{
"_id": "6acc245fa14063b82c3a6098",
"Package": "nprcgenekeepr",
"Type": "Package",
"Title": "Genetic Tools for Colony Management",
"Version": "2.0.0.9000",
"Authors@R": "c(\nperson(\"Michael\", \"Raboin\", role = c(\"aut\")),\nperson(\"Terry\", \"Therneau\", role = c(\"aut\")),\nperson(\"Amanda\", \"Vinson\", role = c(\"aut\", \"dtc\")),\nperson(\"R. Mark\", \"Sharp\", email = \"rmsharp@me.com\",\ncomment = c(ORCID = \"0000-0002-6170-6942\"),\nrole = c(\"aut\", \"cre\", \"cph\", \"dtc\")),\nperson(\"Matthew\", \"Schultz\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-5103-4305\")),\nperson(\"Southwest National Primate Research Center\", role = \"fnd\",\ncomment = \"NIH grant P51 RR13986, work up to and including version 1.0\"),\nperson(\"Oregon National Primate Research Center\", role = \"fnd\",\ncomment = \"NIH grant P51 OD011092, work up to and including version 1.0\"))",
"Description": "Provides genetic tools for colony management and\nimplements a derivation of the work in Amanda Vinson and\nMichael J Raboin (2015)\n \"A\nPractical Approach for Designing Breeding Groups to Maximize\nGenetic Diversity in a Large Colony of Captive Rhesus Macaques\n('Macaca' 'mulatta')\". It provides a 'Shiny' application with\nan exposed API. The application supports these main groups of\nfunctions: (1) Quality control of studbooks contained in text\nfiles or 'Excel' workbooks and of pedigrees within 'LabKey'\nElectronic Health Records (EHR); (2) Creation of pedigrees from\na list of animals using the 'LabKey' EHR integration; (3)\nCreation and display of an age by sex pyramid plot of the\nliving animals within the designated pedigree; (4) Generation\nof genetic value analysis reports; and (5) Creation of\npotential breeding groups with and without proscribed sex\nratios and defined maximum kinships. Further tabs cover mate\npair analysis, genetic diversity, marker genetics, potential\nparents, cross-center identity mapping, de-identified export,\nand genetic-health trends.",
"URL": "https://rmsharp.github.io/nprcgenekeepr/,\nhttps://github.com/rmsharp/nprcgenekeepr",
"BugReports": "https://github.com/rmsharp/nprcgenekeepr/issues",
"Language": "en-US",
"Encoding": "UTF-8",
"License": "MIT + file LICENSE",
"LazyData": "TRUE",
"VignetteBuilder": "knitr",
"Roxygen": "list(markdown = TRUE)",
"Config/renv/profiles/dev/dependencies": "checkhelper, devtools, httpuv,\nqpdf, markdown, pak, roxygen2, spelling, usethis",
"Config/Needs/website": "quarto",
"Config/Needs/coverage": "covr",
"Config/Needs/dev": "devtools, roxygen2",
"Config/roxygen2/version": "8.0.0",
"Repository": "https://rmsharp.r-universe.dev",
"Date/Publication": "2026-10-11 19:14:17 UTC",
"RemoteUrl": "https://github.com/rmsharp/nprcgenekeepr",
"RemoteRef": "HEAD",
"RemoteSha": "5a41dbbdd427e682bb403bd60ff06fb777ac981f",
"NeedsCompilation": "no",
"Packaged": {
"Date": "2026-10-11 23:53:07 UTC",
"User": "root"
},
"Author": "Michael Raboin [aut],\nTerry Therneau [aut],\nAmanda Vinson [aut, dtc],\nR. Mark Sharp [aut, cre, cph, dtc] (ORCID:\n),\nMatthew Schultz [aut] (ORCID: ),\nSouthwest National Primate Research Center [fnd] (NIH grant P51\nRR13986, work up to and including version 1.0),\nOregon National Primate Research Center [fnd] (NIH grant P51 OD011092,\nwork up to and including version 1.0)",
"Maintainer": "R. Mark Sharp ",
"_user": "rmsharp",
"_type": "src",
"_file": "nprcgenekeepr_2.0.0.9000.tar.gz",
"_fileid": "https://r2.ropensci.org/669757b8f19ea953d02b63ba36cd55ba6b4d471d4a817a03ef0b772fb7b2a99b",
"_filesize": 3827643,
"_sha256": "669757b8f19ea953d02b63ba36cd55ba6b4d471d4a817a03ef0b772fb7b2a99b",
"_expires": "2027-01-20T00:05:49.000Z",
"_created": "2026-10-11T23:53:07.000Z",
"_published": "2026-10-12T00:05:51.451Z",
"_buildurl": "https://github.com/r-universe/rmsharp/actions/runs/38185661136",
"_status": "success",
"_host": "GitHub-Actions",
"_jobs": [
{
"job": 114608270672,
"time": 571,
"config": "linux-devel-x86_64",
"r": "4.7.0",
"check": "OK",
"artifact": "11719183447"
},
{
"job": 114608270673,
"time": 618,
"config": "linux-release-x86_64",
"r": "4.6.1",
"check": "ERROR",
"artifact": "11720335468"
},
{
"job": 114608270667,
"time": 460,
"config": "macos-oldrel-arm64",
"r": "4.5.3",
"check": "OK",
"artifact": "11719412866"
},
{
"job": 114608270712,
"time": 545,
"config": "macos-release-arm64",
"r": "4.6.1",
"check": "ERROR",
"artifact": "11720001331"
},
{
"job": 114607356593,
"time": 298,
"config": "source",
"r": "4.6.1",
"check": "OK",
"artifact": "11719214211"
},
{
"job": 114608270684,
"time": 129,
"config": "wasm-release",
"r": "4.6.0",
"check": "OK",
"artifact": "11719378727"
},
{
"job": 114608270701,
"time": 504,
"config": "windows-devel-x86_64",
"r": "4.7.0",
"check": "OK",
"artifact": "11720400057"
},
{
"job": 114608270650,
"time": 694,
"config": "windows-oldrel-x86_64",
"r": "4.5.3",
"check": "ERROR",
"artifact": "11719657553"
},
{
"job": 114608270655,
"time": 703,
"config": "windows-release-x86_64",
"r": "4.6.1",
"check": "ERROR",
"artifact": "11719712473"
}
],
"_upstream": "https://github.com/rmsharp/nprcgenekeepr",
"_commit": {
"id": "5a41dbbdd427e682bb403bd60ff06fb777ac981f",
"author": "R. Mark Sharp ",
"committer": "R. Mark Sharp ",
"message": "chore(methodology): put the project's SESSION_NOTES.md ledger spec back into methodology/methodology_trim.py\n\nThe sync overlay dropped the project's 49-line S518 addition; re-applied at the file's\nnew place after the move. The dry run plans the same 38-of-39 archive as before the sync.\n\nCo-Authored-By: Claude Sonnet 5.5 \n",
"time": 1791746057
},
"_maintainer": {
"name": "R. Mark Sharp",
"email": "rmsharp@me.com",
"login": "rmsharp",
"orcid": "0000-0002-6170-6942",
"description": "Immunogenetics Scientist 1976-1993; Statistical Analyst 1978-present; Data Science 1993 to present; Database development supervisor 1993-2017. ",
"uuid": 386848
},
"_distro": "resolute",
"_registered": true,
"_dependencies": [
{
"package": "R",
"version": ">= 4.1.0",
"role": "Depends"
},
{
"package": "anytime",
"role": "Imports"
},
{
"package": "bslib",
"role": "Imports"
},
{
"package": "data.table",
"role": "Imports"
},
{
"package": "DT",
"role": "Imports"
},
{
"package": "futile.logger",
"role": "Imports"
},
{
"package": "ggplot2",
"role": "Imports"
},
{
"package": "htmlTable",
"role": "Imports"
},
{
"package": "lifecycle",
"role": "Imports"
},
{
"package": "lubridate",
"role": "Imports"
},
{
"package": "Matrix",
"role": "Imports"
},
{
"package": "openxlsx",
"role": "Imports"
},
{
"package": "plotrix",
"role": "Imports"
},
{
"package": "quadprog",
"role": "Imports"
},
{
"package": "readxl",
"role": "Imports"
},
{
"package": "Rlabkey",
"version": ">= 3.2.0",
"role": "Imports"
},
{
"package": "sessioninfo",
"role": "Imports"
},
{
"package": "shiny",
"role": "Imports"
},
{
"package": "stringi",
"role": "Imports"
},
{
"package": "utils",
"role": "Imports"
},
{
"package": "visNetwork",
"role": "Imports"
},
{
"package": "chromote",
"role": "Suggests"
},
{
"package": "dplyr",
"role": "Suggests"
},
{
"package": "shinytest2",
"role": "Suggests"
},
{
"package": "htmltools",
"role": "Suggests"
},
{
"package": "htmlwidgets",
"role": "Suggests"
},
{
"package": "kableExtra",
"role": "Suggests"
},
{
"package": "kinship2",
"role": "Suggests"
},
{
"package": "knitr",
"role": "Suggests"
},
{
"package": "markdown",
"role": "Suggests"
},
{
"package": "mockery",
"role": "Suggests"
},
{
"package": "pkgdown",
"role": "Suggests"
},
{
"package": "rmarkdown",
"role": "Suggests"
},
{
"package": "shinyBS",
"role": "Suggests"
},
{
"package": "spelling",
"role": "Suggests"
},
{
"package": "testthat",
