{ "_id": "6a1fcab2b401979e7343255d", "Package": "BGmisc", "Title": "An R Package for Extended Behavior Genetics Analysis", "Version": "1.8.0", "Authors@R": "c(\nperson(\"S. Mason\", \"Garrison\", , \"garrissm@wfu.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-4804-6003\")),\nperson(c(\"Michael\", \"D.\"), \"Hunter\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-3651-6709\")),\nperson(\"Xuanyu\", \"Lyu\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-2841-5529\")),\nperson(c(\"Rachel\", \"N.\"), \"Good\", role = \"ctb\"),\nperson(c(\"Jonathan\", \"D.\"), \"Trattner\", , \"code@jdtrat.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-1097-7603\")),\nperson(c(\"S.\", \"Alexandra\"), \"Burt\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-5538-7431\"))\n)", "Description": "Provides functions for behavior genetics analysis,\nincluding variance component model identification [Hunter et\nal. (2021) ], calculation of\nrelatedness coefficients using path-tracing methods [Wright\n(1922) ; McArdle & McDonald (1984)\n], inference of\nrelatedness, pedigree conversion, and simulation of\nmulti-generational family data [Lyu et al. (2025)\n]. For a full overview, see\n[Garrison et al. (2024) ]. For a big\ndata application see [Burt et al. (2025) ].", "License": "GPL-3", "URL": "https://github.com/R-Computing-Lab/BGmisc/,\nhttps://r-computing-lab.github.io/BGmisc/", "BugReports": "https://github.com/R-Computing-Lab/BGmisc/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Language": "en-US", "LazyData": "true", "Config/roxygen2/version": "8.0.0", "RoxygenNote": "8.0.0", "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev", "Repository": "https://r-computing-lab.r-universe.dev", "Date/Publication": "2026-06-02 17:03:47 UTC", "RemoteUrl": "https://github.com/r-computing-lab/bgmisc", "RemoteRef": "HEAD", "RemoteSha": "bbef98b9049d7c3f8db39a061561522eb91c199b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 18:49:55 UTC", "User": "root" }, "Author": "S. Mason Garrison [aut, cre] (ORCID:\n),\nMichael D. Hunter [aut] (ORCID:\n),\nXuanyu Lyu [aut] (ORCID: ),\nRachel N. Good [ctb],\nJonathan D. Trattner [aut] (ORCID:\n),\nS. Alexandra Burt [aut] (ORCID:\n)", "Maintainer": "S. Mason Garrison ", "MD5sum": "19013598c1513aada1edd10b852d210c", "_user": "r-computing-lab", "_type": "src", "_file": "BGmisc_1.8.0.tar.gz", "_fileid": "ffc8d1c8b71b59d0758eb926b5aec7edd920c018308e273dbbd745a16f8e3f1b", "_filesize": 2674079, "_sha256": "ffc8d1c8b71b59d0758eb926b5aec7edd920c018308e273dbbd745a16f8e3f1b", "_created": "2026-06-02T18:49:55.000Z", "_published": "2026-06-03T06:33:22.529Z", "_distro": "noble", "_jobs": [ { "job": 79235334712, "time": 335, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7367066999" }, { "job": 79235334742, "time": 242, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7367034000" }, { "job": 79235335019, "time": 159, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7367047290" }, { "job": 79235335087, "time": 159, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7367029688" }, { "job": 79235334485, "time": 294, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7366942117" }, { "job": 79235334425, "time": 157, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7377337458" }, { "job": 79235335011, "time": 196, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7367017122" }, { "job": 79235334515, "time": 186, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7377344284" }, { "job": 79235334950, "time": 179, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7367010338" } ], "_buildurl": "https://github.com/r-universe/r-computing-lab/actions/runs/26840758508", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/r-computing-lab/bgmisc", "_commit": { "id": "bbef98b9049d7c3f8db39a061561522eb91c199b", "author": "Mason Garrison ", "committer": "GitHub ", "message": "Merge pull request #152 from R-Computing-Lab/dev_main\n\nSlim down dataset and clean up related scripts", "time": 1780419827 }, "_maintainer": { "name": "S. Mason Garrison", "email": "garrissm@wfu.edu", "login": "smasongarrison", "orcid": "0000-0002-4804-6003", "twitter": "@SMasonGarrison", "description": "Assistant Professor of Quantitative Psychology", "uuid": 6001608 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "corrplot", "role": "Suggests" }, { "package": "discord", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "EasyMx", "role": "Suggests" }, { "package": "ggpedigree", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "kinship2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "mvtnorm", "role": "Suggests" 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"sex", "dadID", "momID", "famID", "gen", "proband" ], "rows": 134, "table": true, "tojson": true }, { "name": "potter", "title": "Fictional pedigree data on a wizarding family", "object": "potter", "class": [ "data.frame" ], "fields": [ "personID", "famID", "name", "first_name", "surname", "gen", "momID", "dadID", "spouseID", "sex", "twinID", "zygosity" ], "rows": 36, "table": true, "tojson": true }, { "name": "royal92", "title": "Royal pedigree data from 1992", "object": "royal92", "class": [ "data.frame" ], "fields": [ "personID", "momID", "dadID", "famID", "twinID", "name", "sex", "birth_date", "death_date", "title" ], "rows": 3010, "table": true, "tojson": true } ], "_help": [ { "page": "dot-adjBeta", "title": "Construct Adjacency Matrix for Parent-Child Relationships Using Beta Methods This function constructs an adjacency matrix for parent-child relationships using a method in beta testing. It identifies parent-child pairs based on the specified component of relatedness.", "topics": [ ".adjBeta" ] }, { "page": "dot-adjDirect", "title": "Construct Adjacency Matrix for Parent-Child Relationships Using Direct Method", "topics": [ ".adjDirect" ] }, { "page": "dot-adjIndexed", "title": "Construct Adjacency Matrix for Parent-Child Relationships Using Indexed Method", "topics": [ ".adjIndexed" ] }, { "page": "dot-assignParentValue", "title": "Assign parent values based on component type", "topics": [ ".assignParentValue" ] }, { "page": "dot-computeTranspose", "title": "Compute the transpose multiplication for the relatedness matrix", "topics": [ ".computeTranspose" ] }, { "page": "dot-loadOrComputeIsChild", "title": "Load or compute the isChild matrix", "topics": [ ".loadOrComputeIsChild" ] }, { "page": "dot-postProcessGedcom.legacy", "title": "Post-process GEDCOM Data Frame", "topics": [ ".postProcessGedcom.legacy" ] }, { "page": "addParentRow", "title": "Create a properly formatted parent row for the pedigree", "topics": [ "addParentRow" ] }, { "page": "addPersonToPed", "title": "addPersonToPed", "topics": [ "addPersonToPed" ] }, { "page": "addRowlessParents", "title": "Add addRowlessParents", "topics": [ "addRowlessParents" ] }, { "page": "alignPhenToMatrix", "title": "Align Phenotype Vector to Matrix Format for OpenMx", "topics": [ "alignPhenToMatrix" ] }, { "page": "applyTagMappings", "title": "Apply Tag Mappings to a Line", "topics": [ "applyTagMappings" ] }, { "page": "buildBtwnGenerations", "title": "Process Generation Connections", "topics": [ "buildBtwnGenerations" ] }, { "page": "buildFamilyGroups", "title": "Build family group models", "topics": [ "buildFamilyGroups" ] }, { "page": "buildOneFamilyGroup", "title": "Build one family group model", "topics": [ "buildOneFamilyGroup" ] }, { "page": "buildPedigreeModelCovariance", "title": "Create an mxModel for a pedigree", "topics": [ "buildPedigreeModelCovariance" ] }, { "page": "buildPedigreeMx", "title": "Build Pedigree mxModel", "topics": [ "buildPedigreeMx" ] }, { "page": "buildWithinGenerations", "title": "Process