{ "_id": "6a1f1d49b401979e7341fb42", "Package": "updog", "Title": "Flexible Genotyping for Polyploids", "Version": "2.1.7", "Authors@R": "person(\"David\", \n\"Gerard\",\nemail = \"gerard.1787@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9450-5023\"))", "Description": "Implements empirical Bayes approaches to genotype\npolyploids from next generation sequencing data while\naccounting for allele bias, overdispersion, and sequencing\nerror. The main functions are flexdog() and multidog(), which\nallow the specification of many different genotype\ndistributions. Also provided are functions to simulate\ngenotypes, rgeno(), and read-counts, rflexdog(), as well as\nfunctions to calculate oracle genotyping error rates,\noracle_mis(), and correlation with the true genotypes,\noracle_cor(). These latter two functions are useful for read\ndepth calculations. Run browseVignettes(package = \"updog\") in R\nfor example usage. See Gerard et al. (2018)\n and Gerard and Ferrao (2020)\n for details on the\nimplemented methods.", "License": "GPL (>= 3)", "BugReports": "https://github.com/dcgerard/updog/issues", "URL": "https://dcgerard.github.io/updog/", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://dcgerard.r-universe.dev", "Date/Publication": "2026-03-17 16:54:46 UTC", "RemoteUrl": "https://github.com/dcgerard/updog", "RemoteRef": "HEAD", "RemoteSha": "04e8c4243f288c8bac92cf8df52141a28dcb2171", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-16 08:39:52 UTC", "User": "root" }, "Author": "David Gerard [aut, cre] (ORCID:\n)", "Maintainer": "David Gerard ", "MD5sum": "48e84ca8701bdcd131a3cf4f706f3b51", "_user": "dcgerard", "_type": "src", "_file": "updog_2.1.7.tar.gz", "_fileid": "3f5395f7bec437b054ecced661df37a2257aba69257511722871c004a4bf972e", "_filesize": 1051045, "_sha256": 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"Subset of individuals and SNPs from Uitdewilligen et al (2013).", "object": "uitdewilligen", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "betabinom", "title": "The Beta-Binomial Distribution", "topics": [ "betabinom", "dbetabinom", "pbetabinom", "qbetabinom", "rbetabinom" ] }, { "page": "filter_snp", "title": "Filter SNPs based on the output of 'multidog()'.", "topics": [ "filter_snp" ] }, { "page": "flexdog", "title": "Flexible genotyping for polyploids from next-generation sequencing data.", "topics": [ "flexdog" ] }, { "page": "flexdog_full", "title": "Flexible genotyping for polyploids from next-generation sequencing data.", "topics": [ "flexdog_full" ] }, { "page": "format_multidog", "title": "Return arrayicized elements from the output of 'multidog'.", "topics": [ "format_multidog" ] }, { "page": "get_q_array", "title": "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.", "topics": [ "get_q_array" ] }, { "page": "is.flexdog", "title": "Tests if an argument is a 'flexdog' object.", "topics": [ "is.flexdog" ] }, { "page": "is.multidog", "title": "Tests if an argument is a 'multidog' object.", "topics": [ "is.multidog" ] }, { "page": "log_sum_exp", "title": "Log-sum-exponential trick.", "topics": [ "log_sum_exp" ] }, { "page": "log_sum_exp_2", "title": "Log-sum-exponential trick using just two doubles.", "topics": [ "log_sum_exp_2" ] }, { "page": "multidog", "title": "Fit 'flexdog' to multiple SNPs.", "topics": [ "multidog" ] }, { "page": "oracle_cor", "title": "Calculates the correlation between the true genotype and an oracle estimator.", "topics": [ "oracle_cor" ] }, { "page": "oracle_cor_from_joint", "title": "Calculate the correlation of the oracle estimator with the true genotype from the joint distribution matrix.", "topics": [ "oracle_cor_from_joint" ] }, { "page": "oracle_joint", "title": "The joint probability of the genotype and the genotype estimate of an oracle estimator.", "topics": [ "oracle_joint" ] }, { "page": "oracle_mis", "title": "Calculate oracle misclassification error rate.", "topics": [ "oracle_mis" ] }, { "page": "oracle_mis_from_joint", "title": "Get the oracle misclassification error rate directly from the joint distribution of the genotype and the oracle estimator.", "topics": [ "oracle_mis_from_joint" ] }, { "page": "oracle_mis_vec", "title": "Returns the oracle misclassification rates for each genotype.", "topics": [ "oracle_mis_vec" ] }, { "page": "oracle_mis_vec_from_joint", "title": "Get the oracle misclassification error rates (conditional on true genotype) directly from the joint distribution of the genotype and the oracle estimator.", "topics": [ "oracle_mis_vec_from_joint" ] }, { "page": "oracle_plot", "title": "Construct an oracle plot from the output of 'oracle_joint'.", "topics": [ "oracle_plot" ] }, { 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