"role": "Suggests"
},
{
"package": "withr",
"role": "Suggests"
},
{
"package": "yaml",
"role": "Suggests"
}
],
"_owner": "rmsharp",
"_selfowned": true,
"_usedby": 0,
"_updates": [
{
"week": "2026-24",
"n": 2
},
{
"week": "2026-25",
"n": 18
},
{
"week": "2026-26",
"n": 79
},
{
"week": "2026-27",
"n": 55
},
{
"week": "2026-28",
"n": 276
},
{
"week": "2026-29",
"n": 107
},
{
"week": "2026-30",
"n": 12
},
{
"week": "2026-31",
"n": 183
},
{
"week": "2026-32",
"n": 190
},
{
"week": "2026-33",
"n": 383
},
{
"week": "2026-34",
"n": 131
},
{
"week": "2026-35",
"n": 214
},
{
"week": "2026-36",
"n": 76
},
{
"week": "2026-37",
"n": 60
},
{
"week": "2026-38",
"n": 303
},
{
"week": "2026-39",
"n": 299
},
{
"week": "2026-40",
"n": 430
},
{
"week": "2026-41",
"n": 344
}
],
"_tags": [
{
"name": "v2.0.0",
"date": "2026-07-17"
}
],
"_stars": 0,
"_contributors": [
{
"user": "rmsharp",
"count": 4554,
"uuid": 386848
}
],
"_userbio": {
"uuid": 386848,
"type": "user",
"name": "R. Mark Sharp",
"followers": 14,
"description": "Immunogenetics Scientist 1976-1993; Statistical Analyst 1978-present; Data Science 1993 to present; Database development supervisor 1993-2017. "
},
"_downloads": {
"count": 308,
"source": "https://cranlogs.r-pkg.org/downloads/total/last-month/nprcgenekeepr"
},
"_devurl": "https://github.com/rmsharp/nprcgenekeepr",
"_pkgdown": "https://rmsharp.github.io/nprcgenekeepr/",
"_searchresults": 510,
"_rbuild": "4.6.1",
"_assets": [
"extra/citation.cff",
"extra/citation.html",
"extra/citation.json",
"extra/citation.txt",
"extra/contents.json",
"extra/manual.pdf",
"extra/NEWS.html",
"extra/NEWS.txt",
"extra/nprcgenekeepr.html",
"extra/readme.html",
"extra/readme.md",
"LICENSE"
],
"_homeurl": "https://github.com/rmsharp/nprcgenekeepr",
"_realowner": "rmsharp",
"_cranurl": true,
"_releases": [
{
"version": "1.0.3",
"date": "2020-06-02"
},
{
"version": "1.0.5",
"date": "2021-03-31"
},
{
"version": "1.0.7",
"date": "2025-04-24"
},
{
"version": "1.0.8",
"date": "2025-07-26"
},
{
"version": "2.0.0",
"date": "2026-07-26"
}
],
"_exports": [
"addAnimalsWithNoRelative",
"addBackSecondParents",
"addGenotype",
"addIdRecords",
"addParents",
"addSexAndAgeToGroup",
"addUIds",
"alleleFreq",
"appendColonySnapshot",
"applyKinshipOverrides",
"appServer",
"appUI",
"assignAlleles",
"buildMarkerGenotypeMatrix",
"calcA",
"calcAge",
"calcFE",
"calcFEFG",
"calcFG",
"calcFGSE",
"calcGeneDiversity",
"calcGU",
"calcGUSE",
"calcKurtosis",
"calcNeSexRatio",
"calcNeVariance",
"calcRetention",
"calcSkewness",
"calcSnapshotDeltas",
"calculateSexRatio",
"checkAncestryRules",
"checkChangedColsLst",
"checkCrossCenterMapping",
"checkErrorLst",
"checkGenotypeFile",
"checkKinshipOverrides",
"checkLinkageMarkerGenotypeFile",
"checkLocusMetadata",
"checkMarkerGenotypeFile",
"checkMhcHaplotypeFile",
"checkParentAge",
"checkRequiredCols",
"checkSequenceGenotypeFile",
"checkSnapshotHistory",
"checkTwinRelations",
"chooseAlleles",
"chooseDate",
"computeGenomicROH",
"convertAncestry",
"convertDate",
"convertFromCenter",
"convertRelationships",
"convertSexCodes",
"convertStatusCodes",
"correctParentSex",
"countFirstOrder",
"countKinshipValues",
"countLoops",
"create_wkbk",
"createColonySnapshot",
"createExampleFiles",
"createPedTree",
"createSimKinships",
"cumulateSimKinships",
"dataframe2string",
"fillGroupMembersWithSexRatio",
"filterKinMatrix",
"filterPairs",
"filterReport",
"filterThreshold",
"findGeneration",
"findLoops",
"findOffspring",
"findPedigreeNumber",
"fixColumnNames",
"geneDrop",
"get_and_or_list",
"get_elapsed_time_str",
"getAncestors",
"getAnimalsWithHighKinship",
"getAutoIdFormat",
"getBoxWhiskerDescription",
"getChangedColsTab",
"getConfigFileName",
"getCurrentAge",
"getDatedFilename",
"getDateErrorsAndConvertDatesInPed",
"getDemographics",
"getDescendantPedigree",
"getEmptyErrorLst",
"getErrorTab",
"getFileDirectRelatives",
"getFocalAnimalPed",
"getFocalAnimalPedFromFile",
"getFounders",
"getGeneticDiversityStats",
"getGenotypes",
"getGVGenotype",
"getGVPopulation",
"getIdsWithOneParent",
"getIncludeColumns",
"getLkDirectAncestors",
"getLkDirectRelatives",
"getOffspring",
"getParents",
"getPedDirectRelatives",
"getPedigree",
"getPedMaxAge",
"getPossibleCols",
"getPotentialParents",
"getPotentialSires",
"getProbandPedigree",
"getPyramidAgeDist",
"getPyramidPlot",
"getRequiredCols",
"getSiteInfo",
"getSpeciesGestation",
"getSpeciesMinBreedingAge",
"getTokenList",
"getVersion",
"groupAddAssign",
"gvaConvergence",
"hasBothParents",
"hasGenotype",
"headerDisplayNames",
"is_valid_date_str",
"isFounder",
"kinMatrix2LongForm",
"kinship",
"kinshipMatricesToKValues",
"kinshipMatrixToKValues",
"loadSiteConfig",
"loadSpeciesOverrides",
"logModuleEvent",
"makeCEPH",
"makeExamplePedigreeFile",
"makeFounderStatsTable",
"makeGeneticDiversityHeatmap",
"makeGeneticSummaryTable",
"makeGroupMembers",
"makeGroupNum",
"makeGrpNum",
"makePedigreeDiagramData",
"makePedigreeMatingLayout",
"makeRelationClassesTable",
"makeSimPed",
"mapIdsToObfuscated",
"markerExpectedHeterozygosity",
"markerFst",
"markerKinship",
"markerLdBlock",
"markerObservedHeterozygosity",
"markerParentageExclusion",
"markerParentageLikelihood",
"markerRealizedRelatednessVariance",
"meanKinship",
"mhcHaplotypeCarriers",
"mhcHaplotypeFrequency",
"modBreedingGroupsServer",
"modBreedingGroupsUI",
"modCrossCenterIdentityServer",
"modCrossCenterIdentityUI",
"modDeidentifiedExportServer",
"modDeidentifiedExportUI",
"modGeneticDiversityServer",
"modGeneticDiversityUI",
"modGeneticValueServer",
"modGeneticValueUI",
"modGvAndBgDescServer",
"modGvAndBgDescUI",
"modInputServer",
"modInputUI",
"modMarkerGeneticsServer",
"modMarkerGeneticsUI",
"modMatePairServer",
"modMatePairUI",
"modORIPReportingServer",
"modORIPReportingUI",
"modPedigreeServer",
"modPedigreeUI",
"modPotentialParentsServer",
"modPotentialParentsUI",
"modPyramidServer",
"modPyramidUI",
"modSnapshotTrendsServer",
"modSnapshotTrendsUI",
"modSummaryStatsServer",
"modSummaryStatsUI",
"obfuscateDate",
"obfuscateGenomicROH",
"obfuscateGenotypeMatrix",
"obfuscateId",
"obfuscateLdBlocks",
"obfuscateMhcHaplotypes",
"obfuscatePed",
"obfuscateTwinRelations",
"offspringCounts",
"plotSnapshotTrends",
"processQcStudbookResult",
"qcStudbook",
"rankSubjects",
"readAncestryRules",
"readKinshipOverrides",
"readSnapshotHistory",
"readTwinRelations",
"removeAutoGenIds",
"removeDuplicates",
"removeEarlyDates",
"removePotentialSires",
"removeUninformativeFounders",
"removeUnknownAnimals",
"reportAncestryViolations",
"reportGV",
"reportMatePairs",
"resolveCrossCenterIds",
"runGeneKeepR",
"runModularApp",
"runQcStudbook",
"safeExecute",
"saveDataframesAsFiles",
"savePlotToFile",
"set_seed",
"setAutoIdFormat",
"setExit",
"setLabKeyDefaults",
"setPopulation",
"shouldShowChangedColsTab",
"shouldShowOripTab",
"shrinkPedigree",
"summarizeKinshipValues",
"toCharacter",
"trimPedigree",
"withinIntegerRange"
],
"_datasets": [
{
"name": "exampleNprcgenekeeprConfig",
"title": "Example nprcgenekeepr configuration file (loadable)",
"object": "exampleNprcgenekeeprConfig",
"class": [
"character"
],
"fields": [],
"table": false,
"tojson": true
},
{
"name": "examplePedigree",
"title": "Example pedigree object (from ExamplePedigree.csv)",
"object": "examplePedigree",
"class": [
"data.frame"
],
"fields": [
"id",
"sire",
"dam",
"sex",
"gen",
"birth",
"exit",
"age",
"ancestry",
"origin",
"status",
"recordStatus",
"fromCenter"
],
"rows": 3694,
"table": true,
"tojson": true
},
{
"name": "finalRpt",
"title": "Genetic-value report list prior to ranking",
"object": "finalRpt",
"class": [
"list"
],
"fields": [],
"table": false,
"tojson": true
},
{
