{ "_id": "6a1eba20b25058d4daadfc5c", "Package": "tidypopgen", "Title": "Tidy Population Genetics", "Version": "0.4.4.9001", "Authors@R": "c(person(\"Evie\", \"Carter\", role = c(\"aut\")),\nperson(\"Eirlys\", \"Tysall\", role = c(\"aut\")),\nperson(\"Andrea\", \"Manica\", email = \"am315@cam.ac.uk\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-1895-450X\")),\nperson(\"Chang\", \"Christopher\", role = c(\"ctb\"),\ncomment = \"Author of Hardy-Weinberg Equilibrium algorithm in PLINK 1.90, used in loci_hwe()\"),\nperson(\"Shaun\", \"Purcell\", role = c(\"ctb\"),\ncomment = \"Author of Hardy-Weinberg Equilibrium algorithm in PLINK 1.90, used in loci_hwe()\"),\nperson(\"Bengtsson\", \"Henrik\", role = c(\"ctb\"),\ncomment = \"Author of countLines in R.utils, modified for .vcf in count_vcf_variants()\"))", "Description": "We provide a tidy grammar of population genetics,\nfacilitating the manipulation and analysis of data on biallelic\nsingle nucleotide polymorphisms (SNPs). 'tidypopgen' scales to\nvery large genetic datasets by storing genotypes on disk, and\nperforming operations on them in chunks, without ever loading\nall data in memory. The full functionalities of the package are\ndescribed in Carter et al. (2025)\n.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "Language": "en-GB", "URL": "https://github.com/EvolEcolGroup/tidypopgen,\nhttps://evolecolgroup.github.io/tidypopgen/", "BugReports": "https://github.com/EvolEcolGroup/tidypopgen/issues", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Additional_repositories": "https://evolecolgroup.r-universe.dev/", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "LazyData": "true", "Config/Needs/website": "rmarkdown", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibicu-dev libssl-dev libproj-dev libsqlite3-dev\nlibudunits2-dev", "Repository": "https://evolecolgroup.r-universe.dev", "Date/Publication": "2026-05-28 05:04:43 UTC", "RemoteUrl": "https://github.com/EvolEcolGroup/tidypopgen", "RemoteRef": "dev", "RemoteSha": "dc6885bc8c1e99716bdc9305554b00c7e66ec810", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-02 10:56:18 UTC", "User": "root" }, "Author": "Evie Carter 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principal components", "topics": [ "gt_cluster_pca_best_k" ] }, { "page": "gt_dapc", "title": "Discriminant Analysis of Principal Components for gen_tibble", "topics": [ "gt_dapc" ] }, { "page": "gt_extract_f2", "title": "Compute and store blocked f2 statistics for ADMIXTOOLS 2", "topics": [ "gt_extract_f2" ] }, { "page": "gt_from_genlight", "title": "Convert a 'genlight' object from adegenet to a 'gen_tibble'", "topics": [ "gt_from_genlight" ] }, { "page": "gt_get_file_names", "title": "Get the names of files storing the genotypes of a 'gen_tibble'", "topics": [ "gt_get_file_names" ] }, { "page": "gt_has_imputed", "title": "Checks if a 'gen_tibble' has been imputed", "topics": [ "gt_has_imputed" ] }, { "page": "gt_impute_simple", "title": "Simple imputation based on allele frequencies", "topics": [ "gt_impute_simple" ] }, { "page": "gt_impute_xgboost", "title": "Imputation based XGBoost", "topics": [ "gt_impute_xgboost" ] }, { "page": "gt_load", "title": "Load a gen_tibble", "topics": [ "gt_load" ] }, { "page": "gt_order_loci", "title": "Order the loci table of a gen_tibble", "topics": [ "gt_order_loci" ] }, { "page": "gt_pca", "title": "Principal Component Analysis for 'gen_tibble' objects", "concept": [ "gt_pca_functions" ], "topics": [ "gt_pca" ] }, { "page": "gt_pca_autoSVD", "title": "PCA controlling for LD for 'gen_tibble' objects", "concept": [ "gt_pca_functions" ], "topics": [ "gt_pca_autoSVD" ] }, { "page": "gt_pca_partialSVD", "title": "PCA for 'gen_tibble' objects by partial SVD", "concept": [ "gt_pca_functions" ], "topics": [ "gt_pca_partialSVD" ] }, { "page": "gt_pca_randomSVD", "title": "PCA for 'gen_tibble' objects by randomized partial SVD", "concept": [ "gt_pca_functions" ], "topics": [ "gt_pca_randomSVD" ] }, { "page": "gt_pcadapt", "title": "pcadapt analysis on a 'gen_tibble' object", "topics": [ "gt_pcadapt" ] }, { "page": "gt_pseudohaploid", "title": "Set the ploidy of a 'gen_tibble' to include pseudohaploids", "topics": [ "gt_pseudohaploid" ] }, { "page": "gt_save", "title": "Save a gen_tibble", "topics": [ "gt_save" ] }, { "page": "gt_set_imputed", "title": "Sets a 'gen_tibble' to use imputed data", "topics": [ "gt_set_imputed" ] }, { "page": "gt_snmf", "title": "Run SNMF from R in tidypopgen", "topics": [ "gt_snmf" ] }, { "page": "gt_update_backingfile", "title": "Update the backing matrix", "topics": [ "gt_update_backingfile" ] }, { "page": "gt_uses_imputed", "title": "Checks if a 'gen_tibble' uses imputed data", "topics": [ "gt_uses_imputed" ] }, { "page": "heatmap_add_dendro", "title": "Add dendrograms to a heatmap of pairwise distances", "topics": [ "heatmap_add_dendro" ] }, { "page": "heatmap_pairwise", "title": "Pairwise distance heatmap", "topics": [ "heatmap_pairwise" ] }, { "page": "indiv_het_obs", "title": "Estimate individual observed heterozygosity", "topics": [ "indiv_het_obs", "indiv_het_obs.tbl_df", "indiv_het_obs.vctrs_bigSNP" ] }, { "page": "indiv_inbreeding", "title": "Individual inbreeding coefficient", 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