# Flexible Genotyping for Polyploids

## Documentation for package ‘updog’ version 2.1.6

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

betabinom | The Beta-Binomial Distribution
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'.
pbetabinom | The Beta-Binomial Distribution
plot.flexdog | Draw a genotype plot from the output of 'flexdog'.
plot.multidog | Plot the output of 'multidog'.
plot_geno | Make a genotype plot.
qbetabinom | The Beta-Binomial Distribution
rbetabinom | The Beta-Binomial Distribution
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.