"name": "focalAnimals",
"title": "Focal animal IDs from examplePedigree",
"object": "focalAnimals",
"class": [
"data.frame"
],
"fields": [
"id"
],
"rows": 327,
"table": true,
"tojson": true
},
{
"name": "lacy1989Ped",
"title": "Small hypothetical pedigree (Lacy 1989)",
"object": "lacy1989Ped",
"class": [
"data.frame"
],
"fields": [
"id",
"sire",
"dam",
"gen",
"population"
],
"rows": 7,
"table": true,
"tojson": true
},
{
"name": "lacy1989PedAlleles",
"title": "Gene-drop alleles for lacy1989Ped (5000 iterations)",
"object": "lacy1989PedAlleles",
"class": [
"data.frame"
],
"fields": [],
"rows": 14,
"table": true,
"tojson": true
},
{
"name": "ped1Alleles",
"title": "Gene-drop alleles example (baboon pedigree)",
"object": "ped1Alleles",
"class": [
"data.frame"
],
"fields": [
"V1",
"V2",
"V3",
"V4",
"id",
"parent"
],
"rows": 554,
"table": true,
"tojson": true
},
{
"name": "pedDuplicateIds",
"title": "Example studbook with a duplicated record",
"object": "pedDuplicateIds",
"class": [
"data.frame"
],
"fields": [
"ego_id",
"sire.id",
"dam_id",
"sex",
"birth_date"
],
"rows": 9,
"table": true,
"tojson": true
},
{
"name": "pedFemaleSireMaleDam",
"title": "Example studbook with sex-mismatched parents",
"object": "pedFemaleSireMaleDam",
"class": [
"data.frame"
],
"fields": [
"ego_id",
"sire.id",
"dam_id",
"sex",
"birth_date"
],
"rows": 8,
"table": true,
"tojson": true
},
{
"name": "pedGood",
"title": "Valid example studbook (no QC errors)",
"object": "pedGood",
"class": [
"data.frame"
],
"fields": [
"ego_id",
"sire.id",
"dam_id",
"sex",
"birth_date"
],
"rows": 8,
"table": true,
"tojson": true
},
{
"name": "pedInvalidDates",
"title": "Example studbook with invalid birth dates",
"object": "pedInvalidDates",
"class": [
"data.frame"
],
"fields": [
"id",
"sire",
"dam",
"sex",
"birth"
],
"rows": 8,
"table": true,
"tojson": true
},
{
"name": "pedMissingBirth",
"title": "Example studbook missing the birth date column",
"object": "pedMissingBirth",
"class": [
"data.frame"
],
"fields": [
"ego_id",
"sire.id",
"dam_id",
"sex"
],
"rows": 8,
"table": true,
"tojson": true
},
{
"name": "pedOne",
"title": "Raw pedigree-file fragment for testing (5 columns)",
"object": "pedOne",
"class": [
"data.frame"
],
"fields": [
"ego_id",
"sire.id",
"dam_id",
"sex",
"birth_date"
],
"rows": 8,
"table": true,
"tojson": true
},
{
"name": "pedSameMaleIsSireAndDam",
"title": "Example studbook with a male as both sire and dam",
"object": "pedSameMaleIsSireAndDam",
"class": [
"data.frame"
],
"fields": [
"ego_id",
"sire.id",
"dam_id",
"sex",
"birth_date"
],
"rows": 8,
"table": true,
"tojson": true
},
{
"name": "pedSix",
"title": "Raw pedigree-file fragment for testing (7 columns)",
"object": "pedSix",
"class": [
"data.frame"
],
"fields": [
"Ego Id",
"Sire Id",
"Dam",
"Sex",
"Birth Date",
"Departure",
"Death"
],
"rows": 8,
"table": true,
"tojson": true
},
{
"name": "pedWithGenotype",
"title": "Pedigree with simulated genotypes (from qcPed)",
"object": "pedWithGenotype",
"class": [
"data.frame"
],
"fields": [
"id",
"sire",
"dam",
"sex",
"gen",
"birth",
"exit",
"age",
"first",
"second",
"first_name",
"second_name"
],
"rows": 280,
"table": true,
"tojson": true
},
{
"name": "pedWithGenotypeReport",
"title": "Genetic-value report for pedWithGenotype",
"object": "pedWithGenotypeReport",
"class": [
"list",
"nprcgenekeeprGV"
],
"fields": [],
"table": false,
"tojson": true
},
{
"name": "qcBreeders",
"title": "Potential breeder IDs (29 baboons)",
"object": "qcBreeders",
"class": [
"character"
],
"fields": [],
"table": false,
"tojson": true
},
{
"name": "qcPed",
"title": "Example quality-controlled baboon pedigree",
"object": "qcPed",
"class": [
"data.frame"
],
"fields": [
"id",
"sire",
"dam",
"sex",
"gen",
"birth",
"exit",
"age"
],
"rows": 280,
"table": true,
"tojson": true
},
{
"name": "qcPedGvReport",
"title": "Genetic-value report for qcPed",
"object": "qcPedGvReport",
"class": [
"list",
"nprcgenekeeprGV"
],
"fields": [],
"table": false,
"tojson": true
},
{
"name": "rhesusGenotypes",
"title": "Rhesus genotypes (two haplotypes per animal)",
"object": "rhesusGenotypes",
"class": [
"data.frame"
],
"fields": [
"id",
"first_name",
"second_name"
],
"rows": 31,
"table": true,
"tojson": true
},
{
"name": "rhesusPedigree",
"title": "Obfuscated rhesus pedigree object",
"object": "rhesusPedigree",
"class": [
"data.frame"
],
"fields": [
"id",
"sire",
"dam",
"sex",
"gen",
"birth",
"exit",
"age"
],
"rows": 375,
"table": true,
"tojson": true
},
{
"name": "smallPed",
"title": "Hypothetical 17-animal pedigree",
"object": "smallPed",
"class": [
"data.frame"
],
"fields": [
"id",
"sire",
"dam",
"sex",
"gen",
"population"
],
"rows": 17,
"table": true,
"tojson": true
},
{
"name": "smallPedTree",
"title": "Pedigree tree built from smallPed",
"object": "smallPedTree",
"class": [
"list"
],
"fields": [],
"table": true,
"tojson": true
},
{
"name": "speciesGestation",
"title": "Per-species reproductive parameters",
"object": "speciesGestation",
"class": [
"data.frame"
],
"fields": [
"species",
"gestation",
"minMaleBreedingAge",
"minFemaleBreedingAge"
],
"rows": 14,
"table": true,
"tojson": true
}
],
"_help": [
{
"page": "addAnimalsWithNoRelative",
"title": "Add an NA value for animals with no relative",
"topics": [
"addAnimalsWithNoRelative"
]
},
{
"page": "addBackSecondParents",
"title": "Add back second parents to a trimmed pedigree",
"topics": [
"addBackSecondParents"
]
},
{
"page": "addGenotype",
"title": "Add genotype data to pedigree file",
"topics": [
"addGenotype"
]
},
{
"page": "addIdRecords",
"title": "Add ego records with NA parent IDs",
"topics": [
"addIdRecords"
]
},
{
"page": "addParents",
"title": "Add parents",
"topics": [
"addParents"
]
},
{
"page": "addSexAndAgeToGroup",
"title": "Build a group data frame with ID, sex, and age",
"topics": [
"addSexAndAgeToGroup"
]
},
{
"page": "addUIds",
"title": "Add placeholder IDs for unknown parents",
"topics": [
"addUIds"
]
},
{
"page": "alleleFreq",
"title": "Count each allele in a vector",
"topics": [
"alleleFreq"
]
},
{
"page": "appendColonySnapshot",
"title": "Append a colony snapshot to a snapshot history",
"topics": [
"appendColonySnapshot"
]
},
{
"page": "applyKinshipOverrides",
"title": "Apply outside-information kinship overrides to a kinship matrix",
"topics": [
"applyKinshipOverrides"
]
},
{
"page": "appServer",
"title": "Main Application Server for nprcgenekeepr",
"topics": [
"appServer"
]
},
{
"page": "appUI",
"title": "Main Application UI for nprcgenekeepr",
"topics": [
"appUI"
]
},
{
"page": "assignAlleles",
"title": "Assign parent alleles randomly",
"topics": [
"assignAlleles"
]
},
{
"page": "buildMarkerGenotypeMatrix",
"title": "Pivot a long-format marker genotype table into a wide genotype matrix",
"topics": [
"buildMarkerGenotypeMatrix"
]
},
{
"page": "calcA",
"title": "Count each individual's rare alleles per simulation",
"concept": [
"genetic value analysis"
],
"topics": [
"calcA"
]
},
{
"page": "calcAge",
"title": "Calculate animal ages",
"topics": [
"calcAge"
]
},
{
"page": "calcFE",
"title": "Calculate founder equivalents",
"concept": [
"genetic value analysis"
],
"topics": [
"calcFE"
]
},
{
"page": "calcFEFG",
"title": "Calculate founder equivalents and founder genome equivalents",
"concept": [
"genetic value analysis"
],
"topics": [
"calcFEFG"
]
},
{
"page": "calcFG",
"title": "Calculate founder genome equivalents",
"concept": [
"genetic value analysis"
],
"topics": [
"calcFG"
]
},
{
"page": "calcFGSE",
"title": "Calculate the standard error of founder genome equivalents",
"concept": [
"genetic value analysis"
],
"topics": [
"calcFGSE"
]
},
{
"page": "calcGeneDiversity",
