{ "_id": "6a1074edacfb0bcc41cac6d7", "Package": "hiphop", "Title": "Parentage Assignment using Bi-Allelic Genetic Markers", "Version": "0.0.1", "Authors@R": "c(\nperson(given = \"Martijn\",\nfamily = \"van de Pol\",\nrole = c(\"aut\", \"cre\"),\nemail = \"martijn@myscience.eu\",\ncomment = c(ORCID = \"0000-0003-4102-4079\")),\nperson(given = \"Lyanne\",\nfamily = \"Brouwer\",\nrole = c(\"aut\"),\nemail = \"lyanne@myscience.eu\",\ncomment = c(ORCID = \"0000-0001-6728-4851\")),\nperson(given = \"Andrew\",\nfamily = \"Cockburn\",\nrole = c(\"aut\"),\nemail = \"andrew.cockburn@anu.edu.au\",\ncomment = c(ORCID = \"0000-0002-8531-3350\")))", "Description": "Can be used for paternity and maternity assignment and\noutperforms conventional methods where closely related\nindividuals occur in the pool of possible parents. The method\ncompares the genotypes of offspring with any combination of\npotentials parents and scores the number of mismatches of these\nindividuals at bi-allelic genetic markers (e.g. Single\nNucleotide Polymorphisms). It elaborates on a prior exclusion\nmethod based on the Homozygous Opposite Test (HOT; Huisman 2017\n) by introducing the additional\nexclusion criterion HIPHOP (Homozygous Identical Parents,\nHeterozygous Offspring are Precluded; Cockburn et al., in\nrevision). Potential parents are excluded if they have more\nmismatches than can be expected due to genotyping error and\nmutation, and thereby one can identify the true genetic parents\nand detect situations where one (or both) of the true parents\nis not sampled. Package 'hiphop' can deal with (a) the case\nwhere there is contextual information about parentage of the\nmother (i.e. a female has been seen to be involved in\nreproductive tasks such as nest building), but paternity is\nunknown (e.g. due to promiscuity), (b) where both parents need\nto be assigned, because there is no contextual information on\nwhich female laid eggs and which male fertilized them (e.g.\npolygynandrous mating system where multiple females and males\ndeposit young in a common nest, or organisms with external\nfertilisation that breed in aggregations). For details:\nCockburn, A., Penalba, J.V.,Jaccoud, D.,Kilian, A., Brouwer,\nL., Double, M.C., Margraf, N., Osmond, H.L., van de Pol, M. and\nKruuk, L.E.B. (in revision). HIPHOP: improved paternity\nassignment among close relatives using a simple exclusion\nmethod for bi-allelic markers. Molecular Ecology Resources, DOI\nto be added upon acceptance.", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.1.1", "URL": "https://groups.google.com/d/forum/r-hiphop", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-07 05:17:40 UTC", "User": "root" }, "Author": "Martijn van de Pol [aut, cre]\n(), Lyanne Brouwer [aut]\n(), Andrew Cockburn\n[aut] ()", "Maintainer": "Martijn van de Pol ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2020-08-19 08:30:03 UTC", "RemoteUrl": "https://github.com/cran/hiphop", "RemoteRef": "HEAD", "RemoteSha": "7738977add592b7d73893ab49f89973aeba7b1af", "MD5sum": "f6c261dad5eb7548dc29563d15cd3d8e", "_user": "cran", "_type": "src", "_file": "hiphop_0.0.1.tar.gz", "_fileid": "b31bb05f9e3d75b835892d068f85af6db0784e507a181c8f952b7b50f9fad22e", "_filesize": 768177, "_sha256": "b31bb05f9e3d75b835892d068f85af6db0784e507a181c8f952b7b50f9fad22e", "_created": "2026-05-07T05:17:40.000Z", "_published": "2026-05-22T15:23:25.086Z", "_distro": "noble", "_jobs": [ { "job": 77409921266, "time": 110, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6847496199" }, { "job": 77409920767, "time": 108, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6847496853" }, { "job": 77409920419, "time": 158, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6847474487" }, { "job": 77409919897, "time": 93, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7164145729" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/25477349118", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/hiphop", "_commit": { "id": "7738977add592b7d73893ab49f89973aeba7b1af", "author": "Martijn van de Pol ", "committer": "cran-robot ", "message": "version 0.0.1\n", "time": 1597825803 }, "_maintainer": { "name": "Martijn van de Pol", "email": "martijn@myscience.eu", "orcid": "0000-0003-4102-4079" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 1, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 230, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hiphop" }, "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/hiphop.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "0.0.1", "date": "2020-08-19" } ], "_exports": [ "hothiphop", "inspect", "topmatch" ], 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individuals", "topics": [ "inspect" ] }, { "page": "topmatch", "title": "A function selecting the dams and sires with the fewest genetic mismatches to an offspring", "topics": [ "topmatch" ] } ], "_readme": "https://github.com/cran/hiphop/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "intro_hiphop.Rmd", "filename": "intro_hiphop.html", "title": "intro_hiphop", "engine": "knitr::rmarkdown", "headings": [ "Authors", "What is R package hiphop for?", "The basic idea", "Parentage analysis: single parent versus parent pair assignment.", "1. Parentage assignment when one genetic parent is known: single parent analysis", "2. Parentage assignment when no genetic parents are known: parent pair analysis", "How does it work?", "Example dataset", "individuals dataframe", "genotypes dataframe", "The functions", "A worked example to illustrate how the functions work", "select a cohort", "inspect the data", "calculate the mismatch scores", "summarize the best matching parents", "options to summarize the best matches in different ways", "Recommendations for the two different type of parentage analysis cases", "In conclusion", "Troubleshooting", "Asking questions, suggesting improvements and reporting bugs", "Dealing with very large datasets" ], "created": "2020-08-19 08:30:03", "modified": "2020-08-19 08:30:03", "commits": 1 } ], "_score": 2.740362689494244, "_indexed": true, "_nocasepkg": "hiphop", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.1", "date": "2026-05-07T05:19:33.000Z", "distro": "noble", "commit": "7738977add592b7d73893ab49f89973aeba7b1af", "fileid": "e894264360022eadc4683fb6867e19392344affd769d1284b3de2792e81a4b0c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25477349118" }, { "r": "4.6.0", "os": "linux", "version": "0.0.1", "date": "2026-05-07T05:19:37.000Z", "distro": "noble", "commit": "7738977add592b7d73893ab49f89973aeba7b1af", "fileid": "5c43e7a590e9ddfef8b105e84b186a27dad6a3f1969c8249a6495ddc48d00aae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25477349118" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.1", "date": "2026-05-22T15:23:11.000Z", "commit": "7738977add592b7d73893ab49f89973aeba7b1af", "fileid": "68ac8ba1308b847fcfa5a0c13f3c7d46c16d865de53a12d82458ec7de4c923a8", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/25477349118" } ] }