh | MCMC from a hierarchical GSI model for rho, pi, and the... |

Hasselman_sim_colls | Generate a random population structure and mixture sample, as... |

Hasselman_simulation_pipeline | Recreate the simulations of Hasselman _et al._ (2015) with... |

infer_mixture | Estimate mixing proportions and origin probabilities from one... |

list_diploid_params | Collect essential data values before mixture proportion... |

mixture_draw | Separate a chosen proportion of a reference dataset into a... |

perfect_chinook | perfect-assignment genetic data for chinook. |

perfect_chinook_mix | perfect-assignment mixture genetic data for chinook. |

per_locus_means_and_vars | Compute the mean and variance of the single-locus genotype... |

pipe | Pipe operator |

rcpp_indiv_specific_logl_means_and_vars | From the pattern of missing data at each individual, compute... |

rcpp_per_locus_logls | Return a matrix of locus-specific self-assignment logls |

read_gsi_sim | read a gsi_sim formatted input file into a tibble that rubias... |

ref_and_mix_pipeline | Estimate mixing proportions from reference and mixture... |

reference_allele_counts | Tabulate occurences of all observed alleles in reference... |

round2 | Round a given number, with 5 always rounded up |

rubias | rubias: A package for bias correction in hierarchical GSI |

samp_from_mat | Sample 1 observation from cell probabilities that are columns... |

self_assign | Do leave-one-out self-assignment of individuals in a... |

sim_spec_examples | List of example ways of specifying repunit and collection... |

simulate_random_samples | Generate a samples for a mixture. |

tcf2long | Convert Two-Column Genetic Data to Long Format |

tcf2param_list | Generate MCMC parameter list from two-column genetic data &... |

tidy_mcmc_coll_rep_stuff | A helper function to tidy up the output from the gsi_mcmc... |

tidy_mcmc_pofz | A helper function to tidy up the PofZ-like output from the... |

tidy_pi_traces | a helper function to tidy up the pi-traces that come out of... |

write_gsi_sim_mixture | Write a mixerence data frame to gsi_sim format baseline and... |

write_gsi_sim_reference | Write a reference data frame to gsi_sim format baseline and... |

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