"title": "Calculate gene diversity from founder genome equivalents",
"concept": [
"genetic value analysis"
],
"topics": [
"calcGeneDiversity"
]
},
{
"page": "calcGU",
"title": "Calculate genome uniqueness for each population ID",
"concept": [
"genetic value analysis"
],
"topics": [
"calcGU"
]
},
{
"page": "calcGUSE",
"title": "Calculate the standard error of genome uniqueness",
"concept": [
"genetic value analysis"
],
"topics": [
"calcGUSE"
]
},
{
"page": "calcKurtosis",
"title": "Calculate bias-adjusted sample excess kurtosis",
"concept": [
"genetic value analysis"
],
"topics": [
"calcKurtosis"
]
},
{
"page": "calcNeSexRatio",
"title": "Calculate the demographic sex-ratio effective population size",
"concept": [
"genetic value analysis"
],
"topics": [
"calcNeSexRatio"
]
},
{
"page": "calcNeVariance",
"title": "Calculate the variance effective population size",
"concept": [
"genetic value analysis"
],
"topics": [
"calcNeVariance"
]
},
{
"page": "calcRetention",
"title": "Calculate allelic retention",
"concept": [
"genetic value analysis"
],
"topics": [
"calcRetention"
]
},
{
"page": "calcSkewness",
"title": "Calculate bias-adjusted sample skewness",
"concept": [
"genetic value analysis"
],
"topics": [
"calcSkewness"
]
},
{
"page": "calcSnapshotDeltas",
"title": "Compare two colony snapshots metric by metric",
"topics": [
"calcSnapshotDeltas"
]
},
{
"page": "calculateSexRatio",
"title": "Calculate the sex ratio of a set of animals",
"topics": [
"calculateSexRatio"
]
},
{
"page": "checkAncestryRules",
"title": "Validate an ancestry compatibility rules table",
"topics": [
"checkAncestryRules"
]
},
{
"page": "checkChangedColsLst",
"title": "Check a changed-columns list for non-empty fields",
"topics": [
"checkChangedColsLst"
]
},
{
"page": "checkCrossCenterMapping",
"title": "Collect every cross-center identity-mapping problem, without stopping",
"topics": [
"checkCrossCenterMapping"
]
},
{
"page": "checkErrorLst",
"title": "Check an error list for non-empty fields",
"topics": [
"checkErrorLst"
]
},
{
"page": "checkGenotypeFile",
"title": "Check genotype file",
"topics": [
"checkGenotypeFile"
]
},
{
"page": "checkKinshipOverrides",
"title": "Validate a kinship overrides table",
"topics": [
"checkKinshipOverrides"
]
},
{
"page": "checkLinkageMarkerGenotypeFile",
"title": "Check a long-format multi-locus marker genotype file, multiallelic-tolerant",
"topics": [
"checkLinkageMarkerGenotypeFile"
]
},
{
"page": "checkLocusMetadata",
"title": "Check a locus-metadata sidecar table and classify per-locus coverage",
"topics": [
"checkLocusMetadata"
]
},
{
"page": "checkMarkerGenotypeFile",
"title": "Check a long-format multi-locus marker genotype file",
"topics": [
"checkMarkerGenotypeFile"
]
},
{
"page": "checkMhcHaplotypeFile",
"title": "Check a wide-format MHC haplotype designation file",
"topics": [
"checkMhcHaplotypeFile"
]
},
{
"page": "checkParentAge",
"title": "Check parent ages against a minimum age",
"topics": [
"checkParentAge"
]
},
{
"page": "checkRequiredCols",
"title": "Check column names for required columns",
"topics": [
"checkRequiredCols"
]
},
{
"page": "checkSequenceGenotypeFile",
"title": "Check a long-format sequence-derived marker genotype file",
"topics": [
"checkSequenceGenotypeFile"
]
},
{
"page": "checkSnapshotHistory",
"title": "Validate a colony snapshot-history table",
"topics": [
"checkSnapshotHistory"
]
},
{
"page": "checkTwinRelations",
"title": "Validate a twin/zygosity relations table",
"topics": [
"checkTwinRelations"
]
},
{
"page": "chooseAlleles",
"title": "Combine two allele vectors by Mendelian sampling",
"topics": [
"chooseAlleles"
]
},
{
"page": "chooseDate",
"title": "Choose the earlier or later of two dates",
"topics": [
"chooseDate"
]
},
{
"page": "computeGenomicROH",
"title": "Compute genomic Runs of Homozygosity (ROH) and F_ROH",
"topics": [
"computeGenomicROH"
]
},
{
"page": "convertAncestry",
"title": "Convert ancestry information to a standard code",
"topics": [
"convertAncestry"
]
},
{
"page": "convertDate",
"title": "Convert character date columns to Date type",
"topics": [
"convertDate"
]
},
{
"page": "convertFromCenter",
"title": "Convert from-center information to a logical value",
"topics": [
"convertFromCenter"
]
},
{
"page": "convertRelationships",
"title": "Convert pairwise kinship values to relationship categories",
"topics": [
"convertRelationships"
]
},
{
"page": "convertSexCodes",
"title": "Convert a sex indicator to a standardized code",
"topics": [
"convertSexCodes"
]
},
{
"page": "convertStatusCodes",
"title": "Convert status indicators to a standardized code",
"topics": [
"convertStatusCodes"
]
},
{
"page": "correctParentSex",
"title": "Correct the sex of animals listed as a sire or dam",
"topics": [
"correctParentSex"
]
},
{
"page": "countFirstOrder",
"title": "Count first-order relatives",
"topics": [
"countFirstOrder"
]
},
{
"page": "countKinshipValues",
"title": "Count kinship-value occurrences across simulated pedigrees",
"topics": [
"countKinshipValues"
]
},
{
"page": "countLoops",
"title": "Count the number of loops in a pedigree tree",
"topics": [
"countLoops"
]
},
{
"page": "create_wkbk",
"title": "Create an Excel workbook with worksheets",
"topics": [
"create_wkbk"
]
},
{
"page": "createColonySnapshot",
"title": "Create a colony snapshot row from a genetic value report",
"topics": [
"createColonySnapshot"
]
},
{
"page": "createExampleFiles",
"title": "Create example pedigree and ID-list CSV files",
"topics": [
"createExampleFiles"
]
},
{
"page": "createPedTree",
"title": "Create a pedigree tree (PedTree)",
"topics": [
"createPedTree"
]
},
{
"page": "createSimKinships",
"title": "Build kinship matrices from simulated pedigrees",
"topics": [
"createSimKinships"
]
},
{
"page": "cumulateSimKinships",
"title": "Compute kinship summary statistics across simulations",
"topics": [
"cumulateSimKinships"
]
},
{
"page": "dataframe2string",
"title": "Convert a data frame to a character vector",
"topics": [
"dataframe2string"
]
},
{
"page": "exampleNprcgenekeeprConfig",
"title": "Example nprcgenekeepr configuration file (loadable)",
"topics": [
"exampleNprcgenekeeprConfig"
]
},
{
"page": "examplePedigree",
"title": "Example pedigree object (from ExamplePedigree.csv)",
"topics": [
"examplePedigree"
]
},
{
"page": "fillGroupMembersWithSexRatio",
"title": "Form breeding groups to match a target sex ratio",
"topics": [
"fillGroupMembersWithSexRatio"
]
},
{
"page": "filterKinMatrix",
"title": "Filter a kinship matrix to selected IDs",
"topics": [
"filterKinMatrix"
]
},
{
"page": "filterPairs",
"title": "Filter kinship pairs by the animals' sexes",
"topics": [
"filterPairs"
]
},
{
"page": "filterReport",
"title": "Filter a genetic value report to selected animals",
"topics": [
"filterReport"
]
},
{
"page": "filterThreshold",
"title": "Filter out kinship pairs below a threshold",
"topics": [
"filterThreshold"
]
},
{
"page": "finalRpt",
"title": "Genetic-value report list prior to ranking",
"topics": [
"finalRpt"
]
},
{
"page": "findGeneration",
"title": "Determine the generation number for each ID",
"topics": [
"findGeneration"
]
},
{
"page": "findLoops",
"title": "Find loops in a pedigree tree",
"topics": [
"findLoops"
]
},
{
"page": "findOffspring",
"title": "Count total offspring for each animal",
"topics": [
"findOffspring"
]
},
{
"page": "findPedigreeNumber",
"title": "Determine the pedigree number for each ID",
"topics": [
"findPedigreeNumber"
]
},
{
"page": "fixColumnNames",
"title": "Standardize pedigree column names",
"topics": [
"fixColumnNames"
]
},
{
"page": "focalAnimals",
"title": "Focal animal IDs from examplePedigree",