Generations for Pedigree Simulation", "topics": [ "buildWithinGenerations" ] }, { "page": "calcAllGens", "title": "calcAllGens A function to calculate the number of individuals in each generation. This is a supporting function for 'simulatePedigree'.", "topics": [ "allGens", "calcAllGens" ] }, { "page": "calcFamilySize", "title": "calcFamilySize A function to calculate the total number of individuals in a pedigree given parameters. This is a supporting function for function 'simulatePedigree'", "topics": [ "calcFamilySize", "famSizeCal" ] }, { "page": "calcFamilySizeByGen", "title": "calcFamilySizeByGen An internal supporting function for 'simulatePedigree'.", "topics": [ "calcFamilySizeByGen", "sizeAllGens" ] }, { "page": "calculateCIs", "title": "Confidence Intervals for Correlations with Optional Design-Effect Adjustment", "topics": [ "calculateCIs" ] }, { "page": "calculateH", "title": "Falconer's Formula", "topics": [ "calculateH" ] }, { "page": "calculateRelatedness", "title": "Calculate Relatedness Coefficient", "topics": [ "calculateRelatedness", "related_coef" ] }, { "page": "checkIDs", "title": "Validates and Optionally Repairs Unique IDs in a Pedigree Dataframe", "topics": [ "checkIDs" ] }, { "page": "checkIDuniqueness", "title": "Check for duplicated individual IDs", "topics": [ "checkIDuniqueness" ] }, { "page": "checkParentIDs", "title": "Validates and Optionally Repairs Parent IDs in a Pedigree Dataframe", "topics": [ "checkParentIDs" ] }, { "page": "checkParentSex", "title": "Check Parental Role Sex Consistency", "topics": [ "checkParentSex" ] }, { "page": "checkPedigreeNetwork", "title": "Validate Pedigree Network Structure", "topics": [ "checkPedigreeNetwork" ] }, { "page": "checkSex", "title": "Validates and Optionally Repairs Sex Coding in a Pedigree Dataframe", "topics": [ "checkSex" ] }, { "page": "checkWithinRowDuplicates", "title": "Check for within-row duplicates (self-parents, same mom/dad)", "topics": [ "checkWithinRowDuplicates" ] }, { "page": "collapseNames", "title": "collapse Names", "topics": [ "collapseNames" ] }, { "page": "com2links", "title": "Convert Sparse Relationship Matrices to Kinship Links", "topics": [ "com2links" ] }, { "page": "comp2vech", "title": "comp2vech Turn a variance component relatedness matrix into its half-vectorization", "topics": [ "comp2vech" ] }, { "page": "computeParentAdjacency", "title": "Compute Parent Adjacency Matrix with Multiple Approaches", "topics": [ "computeParentAdjacency" ] }, { "page": "condenseMatrixSlots", "title": "Condense Matrix Slots in an OpenMx Model", "topics": [ "condenseMatrixSlots" ] }, { "page": "countPatternRows", "title": "Count GEDCOM Pattern Rows", "topics": [ "countPatternRows" ] }, { "page": "createGenDataFrame", "title": "Create Data Frame for Generation", "topics": [ "createGenDataFrame", "createGenDataFrame_beta" ] }, { "page": "determineSex", "title": "Determine Sex of Offspring", "topics": [ "determineSex", "determineSex_beta" ] }, { "page": "dropIdenticalDuplicateIDs", "title": "Drop Identical Duplicate IDs from Pedigree Data Frame", "topics": [ "dropIdenticalDuplicateIDs" ] }, { "page": "dropLink", "title": "dropLink", "topics": [ "dropLink" ] }, { "page": "findBiggest", "title": "Function to find the biggest families in a pedigree This function finds the biggest families in a pedigree. It is supposed to be used internally by the 'summarize_pedigree' function.", "topics": [ "findBiggest", "findbiggest" ] }, { "page": "findLeaves", "title": "Find Leaf Nodes in a Pedigree", "topics": [ "findLeaves" ] }, { "page": "findOldest", "title": "Function to find the oldest individuals in a pedigree This function finds the oldest families in a pedigree. It is supposed to be used internally by the 'summarize_pedigree' function.", "topics": [ "findOldest", "findoldest" ] }, { "page": "fitComponentModel", "title": "fitComponentModel Fit the estimated variance components of a model to covariance data", "topics": [ "fitComponentModel" ] }, { "page": "fitPedigreeModel", "title": "Fit an OpenMx pedigree model to observed data", "topics": [ "fitPedigreeModel" ] }, { "page": "fuseTwins", "title": "Fuse MZ twin pairs in a pedigree dataset for path tracing This function identifies MZ twin pairs in the pedigree dataset and merges their IDs for path tracing purposes. The second twin in each pair is made a founder (with NA parents), and all children of the second twin are redirected to the first twin. This allows for correct relatedness calculations without diagonal or downstream artifacts.", "topics": [ "fuseTwins" ] }, { "page": "getGenDist", "title": "Compute the generational distance between two individuals", "topics": [ "getGenDist" ] }, { "page": "hazard", "title": "Simulated pedigree with two extended families and an age-related hazard", "topics": [ "hazard" ] }, { "page": "identifyComponentModel", "title": "identifyComponentModel Determine if a variance components model is identified", "topics": [ "identifyComponentModel" ] }, { "page": "inbreeding", "title": "Artificial pedigree data on eight families with inbreeding", "topics": [ "inbreeding" ] }, { "page": "initializeRecord", "title": "Initialize an Empty Individual Record", "topics": [ "initializeRecord" ] }, { "page": "insertEven", "title": "evenInsert A function to insert m elements evenly into a length n vector.", "topics": [ "evenInsert", "insertEven" ] }, { "page": "makeInbreeding", "title": "makeInbreeding", "topics": [ "makeInbreeding" ] }, { "page": "makeTwins", "title": "makeTwins", "topics": [ "makeTwins" ] }, { "page": "mapFAMS2parents", "title": "Create a Mapping from Family IDs to Parent IDs", "topics": [ "mapFAMS2parents" ] }, { "page": "markPotentialChildren", "title": "Mark and Assign children", "topics": [ "markPotentialChildren", "markPotentialChildren_beta" ] }, { "page": "parseNameLine", "title": "Parse Name Line", "topics": [ "parseNameLine" ] }, { "page": "ped2add", "title": "Take a pedigree and turn it into an additive genetics relatedness matrix", "topics": [ "ped2add" ] }, { "page": "ped2addFocal", "title": "Add a focal-person additive relatedness column to a pedigree", "topics": [ "ped2addFocal" ] }, { "page": "ped2ce", "title": "Take a pedigree and turn it into an extended environmental relatedness matrix", "topics": [ "ped2ce" ] }, { "page": "ped2cn", "title": "Take a pedigree and turn it into a common nuclear environmental matrix", "topics": [ "ped2cn" ] }, { "page": "ped2cnFocal", "title": "Add a focal-person common nuclear relatedness column to a pedigree", "topics": [ "ped2cnFocal" ] }, { "page": "ped2com", "title": "Take a pedigree and turn it into a relatedness matrix", "topics": [ "ped2com" ] }, { "page": "ped2fam", "title": "Segment Pedigree into Extended Families", "topics": [ "ped2fam" ] }, { "page": "ped2focal", "title": "Compute relatedness between all individuals and a focal person", "topics": [ "ped2focal" ] }, { "page": "ped2gen", "title": "Take a pedigree and turn it into a generation relatedness matrix. It computes the rank of the generation matrix, which is the number of generations separating two individuals", "topics": [ "ped2gen" ] }, { "page": "ped2genDist", "title": "Compute a full pairwise generational distance matrix", "topics": [ "ped2genDist" ] }, { "page": "ped2genDistFocal", "title": "Compute generational distances from a focal individual to all others", "topics": [ "ped2genDistFocal" ] }, { "page": "ped2genFocal", "title": "Add a focal-person generation relatedness column to a pedigree. It computes the rank of the generation matrix, which is the number of generations separating two individuals", "topics": [ "ped2genFocal" ] }, { "page": "ped2graph", "title": "Turn