{ "_id": "6adb31151206290b6ab76630", "Package": "hybridclock", "Title": "How Long Have Hybrids Been Forming? Hybrid Population Histories\nfrom Diagnostic Markers", "Version": "0.1.1.9000", "Authors@R": "person(\"Paul A.\", \"Maier\", , \"maierpa@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-0851-8827\"))", "Description": "Estimates the history of hybrid populations from\ndiagnostic markers, with or without a genetic map: the average\nage of the hybrids, how long ago the rarer species' ancestry\nentered, the number of backcrosses, and whether pure animals of\nthe rarer species are still arriving. Population samples of\nhybrid index and interspecies heterozygosity, as defined by\nFitzpatrick (2012) , are compared\nwith forward simulations that include drift, small breeding\ngroups, sibling mating and separate breeding pools, so that\ninbreeding is not mistaken for age. Estimates come from\n'Cubist' models with split-conformal intervals. Recent hybrids\nare also classified individually, and the number of markers\nneeded to detect backcrossed hybrids follows Boecklen and\nHoward (1997)\n.", "License": "MIT + file LICENSE", "URL": "https://github.com/paulmaier/hybridclock,\nhttps://paulmaier.github.io/hybridclock/", "BugReports": "https://github.com/paulmaier/hybridclock/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/roxygen2/version": "8.1.0", "LazyData": "true", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://paulmaier.r-universe.dev", "Date/Publication": "2026-10-22 17:52:13 UTC", "RemoteUrl": "https://github.com/paulmaier/hybridclock", "RemoteRef": "HEAD", "RemoteSha": "e2b25b9537c2987acf77faa3a27c50d44b4ae4c9", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-23 09:59:46 UTC", "User": "root" }, "Author": "Paul A. Maier [aut, cre, cph] (ORCID:\n)", "Maintainer": "Paul A. Maier ", "_user": "paulmaier", "_type": "src", "_file": "hybridclock_0.1.1.9000.tar.gz", "_fileid": "https://r2.ropensci.org/33349c4f4f90ba5ad4ceff3ee87e579ee5ded298c715d5bc85597cfad445bd26", "_filesize": 599246, "_sha256": "33349c4f4f90ba5ad4ceff3ee87e579ee5ded298c715d5bc85597cfad445bd26", "_expires": "2027-01-31T10:04:03.000Z", "_created": "2026-10-23T09:59:46.000Z", "_published": "2026-10-23T10:04:05.656Z", "_upstream": "https://github.com/paulmaier/hybridclock", "_status": "success", "_maintainer": { "name": "Paul A. Maier", "email": "maierpa@gmail.com", "login": "paulmaier", "description": "I am a Sr Population Geneticist at FamilyTreeDNA (Gene by Gene). Also a wilderness junkie, photographer, musician, pilot, runner, and Dad Joke Artist.", "uuid": 32253629, "orcid": "0000-0003-0851-8827" }, "_jobs": [ { "job": 120355369438, "time": 139, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12493269113" }, { "job": 120355369399, "time": 149, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12494256162" }, { "job": 120355369565, "time": 187, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12494296105" }, { "job": 120355369423, "time": 213, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12493023879" }, { "job": 120352879671, "time": 376, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12493597531" }, { "job": 120355369452, "time": 105, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12494545239" }, { "job": 120355369490, "time": 92, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12493593039" }, { "job": 120355369383, "time": 128, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12494296009" }, { "job": 120355369449, "time": 105, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12493278903" } ], "_buildurl": "https://github.com/r-universe/paulmaier/actions/runs/39935147721", "_commit": { "id": "e2b25b9537c2987acf77faa3a27c50d44b4ae4c9", "author": "Paul Maier <32253629+paulmaier@users.noreply.github.com>", "committer": "Paul Maier <32253629+paulmaier@users.noreply.github.com>", "message": "README: install from CRAN, CRAN badge\n", "time": 1792691533 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "Cubist", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "ranger", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "paulmaier", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-42", "n": 6 }, { "week": "2026-43", "n": 2 } ], "_tags": [ { "name": "v0.1.0", "date": "2026-10-13" }, { "name": "v0.1.1", "date": "2026-10-14" } ], "_topics": [ "admixture", "age-estimation", "conservation-genetics", "cubist", "f1", "f2", "f3", "hiest", "hybrid-zones", "hybridization", "introgression", "junctions", "newhybrids", "population-genetics", "simulation" ], "_stars": 0, "_contributors": [ { "user": "paulmaier", "count": 8, "uuid": 32253629 } ], "_userbio": { "uuid": 32253629, "type": "user", "name": "Paul Maier", "followers": 1, "description": "I am a Sr Population Geneticist at FamilyTreeDNA (Gene by Gene). 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"wolves", "title": "Mexican wolves: crosses between two captive lineages", "object": "wolves", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "bettongs", "title": "Burrowing bettongs: two subspecies mixed in a fenced reserve", "topics": [ "bettongs" ] }, { "page": "build_reference", "title": "Simulate a reference set of hybrid histories", "topics": [ "build_reference" ] }, { "page": "carp", "title": "Bighead and silver carp: an invasive hybrid zone", "topics": [ "carp" ] }, { "page": "check_markers", "title": "Check that markers are diagnostic in the parents that actually bred", "topics": [ "check_markers" ] }, { "page": "chickens", "title": "Chickens: an advanced intercross after eight generations", "topics": [ "chickens" ] }, { "page": "class_settings", "title": "Settings for the classes that choose between the two tiers", "topics": [ "class_settings" ] }, { "page": "classification_power", "title": "Expected accuracy of individual classification", "topics": [ "classification_power" ] }, { "page": "classify_hybrids", "title": "Classify recent hybrids individually", "topics": [ "classify_hybrids" ] }, { "page": "classify_hybrids_microsat", "title": "Classify recent hybrids from microsatellites", "topics": [ "classify_hybrids_microsat" ] }, { "page": "diagnostic_markers", "title": "Find diagnostic markers between two reference groups", "topics": [ "diagnostic_markers" ] }, { "page": "effective_markers", "title": "Effective number of independent markers", "topics": [ "effective_markers" ] }, { "page": "estimate_history", "title": "Estimate the hybrid history of sampled populations", "topics": [ "estimate_history" ] }, { "page": "hybrid_scores", "title": "Hybrid index and interspecies heterozygosity", "topics": [ "hybrid_scores" ] }, { "page": "hybrid_scores_microsat", "title": "Hybrid index and heterozygosity from microsatellites", "topics": [ "hybrid_scores_microsat" ] }, { "page": "hybridclock_example", "title": 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