"topics": [
"focalAnimals"
]
},
{
"page": "geneDrop",
"title": "Simulate gene dropping through a pedigree",
"topics": [
"geneDrop"
]
},
{
"page": "get_and_or_list",
"title": "Join a character vector into an and/or list",
"topics": [
"get_and_or_list"
]
},
{
"page": "get_elapsed_time_str",
"title": "Format the elapsed time since a start time",
"topics": [
"get_elapsed_time_str"
]
},
{
"page": "getAncestors",
"title": "Recursively collect an individual's ancestors",
"topics": [
"getAncestors"
]
},
{
"page": "getAnimalsWithHighKinship",
"title": "List each animal's high-kinship relatives",
"topics": [
"getAnimalsWithHighKinship"
]
},
{
"page": "getAutoIdFormat",
"title": "Get the auto-generated unknown-ID format",
"topics": [
"getAutoIdFormat"
]
},
{
"page": "getBoxWhiskerDescription",
"title": "Get Box and Whisker Plot Description",
"topics": [
"getBoxWhiskerDescription"
]
},
{
"page": "getChangedColsTab",
"title": "Build the changed-columns tab panel",
"topics": [
"getChangedColsTab"
]
},
{
"page": "getConfigFileName",
"title": "Get the configuration file name for the system",
"topics": [
"getConfigFileName"
]
},
{
"page": "getCurrentAge",
"title": "Calculate current age in years from a birth date",
"topics": [
"getCurrentAge"
]
},
{
"page": "getDatedFilename",
"title": "Prepend the date and time to a file name",
"topics": [
"getDatedFilename"
]
},
{
"page": "getDateErrorsAndConvertDatesInPed",
"title": "Find date errors and convert dates in a pedigree",
"topics": [
"getDateErrorsAndConvertDatesInPed"
]
},
{
"page": "getDemographics",
"title": "Get demographic data",
"topics": [
"getDemographics"
]
},
{
"page": "getDescendantPedigree",
"title": "Reduce a pedigree to a group and its descendants",
"topics": [
"getDescendantPedigree"
]
},
{
"page": "getEmptyErrorLst",
"title": "Create an empty errorLst object",
"topics": [
"getEmptyErrorLst"
]
},
{
"page": "getErrorTab",
"title": "Build the error-list tab panel",
"topics": [
"getErrorTab"
]
},
{
"page": "getFileDirectRelatives",
"title": "Get the direct relatives of selected animals from a pedigree file",
"concept": [
"direct relatives"
],
"topics": [
"getFileDirectRelatives"
]
},
{
"page": "getFocalAnimalPed",
"title": "Get pedigree based on list of focal animals",
"topics": [
"getFocalAnimalPed"
]
},
{
"page": "getFocalAnimalPedFromFile",
"title": "Get a focal-animal pedigree from a pedigree file",
"topics": [
"getFocalAnimalPedFromFile"
]
},
{
"page": "getFounders",
"title": "Get the founder ids from a pedigree",
"topics": [
"getFounders"
]
},
{
"page": "getGeneticDiversityStats",
"title": "Assemble breeding-group genetic diversity heat-map statistics",
"topics": [
"getGeneticDiversityStats"
]
},
{
"page": "getGenotypes",
"title": "Get genotypes from file",
"topics": [
"getGenotypes"
]
},
{
"page": "getGVGenotype",
"title": "Extract genotype data for a genetic value report",
"topics": [
"getGVGenotype"
]
},
{
"page": "getGVPopulation",
"title": "Get the population of interest for the Genetic Value analysis",
"topics": [
"getGVPopulation"
]
},
{
"page": "getIdsWithOneParent",
"title": "Get ids of animals with only one parent",
"topics": [
"getIdsWithOneParent"
]
},
{
"page": "getIncludeColumns",
"title": "Get the superset of report-inclusion columns",
"topics": [
"getIncludeColumns"
]
},
{
"page": "getLkDirectAncestors",
"title": "Get the direct ancestors of selected animals",
"concept": [
"direct relatives"
],
"topics": [
"getLkDirectAncestors"
]
},
{
"page": "getLkDirectRelatives",
"title": "Get the direct relatives of selected animals from the LabKey EHR",
"concept": [
"direct relatives"
],
"topics": [
"getLkDirectRelatives"
]
},
{
"page": "getOffspring",
"title": "Get offspring to corresponding animal IDs provided",
"topics": [
"getOffspring"
]
},
{
"page": "getParents",
"title": "Get parents to corresponding animal IDs provided",
"topics": [
"getParents"
]
},
{
"page": "getPedDirectRelatives",
"title": "Get the direct relatives of selected animals from a pedigree",
"concept": [
"direct relatives"
],
"topics": [
"getPedDirectRelatives"
]
},
{
"page": "getPedigree",
"title": "Get pedigree from file",
"topics": [
"getPedigree"
]
},
{
"page": "getPedMaxAge",
"title": "Get the maximum age of any animal in the pedigree",
"topics": [
"getPedMaxAge"
]
},
{
"page": "getPossibleCols",
"title": "Get possible column names for a studbook",
"topics": [
"getPossibleCols"
]
},
{
"page": "getPotentialParents",
"title": "Get potential parents for animals with unknown parents",
"topics": [
"getPotentialParents"
]
},
{
"page": "getPotentialSires",
"title": "List potential sires",
"topics": [
"getPotentialSires"
]
},
{
"page": "getProbandPedigree",
"title": "Reduce a pedigree to probands and their ancestors",
"topics": [
"getProbandPedigree"
]
},
{
"page": "getPyramidAgeDist",
"title": "Get the age distribution for the pedigree",
"topics": [
"getPyramidAgeDist"
]
},
{
"page": "getPyramidPlot",
"title": "Create an age-sex pyramid plot of a pedigree",
"topics": [
"getPyramidPlot"
]
},
{
"page": "getRequiredCols",
"title": "Get required column names for a studbook",
"topics": [
"getRequiredCols"
]
},
{
"page": "getSiteInfo",
"title": "Get site information",
"topics": [
"getSiteInfo"
]
},
{
"page": "getSpeciesGestation",
"title": "Look up the maximum gestation period (days) for one or more species",
"topics": [
"getSpeciesGestation"
]
},
{
"page": "getSpeciesMinBreedingAge",
"title": "Look up the minimum breeding age (years) for one or more species and sexes",
"topics": [
"getSpeciesMinBreedingAge"
]
},
{
"page": "getTokenList",
"title": "Get tokens from a character vector of lines",
"topics": [
"getTokenList"
]
},
{
"page": "getVersion",
"title": "Get the version number of nprcgenekeepr",
"topics": [
"getVersion"
]
},
{
"page": "groupAddAssign",
"title": "Add animals to a breeding group or form new groups",
"topics": [
"groupAddAssign"
]
},
{
"page": "gvaConvergence",
"title": "Recommend gene-drop iterations for a pedigree",
"topics": [
"gvaConvergence"
]
},
{
"page": "hasBothParents",
"title": "Check whether an animal has both parents",
"topics": [
"hasBothParents"
]
},
{
"page": "hasGenotype",
"title": "Check for genotype data in dataframe",
"topics": [
"hasGenotype"
]
},
{
"page": "headerDisplayNames",
"title": "Convert internal column names to display or header names",
"topics": [
"headerDisplayNames"
]
},
{
"page": "is_valid_date_str",
"title": "Test whether a string is a valid date",
"topics": [
"is_valid_date_str"
]
},
{
"page": "isFounder",
"title": "Identify the founders in a pedigree",
"topics": [
"isFounder"
]
},
{
"page": "kinMatrix2LongForm",
"title": "Reformat a kinship matrix into long form",
"topics": [
"kinMatrix2LongForm"
]
},
{
"page": "kinship",
"title": "Generate a kinship matrix",
"topics": [
"kinship"
]
},
{
"page": "kinshipMatricesToKValues",
"title": "Build a kValue table from a list of kinship matrices",
"topics": [
"kinshipMatricesToKValues"
]
},
{
"page": "kinshipMatrixToKValues",
"title": "Extract a kValue table from a kinship matrix",
"topics": [
"kinshipMatrixToKValues"
]
},
{
"page": "lacy1989Ped",
"title": "Small hypothetical pedigree (Lacy 1989)",
"topics": [
"lacy1989Ped"
]
},
{
"page": "lacy1989PedAlleles",
"title": "Gene-drop alleles for lacy1989Ped (5000 iterations)",
"topics": [
"lacy1989PedAlleles"
]
},
{
"page": "loadSiteConfig",
"title": "Load the site configuration for the modular Shiny application",
"topics": [
"loadSiteConfig"
]
},
{
"page": "loadSpeciesOverrides",
"title": "Load user-configurable species reproductive-parameter overrides",
"topics": [
"loadSpeciesOverrides"