a pedigree into a graph", "topics": [ "ped2graph" ] }, { "page": "ped2maternal", "title": "Add a maternal line ID variable to a pedigree", "topics": [ "ped2maternal" ] }, { "page": "ped2mit", "title": "Take a pedigree and turn it into a mitochondrial relatedness matrix", "topics": [ "ped2mit", "ped2mt" ] }, { "page": "ped2mitFocal", "title": "Add a focal-person mitochondrial relatedness column to a pedigree", "topics": [ "ped2mitFocal", "ped2mtFocal" ] }, { "page": "ped2paternal", "title": "Add a paternal line ID variable to a pedigree", "topics": [ "ped2paternal" ] }, { "page": "postProcessGedcom", "title": "Post-process GEDCOM Data Frame", "topics": [ "postProcessGedcom" ] }, { "page": "potter", "title": "Fictional pedigree data on a wizarding family", "topics": [ "potter" ] }, { "page": "prepSummarizePedigrees", "title": "Function to prepare the pedigree for summarization This function prepares the pedigree for summarization by ensuring that the necessary IDs are present and that the pedigree is built correctly.", "topics": [ "prepSummarizePedigrees" ] }, { "page": "processEventLine", "title": "Process Event Lines (Birth or Death)", "topics": [ "processEventLine" ] }, { "page": "processParents", "title": "Process Parents Information from GEDCOM Data", "topics": [ "processParents" ] }, { "page": "readGedcom", "title": "Read a GEDCOM File", "topics": [ "readGed", "readGedcom", "readgedcom" ] }, { "page": "readWikifamilytree", "title": "Read Wiki Family Tree", "topics": [ "readWikifamilytree" ] }, { "page": "recodeSex", "title": "Recodes Sex Variable in a Pedigree Dataframe", "topics": [ "recodeSex" ] }, { "page": "repairIDs", "title": "Repair Missing IDs", "topics": [ "repairIDs" ] }, { "page": "repairParentIDs", "title": "Repair Parent IDs", "topics": [ "repairParentIDs" ] }, { "page": "repairSex", "title": "Repairs Sex Coding in a Pedigree Dataframe", "topics": [ "repairSex" ] }, { "page": "restorePedColnames", "title": "Restore Original Column Names in a Pedigree Dataframe", "topics": [ "restorePedColnames" ] }, { "page": "royal92", "title": "Royal pedigree data from 1992", "topics": [ "royal92" ] }, { "page": "simulatePedigree", "title": "Simulate Pedigrees This function simulates \"balanced\" pedigrees based on a group of parameters: 1) k - Kids per couple; 2) G - Number of generations; 3) p - Proportion of males in offspring; 4) r - Mating rate.", "topics": [ "SimPed", "simulatePedigree" ] }, { "page": "simulatePedigrees", "title": "Simulate Multiple Pedigrees", "topics": [ "simulatePedigrees" ] }, { "page": "sliceFamilies", "title": "sliceFamilies", "topics": [ "sliceFamilies" ] }, { "page": "summarizeFamilies", "title": "Summarize the families in a pedigree", "topics": [ "summariseFamilies", "summarisefamilies", "summarizeFamilies", "summarizefamilies" ] }, { "page": "summarizeMatrilines", "title": "Summarize the maternal lines in a pedigree", "topics": [ "summariseMatrilines", "summarisematrilines", "summarizeMatrilines", "summarizematrilines" ] }, { "page": "summarizePatrilines", "title": "Summarize the paternal lines in a pedigree", "topics": [ "summarisePatrilines", "summarisepatrilines", "summarizePatrilines", "summarizepatrilines" ] }, { "page": "summarizePedigrees", "title": "Summarize Pedigree Data", "topics": [ "summarisePedigrees", "summarisepedigrees", "summarizePedigrees", "summarizepedigrees" ] }, { "page": "traceTreePaths", "title": "Trace paths between individuals in a family tree grid", "topics": [ "traceTreePaths" ] }, { "page": "trimPedigree", "title": "Iteratively Trim Leaf Nodes from a Pedigree", "topics": [ "trimPedigree" ] }, { "page": "validate_and_convert_matrix", "title": "validate_and_convert_matrix", "topics": [ "validate_and_convert_matrix" ] }, { "page": "vech", 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