{ "_id": "6a115f29acfb0bcc41cecfe7", "Package": "admixr", "Title": "An Interface for the Software Package 'ADMIXTOOLS'", "Version": "0.9.2.9000", "Authors@R": "person(given = \"Martin\",\nfamily = \"Petr\",\nrole = c(\"aut\", \"cre\"),\nemail = \"contact@bodkan.net\",\ncomment = c(ORCID = \"0000-0003-4879-8421\"))", "Description": "An interface for various command-line tools provided by\nthe software suite 'ADMIXTOOLS'\n(). Wrapper functions\ncompletely automate the generation of intermediate\nconfiguration files, run 'ADMIXTOOLS' programs on the\ncommand-line in the background, and extract statistics of\ninterest from plain-text files which they produce. This allows\nusers to avoid dealing with low-level technical details of\nshell scripting (which is requried by traditional 'ADMIXTOOLS'\nworkflows) and focus on their research problem at hand instead.\nA set of complementary functions for processing and filtering\nof data in the 'EIGENSTRAT' format is also provided.", "License": "MIT + file LICENSE", "URL": "https://github.com/bodkan/admixr", "BugReports": "https://github.com/bodkan/admixr/issues", "SystemRequirements": "ADMIXTOOLS suite of command-line utilities for\npopulation genetics. See\n for the most recent\ninstallation instructions and further information.", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev libx11-dev", "Repository": "https://bodkan.r-universe.dev", "Date/Publication": "2025-11-24 17:41:15 UTC", "RemoteUrl": "https://github.com/bodkan/admixr", "RemoteRef": "HEAD", "RemoteSha": "5def1e935e3cbd430b9a73a9cd890548d4582422", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-23 07:59:32 UTC", "User": "root" }, "Author": "Martin Petr [aut, cre] (ORCID: )", "Maintainer": "Martin Petr ", "MD5sum": "c349414f7abd36d704ba3709faeca037", "_user": "bodkan", "_type": "src", "_file": "admixr_0.9.2.9000.tar.gz", "_fileid": "5573e27beda4eb5ab0ea85d0646f6b306bd16b9bb124a2cdcb8e432556c36878", "_filesize": 437151, "_sha256": "5573e27beda4eb5ab0ea85d0646f6b306bd16b9bb124a2cdcb8e432556c36878", "_created": "2026-05-23T07:59:32.000Z", "_published": "2026-05-23T08:02:49.101Z", "_distro": "noble", "_jobs": [ 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"config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7175482508" } ], "_buildurl": "https://github.com/r-universe/bodkan/actions/runs/26327482709", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bodkan/admixr", "_commit": { "id": "5def1e935e3cbd430b9a73a9cd890548d4582422", "author": "Martin Petr ", "committer": "Martin Petr ", "message": "Re-render the website\n", "time": 1764006075 }, "_maintainer": { "name": "Martin Petr", "email": "contact@bodkan.net", "orcid": "0000-0003-4879-8421" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "glue", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "forcats", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bodkan", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-47", "n": 28 }, { "week": "2025-48", "n": 15 } ], "_tags": [ { "name": "v0.9.2", "date": "2025-11-21" } ], "_topics": [ "bioinformatics", "popgen", "population-genetics" ], "_stars": 37, "_contributors": [ { "user": "bodkan", "count": 755, "uuid": 16516593 } ], "_userbio": { "uuid": 16516593, "type": "user", "name": "Martin Petr" }, "_downloads": { "count": 376, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/admixr" }, "_mentions": 5, "_devurl": "https://github.com/bodkan/admixr", "_searchresults": 84, "_rbuild": "4.6.0", "_assets": [ "extra/admixr.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/bodkan/admixr", "_realowner": "bodkan", "_cranurl": true, "_releases": [ { "version": "0.9.1", "date": "2020-07-03" }, { "version": "0.9.2", "date": "2025-11-22" } ], "_exports": [ "%>%", "count_snps", "d", "download_data", "eigenstrat", "f3", "f4", "f4ratio", "filter_bed", "loginfo", "merge_eigenstrat", "qpAdm", "qpAdm_filter", "qpAdm_rotation", "qpWave", "read_geno", "read_ind", "read_output", "read_snp", "relabel", "reset", "transversions_only", "write_geno", "write_ind", "write_snp" ], "_help": [ { "page": "count_snps", "title": "Count the number/proportion of present/missing sites in each sample", "topics": [ "count_snps" ] }, { "page": "download_data", "title": "Download example SNP data.", "topics": [ "download_data" ] }, { "page": "eigenstrat", "title": "EIGENSTRAT data constructor", "topics": [ "eigenstrat" ] }, { "page": "f4ratio", "title": "Calculate the D, f4, f4-ratio, or f3 statistic.", "topics": [ "d", "f3", "f4", "f4ratio" ] }, { "page": "filter_bed", "title": "Filter EIGENSTRAT data based on a given BED file", "topics": [ "filter_bed" ] }, { "page": "loginfo", "title": "Print the full log output of an admixr wrapper to the console.", "topics": [ "loginfo" ] }, { "page": "merge_eigenstrat", "title": "Merge two sets of EIGENSTRAT datasets", "topics": [ "merge_eigenstrat" ] }, { "page": "print.admixr_result", "title": "Print out the admixr result object (dataframe or a list) without showing the hidden attributes.", "topics": [ "print.admixr_result" ] }, { "page": "print.EIGENSTRAT", "title": "EIGENSTRAT print method", "topics": [ "print.EIGENSTRAT" ] }, { "page": "qpAdm", "title": "Calculate ancestry proportions in a set of target populations.", "topics": [ "qpAdm" ] }, { "page": "qpAdm_filter", "title": "Filter qpAdm rotation results for only 'sensible' models", "topics": [ "qpAdm_filter" ] }, { "page": "qpAdm_rotation", "title": "Fit qpAdm models based on the rotation strategy described in Harney et al. 2020 (bioRxiv)", "topics": [ "qpAdm_rotation" ] }, { "page": "qpWave", "title": "Find the most likely number of ancestry waves using the qpWave method.", "topics": [ "qpWave" ] }, { "page": "read_ind", "title": "Read an EIGENSTRAT ind/snp/geno file.", "topics": [ "read_geno", "read_ind", "read_snp" ] }, { "page": "read_output", "title": "Read an output file from one of the ADMIXTOOLS programs.", "topics": [ "read_output" ] }, { "page": "relabel", "title": "Change labels of populations or samples", "topics": [ "relabel" ] }, { "page": "reset", "title": "Reset modifications to an EIGENSTRAT object", "topics": [ "reset" ] }, { "page": "transversions_only", "title": "Remove transversions (C->T and G->A substitutions)", "topics": [ "transversions_only" ] }, { "page": "write_ind", "title": "Write an 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