]
},
{
"page": "logModuleEvent",
"title": "Log module events",
"topics": [
"logModuleEvent"
]
},
{
"page": "makeCEPH",
"title": "Make a CEPH-style pedigree for each id",
"topics": [
"makeCEPH"
]
},
{
"page": "makeExamplePedigreeFile",
"title": "Write copy of nprcgenekeepr::examplePedigree into a file",
"topics": [
"makeExamplePedigreeFile"
]
},
{
"page": "makeFounderStatsTable",
"title": "Create Founder Statistics HTML Table",
"topics": [
"makeFounderStatsTable"
]
},
{
"page": "makeGeneticDiversityHeatmap",
"title": "Make a genetic diversity heat map",
"topics": [
"makeGeneticDiversityHeatmap"
]
},
{
"page": "makeGeneticSummaryTable",
"title": "Create Genetic Summary Statistics HTML Table",
"topics": [
"makeGeneticSummaryTable"
]
},
{
"page": "makeGroupMembers",
"title": "Make the initial groupMembers animal list",
"topics": [
"makeGroupMembers"
]
},
{
"page": "makeGroupNum",
"title": "Make the initial grpNum list",
"topics": [
"makeGroupNum"
]
},
{
"page": "makeGrpNum",
"title": "Deprecated alias for makeGroupNum",
"topics": [
"makeGrpNum"
]
},
{
"page": "makePedigreeDiagramData",
"title": "Convert a pedigree data frame into visNetwork-ready diagram data",
"topics": [
"makePedigreeDiagramData"
]
},
{
"page": "makePedigreeMatingLayout",
"title": "Combine the mating-unit forest into visNetwork-ready diagram data",
"topics": [
"makePedigreeMatingLayout"
]
},
{
"page": "makeRelationClassesTable",
"title": "Make a relation classes table from kinship pairs",
"topics": [
"makeRelationClassesTable"
]
},
{
"page": "makeSimPed",
"title": "Make a simulated pedigree from representative sires and dams",
"topics": [
"makeSimPed"
]
},
{
"page": "mapIdsToObfuscated",
"title": "Map IDs to Obfuscated IDs",
"concept": [
"obfuscation"
],
"topics": [
"mapIdsToObfuscated"
]
},
{
"page": "markerExpectedHeterozygosity",
"title": "Compute per-locus and population-wide expected heterozygosity",
"topics": [
"markerExpectedHeterozygosity"
]
},
{
"page": "markerFst",
"title": "Compute a between-center allele-frequency differentiation statistic (Fst)",
"topics": [
"markerFst"
]
},
{
"page": "markerKinship",
"title": "Estimate pairwise kinship directly from marker genotypes (KING-robust)",
"topics": [
"markerKinship"
]
},
{
"page": "markerLdBlock",
"title": "Compute a descriptive, same-chromosome pairwise LD/block statistic",
"topics": [
"markerLdBlock"
]
},
{
"page": "markerObservedHeterozygosity",
"title": "Compute per-animal observed heterozygosity from marker genotypes",
"topics": [
"markerObservedHeterozygosity"
]
},
{
"page": "markerParentageExclusion",
"title": "Flag Mendelian-inconsistent recorded parents from marker genotypes",
"topics": [
"markerParentageExclusion"
]
},
{
"page": "markerParentageLikelihood",
"title": "Rank candidate replacement parents by a multilocus likelihood (LOD) score",
"topics": [
"markerParentageLikelihood"
]
},
{
"page": "markerRealizedRelatednessVariance",
"title": "Estimate the variance of realized relatedness around pedigree kinship",
"topics": [
"markerRealizedRelatednessVariance"
]
},
{
"page": "meanKinship",
"title": "Calculate mean kinship for each animal in a kinship matrix",
"topics": [
"meanKinship"
]
},
{
"page": "mhcHaplotypeCarriers",
"title": "List the animals carrying each MHC haplotype",
"topics": [
"mhcHaplotypeCarriers"
]
},
{
"page": "mhcHaplotypeFrequency",
"title": "Summarize MHC haplotype frequencies and flag rare haplotypes",
"topics": [
"mhcHaplotypeFrequency"
]
},
{
"page": "modBreedingGroupsServer",
"title": "Breeding Groups Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modBreedingGroupsServer"
]
},
{
"page": "modBreedingGroupsUI",
"title": "Breeding Groups Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modBreedingGroupsUI"
]
},
{
"page": "modCrossCenterIdentityServer",
"title": "Cross-Center Identity Mapping Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modCrossCenterIdentityServer"
]
},
{
"page": "modCrossCenterIdentityUI",
"title": "Cross-Center Identity Mapping Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modCrossCenterIdentityUI"
]
},
{
"page": "modDeidentifiedExportServer",
"title": "De-Identified Export Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modDeidentifiedExportServer"
]
},
{
"page": "modDeidentifiedExportUI",
"title": "De-Identified Export Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modDeidentifiedExportUI"
]
},
{
"page": "modGeneticDiversityServer",
"title": "Genetic Diversity Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modGeneticDiversityServer"
]
},
{
"page": "modGeneticDiversityUI",
"title": "Genetic Diversity Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modGeneticDiversityUI"
]
},
{
"page": "modGeneticValueServer",
"title": "Genetic Value Analysis Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modGeneticValueServer"
]
},
{
"page": "modGeneticValueUI",
"title": "Genetic Value Analysis Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modGeneticValueUI"
]
},
{
"page": "modGvAndBgDescServer",
"title": "Genetic Value and Breeding Group Description Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modGvAndBgDescServer"
]
},
{
"page": "modGvAndBgDescUI",
"title": "Genetic Value and Breeding Group Description Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modGvAndBgDescUI"
]
},
{
"page": "modInputServer",
"title": "Data Input and Quality Control Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modInputServer"
]
},
{
"page": "modInputUI",
"title": "Data Input and Quality Control Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modInputUI"
]
},
{
"page": "modMarkerGeneticsServer",
"title": "Marker Genetics Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modMarkerGeneticsServer"
]
},
{
"page": "modMarkerGeneticsUI",
"title": "Marker Genetics Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modMarkerGeneticsUI"
]
},
{
"page": "modMatePairServer",
"title": "Mate Pair Analysis Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modMatePairServer"
]
},
{
"page": "modMatePairUI",
"title": "Mate Pair Analysis Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modMatePairUI"
]
},
{
"page": "modORIPReportingServer",
"title": "ORIP Reporting Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modORIPReportingServer"
]
},
{
"page": "modORIPReportingUI",
"title": "ORIP Reporting Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modORIPReportingUI"
]
},
{
"page": "modPedigreeServer",
"title": "Pedigree Browser Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modPedigreeServer"
]
},
{
"page": "modPedigreeUI",
"title": "Pedigree Browser Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modPedigreeUI"
]
},
{
"page": "modPotentialParentsServer",
"title": "Potential Parents Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modPotentialParentsServer"
]
},
{
"page": "modPotentialParentsUI",
"title": "Potential Parents Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modPotentialParentsUI"
]
},
{
"page": "modPyramidServer",
"title": "Age-Sex Pyramid Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modPyramidServer"
]
},
{
"page": "modPyramidUI",
"title": "Age-Sex Pyramid Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modPyramidUI"
]
},
{
"page": "modSnapshotTrendsServer",
"title": "Genetic-Health Trends Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modSnapshotTrendsServer"
]
},
{
"page": "modSnapshotTrendsUI",
"title": "Genetic-Health Trends Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modSnapshotTrendsUI"
]
},
{
"page": "modSummaryStatsServer",
"title": "Summary Statistics Module - Server Function",
"concept": [
"Shiny modules"
