| updog-package | 'updog' Flexible Genotyping for Polyploids |
| betabinom | The Beta-Binomial Distribution |
| dbetabinom | The Beta-Binomial Distribution |
| export_vcf | Save the output of 'multidog()' to a VCF file. |
| 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). |
| updog | 'updog' Flexible Genotyping for Polyploids |
| wem | EM algorithm to fit weighted ash objective. |