dbetabinom              The Beta-Binomial Distribution
filter_snp              Filter SNPs based on the output of
                        'multidog()'.
flexdog                 Flexible genotyping for polyploids from
                        next-generation sequencing data.
flexdog_full            Flexible genotyping for polyploids from
                        next-generation sequencing data.
format_multidog         Return arrayicized elements from the output of
                        'multidog'.
get_q_array             Return the probabilities of an offspring's
                        genotype given its parental genotypes for all
                        possible combinations of parental and offspring
                        genotypes. This is for species with polysomal
                        inheritance and bivalent, non-preferential
                        pairing.
is.flexdog              Tests if an argument is a 'flexdog' object.
is.multidog             Tests if an argument is a 'multidog' object.
log_sum_exp             Log-sum-exponential trick.
log_sum_exp_2           Log-sum-exponential trick using just two
                        doubles.
multidog                Fit 'flexdog' to multiple SNPs.
oracle_cor              Calculates the correlation between the true
                        genotype and an oracle estimator.
oracle_cor_from_joint   Calculate the correlation of the oracle
                        estimator with the true genotype from the joint
                        distribution matrix.
oracle_joint            The joint probability of the genotype and the
                        genotype estimate of an oracle estimator.
oracle_mis              Calculate oracle misclassification error rate.
oracle_mis_from_joint   Get the oracle misclassification error rate
                        directly from the joint distribution of the
                        genotype and the oracle estimator.
oracle_mis_vec          Returns the oracle misclassification rates for
                        each genotype.
oracle_mis_vec_from_joint
                        Get the oracle misclassification error rates
                        (conditional on true genotype) directly from
                        the joint distribution of the genotype and the
                        oracle estimator.
oracle_plot             Construct an oracle plot from the output of
                        'oracle_joint'.
plot.flexdog            Draw a genotype plot from the output of
                        'flexdog'.
plot.multidog           Plot the output of 'multidog'.
plot_geno               Make a genotype plot.
rflexdog                Simulate GBS data from the 'flexdog'
                        likelihood.
rgeno                   Simulate individual genotypes from one of the
                        supported 'flexdog' models.
snpdat                  GBS data from Shirasawa et al (2017)
uitdewilligen           Subset of individuals and SNPs from
                        Uitdewilligen et al (2013).
wem                     EM algorithm to fit weighted ash objective.