],
"topics": [
"modSummaryStatsServer"
]
},
{
"page": "modSummaryStatsUI",
"title": "Summary Statistics Module - UI Function",
"concept": [
"Shiny modules"
],
"topics": [
"modSummaryStatsUI"
]
},
{
"page": "obfuscateDate",
"title": "Obfuscate dates with a random day offset",
"concept": [
"obfuscation"
],
"topics": [
"obfuscateDate"
]
},
{
"page": "obfuscateGenomicROH",
"title": "De-identify a computeGenomicROH() result table",
"concept": [
"obfuscation"
],
"topics": [
"obfuscateGenomicROH"
]
},
{
"page": "obfuscateGenotypeMatrix",
"title": "De-identify a sequence-scale genotype matrix",
"concept": [
"obfuscation"
],
"topics": [
"obfuscateGenotypeMatrix"
]
},
{
"page": "obfuscateId",
"title": "Create ID aliases of a specified length",
"concept": [
"obfuscation"
],
"topics": [
"obfuscateId"
]
},
{
"page": "obfuscateLdBlocks",
"title": "De-identify a markerLdBlock() result table",
"concept": [
"obfuscation"
],
"topics": [
"obfuscateLdBlocks"
]
},
{
"page": "obfuscateMhcHaplotypes",
"title": "De-identify an MHC haplotype carrier table",
"concept": [
"obfuscation"
],
"topics": [
"obfuscateMhcHaplotypes"
]
},
{
"page": "obfuscatePed",
"title": "Obfuscate a pedigree by aliasing IDs and shifting dates",
"concept": [
"obfuscation"
],
"topics": [
"obfuscatePed"
]
},
{
"page": "obfuscateTwinRelations",
"title": "De-identify a twin/zygosity relations table",
"concept": [
"obfuscation"
],
"topics": [
"obfuscateTwinRelations"
]
},
{
"page": "offspringCounts",
"title": "Tabulate offspring counts, optionally by population",
"topics": [
"offspringCounts"
]
},
{
"page": "ped1Alleles",
"title": "Gene-drop alleles example (baboon pedigree)",
"topics": [
"ped1Alleles"
]
},
{
"page": "pedDuplicateIds",
"title": "Example studbook with a duplicated record",
"topics": [
"pedDuplicateIds"
]
},
{
"page": "pedFemaleSireMaleDam",
"title": "Example studbook with sex-mismatched parents",
"topics": [
"pedFemaleSireMaleDam"
]
},
{
"page": "pedGood",
"title": "Valid example studbook (no QC errors)",
"topics": [
"pedGood"
]
},
{
"page": "pedInvalidDates",
"title": "Example studbook with invalid birth dates",
"topics": [
"pedInvalidDates"
]
},
{
"page": "pedMissingBirth",
"title": "Example studbook missing the birth date column",
"topics": [
"pedMissingBirth"
]
},
{
"page": "pedOne",
"title": "Raw pedigree-file fragment for testing (5 columns)",
"topics": [
"pedOne"
]
},
{
"page": "pedSameMaleIsSireAndDam",
"title": "Example studbook with a male as both sire and dam",
"topics": [
"pedSameMaleIsSireAndDam"
]
},
{
"page": "pedSix",
"title": "Raw pedigree-file fragment for testing (7 columns)",
"topics": [
"pedSix"
]
},
{
"page": "pedWithGenotype",
"title": "Pedigree with simulated genotypes (from qcPed)",
"topics": [
"pedWithGenotype"
]
},
{
"page": "pedWithGenotypeReport",
"title": "Genetic-value report for pedWithGenotype",
"topics": [
"pedWithGenotypeReport"
]
},
{
"page": "plotSnapshotTrends",
"title": "Plot colony genetic-health trends from a snapshot history",
"topics": [
"plotSnapshotTrends"
]
},
{
"page": "print",
"title": "Print an nprcgenekeepr summary object",
"topics": [
"print.summary.nprcgenekeeprErr",
"print.summary.nprcgenekeeprGV"
]
},
{
"page": "processQcStudbookResult",
"title": "Process qcStudbook Result into UI-Friendly Format",
"topics": [
"processQcStudbookResult"
]
},
{
"page": "qcBreeders",
"title": "Potential breeder IDs (29 baboons)",
"topics": [
"qcBreeders"
]
},
{
"page": "qcPed",
"title": "Example quality-controlled baboon pedigree",
"topics": [
"qcPed"
]
},
{
"page": "qcPedGvReport",
"title": "Genetic-value report for qcPed",
"topics": [
"qcPedGvReport"
]
},
{
"page": "qcStudbook",
"title": "Run quality control on a studbook or pedigree",
"topics": [
"qcStudbook"
]
},
{
"page": "rankSubjects",
"title": "Rank animals by genetic value",
"topics": [
"rankSubjects"
]
},
{
"page": "readAncestryRules",
"title": "Read an ancestry compatibility rules table from a file",
"topics": [
"readAncestryRules"
]
},
{
"page": "readKinshipOverrides",
"title": "Read a kinship overrides table from a file",
"topics": [
"readKinshipOverrides"
]
},
{
"page": "readSnapshotHistory",
"title": "Read a colony snapshot-history table from a file",
"topics": [
"readSnapshotHistory"
]
},
{
"page": "readTwinRelations",
"title": "Read a twin/zygosity relations table from a file",
"topics": [
"readTwinRelations"
]
},
{
"page": "removeAutoGenIds",
"title": "Remove automatically generated IDs from pedigree",
"topics": [
"removeAutoGenIds"
]
},
{
"page": "removeDuplicates",
"title": "Remove duplicate records from pedigree",
"topics": [
"removeDuplicates"
]
},
{
"page": "removeEarlyDates",
"title": "Remove dates before a specified year",
"topics": [
"removeEarlyDates"
]
},
{
"page": "removePotentialSires",
"title": "Remove potential sires from a list of IDs",
"topics": [
"removePotentialSires"
]
},
{
"page": "removeUninformativeFounders",
"title": "Remove uninformative founders",
"topics": [
"removeUninformativeFounders"
]
},
{
"page": "removeUnknownAnimals",
"title": "Remove placeholder animals added for unknown parents",
"topics": [
"removeUnknownAnimals"
]
},
{
"page": "reportAncestryViolations",
"title": "Report ancestry-rule violations within formed groups",
"topics": [
"reportAncestryViolations"
]
},
{
"page": "reportGV",
"title": "Generate a genetic value report for a pedigree",
"topics": [
"reportGV"
]
},
{
"page": "reportMatePairs",
"title": "Report eligible individual mate pairs with kinship and genetic-value context",
"topics": [
"reportMatePairs"
]
},
{
"page": "resolveCrossCenterIds",
"title": "Merge two centers' pedigrees via a curator-confirmed identity link",
"topics": [
"resolveCrossCenterIds"
]
},
{
"page": "rhesusGenotypes",
"title": "Rhesus genotypes (two haplotypes per animal)",
"topics": [
"rhesusGenotypes"
]
},
{
"page": "rhesusPedigree",
"title": "Obfuscated rhesus pedigree object",
"topics": [
"rhesusPedigree"
]
},
{
"page": "runGeneKeepR",
"title": "Run the GeneKeepR Shiny Application",
"topics": [
"runGeneKeepR"
]
},
{
"page": "runModularApp",
"title": "Run the Modular Version of GeneKeepR (Deprecated)",
"topics": [
"runModularApp"
]
},
{
"page": "runQcStudbook",
"title": "Run Quality Control on Studbook with UI-Friendly Results",
"topics": [
"runQcStudbook"
]
},
{
"page": "safeExecute",
"title": "Execute an expression with error handling",
"topics": [
"safeExecute"
]
},
{
"page": "saveDataframesAsFiles",
"title": "Write copy of dataframes to either CSV, TXT, or Excel file",
"topics": [
"saveDataframesAsFiles"
]
},
{
"page": "savePlotToFile",
"title": "Save Plot to File",
"topics": [
"savePlotToFile"
]
},
{
"page": "set_seed",
"title": "Set a reproducible RNG seed across R versions",
"topics": [
"set_seed"
]
},
{
"page": "setAutoIdFormat",
"title": "Set the auto-generated unknown-ID format",
"topics": [
"setAutoIdFormat"
]
},
{
"page": "setExit",
"title": "Set the exit date when no exit column exists",
"topics": [
"setExit"
]
},
{
"page": "setLabKeyDefaults",
"title": "Configure Rlabkey authentication for the current session",
"topics": [
"setLabKeyDefaults"
]
},
{
"page": "setPopulation",
"title": "Flag animals as the population of interest",
"topics": [
"setPopulation"
]
},
{
"page": "shouldShowChangedColsTab",
"title": "Determine if Changed Columns tab should be displayed",
"topics": [
"shouldShowChangedColsTab"
]
},
{
"page": "shouldShowOripTab",
"title": "Determine if the ORIP Reporting tab should be displayed",
"topics": [
"shouldShowOripTab"
]
},
{
"page": "shrinkPedigree",
"title": "Shrink a pedigree to fit within a bit-size budget",
"topics": [
"shrinkPedigree"
]
},
{
