Man pages for benmoran11/rubias

a_freq_listConvert data frame of allele frequencies to nested lists
alewifeMicrosat data from alewife herring reference populations
allelic_listCreate genotype lists for each locus
assess_pb_bias_correctionTest the effects of the parametric bootstrap bias correction...
assess_reference_looSimulate mixtures and estimate reporting group and collection...
assess_reference_mcPartition a reference dataset and estimate reporting group...
avg_coll2correctRUGet the average within-RU assignment rate for each collection
bias_comparisonTest the effects of bias corrections on a reference dataset...
bluebackMicrosat data from blueback herring reference populations.
bootstrap_rhoPerform a parametric bootstrapping correction on an estimated...
check_refmixA helper function to check that the input data frame is OK
chinookSNP data from chinook reference populations
chinook_allSNP data from Chinook reference and mixtures mixed together
chinook_mixSNP data from Chinook salmon taken in May/August 2015 from...
count_missing_datafor each individual count the number or loci missing and...
dirch_from_allocationsGiven a vector of different categories in 1...n and a prior,...
dirch_from_countsGiven a vector of counts for different categories in 1...n...
geno_logLCalculate a matrix of genotype log-likelihoods for a genetic...
geno_logL_ssqCalculate a matrix of sum-of-squares of genotype...
gprob_sim_gcSimulate genotype log-likelihoods from a population by gene...
gprob_sim_gc_missingSimulate genotypes by gene copy, with missing data from...
gprob_sim_indSimulate genotype log-likelihoods from a population by...
gsi_em_1EM algorithm from the simplest GSI model for pi and the...
gsi_mcmc_1MCMC from the simplest GSI model for pi and the individual...
gsi_mcmc_2MCMC from a hierarchical GSI model for rho, pi, and the...
gsi_mcmc_bhMCMC from a hierarchical GSI model for rho, pi, and the...
Hasselman_sim_collsGenerate a random population structure and mixture sample, as...
Hasselman_simulation_pipelineRecreate the simulations of Hasselman _et al._ (2015) with...
infer_mixtureEstimate mixing proportions and origin probabilities from one...
list_diploid_paramsCollect essential data values before mixture proportion...
mixture_drawSeparate a chosen proportion of a reference dataset into a...
perfect_chinookperfect-assignment genetic data for chinook.
perfect_chinook_mixperfect-assignment mixture genetic data for chinook.
per_locus_means_and_varsCompute the mean and variance of the single-locus genotype...
pipePipe operator
rcpp_indiv_specific_logl_means_and_varsFrom the pattern of missing data at each individual, compute...
rcpp_per_locus_loglsReturn a matrix of locus-specific self-assignment logls
read_gsi_simread a gsi_sim formatted input file into a tibble that rubias...
ref_and_mix_pipelineEstimate mixing proportions from reference and mixture...
reference_allele_countsTabulate occurences of all observed alleles in reference...
round2Round a given number, with 5 always rounded up
rubiasrubias: A package for bias correction in hierarchical GSI
samp_from_matSample 1 observation from cell probabilities that are columns...
self_assignDo leave-one-out self-assignment of individuals in a...
sim_spec_examplesList of example ways of specifying repunit and collection...
simulate_random_samplesGenerate a samples for a mixture.
tcf2longConvert Two-Column Genetic Data to Long Format
tcf2param_listGenerate MCMC parameter list from two-column genetic data &...
tidy_mcmc_coll_rep_stuffA helper function to tidy up the output from the gsi_mcmc...
tidy_mcmc_pofzA helper function to tidy up the PofZ-like output from the...
tidy_pi_tracesa helper function to tidy up the pi-traces that come out of...
write_gsi_sim_mixtureWrite a mixerence data frame to gsi_sim format baseline and...
write_gsi_sim_referenceWrite a reference data frame to gsi_sim format baseline and...
benmoran11/rubias documentation built on Sept. 16, 2017, 3:29 a.m.