"page": "smallPed",
"title": "Hypothetical 17-animal pedigree",
"topics": [
"smallPed"
]
},
{
"page": "smallPedTree",
"title": "Pedigree tree built from smallPed",
"topics": [
"smallPedTree"
]
},
{
"page": "speciesGestation",
"title": "Per-species reproductive parameters",
"topics": [
"speciesGestation"
]
},
{
"page": "summarizeKinshipValues",
"title": "Summarize simulated kinship values",
"topics": [
"summarizeKinshipValues"
]
},
{
"page": "summary",
"title": "Summarize a studbook quality-control error list",
"topics": [
"summary.nprcgenekeeprErr",
"summary.nprcgenekeeprGV"
]
},
{
"page": "toCharacter",
"title": "Force dataframe columns to character",
"topics": [
"toCharacter"
]
},
{
"page": "trimPedigree",
"title": "Trim a pedigree to a group's ancestors",
"topics": [
"trimPedigree"
]
},
{
"page": "withinIntegerRange",
"title": "Get integer within a range",
"topics": [
"withinIntegerRange"
]
}
],
"_pkglogo": "https://github.com/rmsharp/nprcgenekeepr/raw/HEAD/man/figures/logo.png",
"_readme": "https://github.com/rmsharp/nprcgenekeepr/raw/HEAD/README.md",
"_rundeps": [
"anytime",
"askpass",
"backports",
"base64enc",
"BH",
"bit",
"bit64",
"bslib",
"cachem",
"cellranger",
"checkmate",
"cli",
"commonmark",
"cpp11",
"crayon",
"crosstalk",
"curl",
"data.table",
"digest",
"DT",
"evaluate",
"farver",
"fastmap",
"fontawesome",
"formatR",
"fs",
"futile.logger",
"futile.options",
"generics",
"ggplot2",
"glue",
"gtable",
"highr",
"hms",
"htmlTable",
"htmltools",
"htmlwidgets",
"httpuv",
"httr",
"isoband",
"jquerylib",
"jsonlite",
"knitr",
"labeling",
"lambda.r",
"later",
"lattice",
"lazyeval",
"lifecycle",
"lubridate",
"magrittr",
"Matrix",
"memoise",
"mime",
"openssl",
"openxlsx",
"otel",
"pillar",
"pkgconfig",
"plotrix",
"prettyunits",
"progress",
"promises",
"quadprog",
"R6",
"rappdirs",
"RColorBrewer",
"Rcpp",
"readxl",
"rematch",
"Rlabkey",
"rlang",
"rmarkdown",
"rstudioapi",
"S7",
"sass",
"scales",
"sessioninfo",
"shiny",
"sourcetools",
"stringi",
"stringr",
"sys",
"tibble",
"timechange",
"tinytex",
"utf8",
"vctrs",
"viridisLite",
"visNetwork",
"withr",
"xfun",
"xtable",
"yaml",
"zip"
],
"_vignettes": [
{
"source": "gvaConvergence.Rmd",
"filename": "gvaConvergence.html",
"title": "Gene-Drop Iteration Convergence",
"author": "R. Mark Sharp, Ph.D.",
"engine": "knitr::rmarkdown_notangle",
"headings": [
"How many gene-drop iterations does a pedigree need?",
"What it measures",
"A pedigree where the iteration count matters",
"A pedigree that converges immediately",
"Choosing an iteration count"
],
"created": "2026-06-25 23:16:52",
"modified": "2026-09-19 22:30:23",
"commits": 4
},
{
"source": "a3manual.Rmd",
"filename": "a3manual.html",
"title": "Genetic Management Tools Manual",
"author": "Michael Raboin, Amanda Vinson, and R. Mark Sharp",
"engine": "knitr::knitr",
"headings": [],
"created": "2020-04-14 18:15:33",
"modified": "2026-09-19 22:30:23",
"commits": 2
},
{
"source": "a2interactive.Rmd",
"filename": "a2interactive.html",
"title": "Interactive Use of nprcgenekeepr",
"engine": "knitr::rmarkdown_notangle",
"headings": [
"Introduction",
"Installation and Help",
"Reading in a Pedigree",
"Identifying Focal Animals",
"Age Sex Pyramid Plot",
"Pedigree Diagram",
"Direct Edge Style",
"Rectilinear Edge Style",
"Twin/Zygosity Connectors",
"Genetic Value Analysis",
"Detailed look at the Genetic Value Report object",
"Breeding Group Formation",
"Harems",
"Controlling Sex Ratios",
"Individual Mate-Pair Analysis",
"Ancestry Rules for Mate Pairs",
"Pedigree Errors",
"Genetic Loops",
"Marker Genetics",
"Preparing a Marker Genotype File",
"Marker-Based Kinship",
"Heterozygosity Diagnostic",
"Parentage Verification (Mendelian Exclusion)",
"Candidate-Parent Likelihood Ranking",
"Validating a Cross-Center Mapping",
"Cross-Center Identity Linking",
"Cross-Center Differentiation (Fst)",
"Multiallelic Marker Panels and Locus Metadata",
"Realized Relatedness Variance",
"Linkage-Disequilibrium Blocks",
"De-identifying LD-Block Results",
"Aliasing Ids with a Known Placeholder Status"
],
"created": "2020-04-14 18:15:33",
"modified": "2026-10-05 19:40:40",
"commits": 32
},
{
"source": "simulatedKValues.Rmd",
"filename": "simulatedKValues.html",
"title": "Quick Example of Simulated Kinships with Partial Parentage",
"author": "R. Mark Sharp, Ph.D.",
"engine": "knitr::rmarkdown_notangle",
"headings": [
"Introduction",
"Anticipation of further uses of this kinship estimation method",
"Identification of potential parents",
"Creation of example pedigree[^not-realistic]",
"Small Example"
],
"created": "2024-12-18 04:27:24",
"modified": "2026-09-19 22:30:23",
"commits": 12
}
],
"_score": 7.263872676865224,
"_indexed": true,
"_nocasepkg": "nprcgenekeepr",
"_universes": [
"rmsharp"
],
"_binaries": [
{
"r": "4.7.0",
"os": "linux",
"version": "2.0.0.9000",
"date": "2026-10-11T23:56:42.000Z",
"distro": "resolute",
"commit": "5a41dbbdd427e682bb403bd60ff06fb777ac981f",
"fileid": "https://r2.ropensci.org/95374ca2ab0b80b49075324ddc24884e4064f4c8a11777ff5f85b86641283625",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/rmsharp/actions/runs/38185661136"
},
{
"r": "4.6.1",
"os": "linux",
"version": "2.0.0.9000",
"date": "2026-10-11T23:56:01.000Z",
"distro": "resolute",
"commit": "5a41dbbdd427e682bb403bd60ff06fb777ac981f",
"fileid": "https://r2.ropensci.org/204321dbbdd314226cee960436ed59852f7cc08cc6ab4e87ae428eadcdb7d28f",
"status": "failure",
"check": "ERROR",
"buildurl": "https://github.com/r-universe/rmsharp/actions/runs/38185661136"
},
{
"r": "4.5.3",
"os": "mac",
"version": "2.0.0.9000",
"date": "2026-10-11T23:55:22.000Z",
"commit": "5a41dbbdd427e682bb403bd60ff06fb777ac981f",
"fileid": "https://r2.ropensci.org/843da50838a29cc044e3de08514774b58d1fc4f568012911305a3aa74481284d",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/rmsharp/actions/runs/38185661136"
},
{
"r": "4.6.1",
"os": "mac",
"version": "2.0.0.9000",
"date": "2026-10-11T23:55:34.000Z",
"commit": "5a41dbbdd427e682bb403bd60ff06fb777ac981f",
"fileid": "https://r2.ropensci.org/0bfb6d4f558e5e30b7aa18030d54d5219176695afb652bb5bb363d33515337f6",
"status": "failure",
"check": "ERROR",
"buildurl": "https://github.com/r-universe/rmsharp/actions/runs/38185661136"
},
{
"r": "4.6.0",
"os": "wasm",
"version": "2.0.0.9000",
"date": "2026-10-11T23:55:52.000Z",
"commit": "5a41dbbdd427e682bb403bd60ff06fb777ac981f",
"fileid": "https://r2.ropensci.org/cf6e776ef06a83ab06749e4cd3383553d65251a9cd0a0735d28cf35f445a7c93",
"status": "success",
"buildurl": "https://github.com/r-universe/rmsharp/actions/runs/38185661136"
},
{
"r": "4.7.0",
"os": "win",
"version": "2.0.0.9000",
"date": "2026-10-11T23:55:26.000Z",
"commit": "5a41dbbdd427e682bb403bd60ff06fb777ac981f",
"fileid": "https://r2.ropensci.org/7f4e1b51cc3e110f81f343d200339982cbfc862ccbffaf91a8ed73f15960bca1",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/rmsharp/actions/runs/38185661136"
},
{
"r": "4.5.3",
"os": "win",
"version": "2.0.0.9000",
"date": "2026-10-11T23:55:39.000Z",
"commit": "5a41dbbdd427e682bb403bd60ff06fb777ac981f",
"fileid": "https://r2.ropensci.org/920a71a5d864bf91e1e74616730a851e18c24bdf2df220724a9e11013048f343",
"status": "failure",
"check": "ERROR",
"buildurl": "https://github.com/r-universe/rmsharp/actions/runs/38185661136"
},
{
"r": "4.6.1",
"os": "win",
"version": "2.0.0.9000",
"date": "2026-10-11T23:55:06.000Z",
"commit": "5a41dbbdd427e682bb403bd60ff06fb777ac981f",
"fileid": "https://r2.ropensci.org/de6fff6214b660d9c5ece30378099a2c4597c768389620dd8de103837900f247",
"status": "failure",
"check": "ERROR",
"buildurl": "https://github.com/r-universe/rmsharp/actions/runs/38185661136"
}
]
}