Package: BGmisc 1.8.0

S. Mason Garrison

BGmisc: An R Package for Extended Behavior Genetics Analysis

Provides functions for behavior genetics analysis, including variance component model identification [Hunter et al. (2021) <doi:10.1007/s10519-021-10055-x>], calculation of relatedness coefficients using path-tracing methods [Wright (1922) <doi:10.1086/279872>; McArdle & McDonald (1984) <doi:10.1111/j.2044-8317.1984.tb00802.x>], inference of relatedness, pedigree conversion, and simulation of multi-generational family data [Lyu et al. (2025) <doi:10.1007/s10519-025-10225-1>]. For a full overview, see [Garrison et al. (2024) <doi:10.21105/joss.06203>]. For a big data application see [Burt et al. (2025) <doi:10.1016/j.ebiom.2025.105911>].

Authors:S. Mason Garrison [aut, cre], Michael D. Hunter [aut], Xuanyu Lyu [aut], Rachel N. Good [ctb], Jonathan D. Trattner [aut], S. Alexandra Burt [aut]

BGmisc_1.8.0.tar.gz
BGmisc_1.8.0.zip(r-4.7)BGmisc_1.8.0.zip(r-4.6)BGmisc_1.8.0.zip(r-4.5)
BGmisc_1.8.0.tgz(r-4.6-any)BGmisc_1.8.0.tgz(r-4.5-any)
BGmisc_1.8.0.tar.gz(r-4.7-any)BGmisc_1.8.0.tar.gz(r-4.6-any)
BGmisc_1.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
BGmisc/json (API)
NEWS

# Install 'BGmisc' in R:

install.packages('BGmisc', repos = c('https://r-computing-lab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/r-computing-lab/bgmisc/issues

Pkgdown/docs site:https://r-computing-lab.github.io

Datasets:

hazard - Simulated pedigree with two extended families and an age-related hazard
inbreeding - Artificial pedigree data on eight families with inbreeding
potter - Fictional pedigree data on a wizarding family
royal92 - Royal pedigree data from 1992

On CRAN:

behavior-genetics

8.98 score 3 stars 1 packages 134 scripts 935 downloads 70 exports 14 dependencies

Last updated from:bbef98b904. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	335
source / vignettes	OK	294
linux-release-x86_64	OK	242
macos-release-arm64	OK	159
macos-oldrel-arm64	OK	159
windows-devel	OK	196
windows-release	OK	179
windows-oldrel	OK	186
wasm-release	OK	157

Exports:addPersonToPed alignPhenToMatrix buildFamilyGroups buildOneFamilyGroup buildPedigreeModelCovariance buildPedigreeMx buildTreeGrid calcAllGens calcFamilySize calculateCIs calculateRelatedness checkIDs checkParentIDs checkPedigreeNetwork checkSex com2links comp2vech computeParentAdjacency createGenDataFrame determineSex dropLink findLeaves fitComponentModel fitPedigreeModel getGenDist getWikiTreeSummary identifyComponentModel inferRelatedness makeInbreeding makeTwins ped2add ped2addFocal ped2ce ped2cn ped2cnFocal ped2com ped2fam ped2focal ped2gen ped2genDist ped2genDistFocal ped2genFocal ped2graph ped2maternal ped2mit ped2mitFocal ped2paternal readGed readgedcom readGedcom readWikifamilytree recodeSex related_coef repairIDs repairSex SimPed simulatePedigree simulatePedigrees sliceFamilies summariseFamilies summariseMatrilines summarisePatrilines summarisePedigrees summarizeFamilies summarizeMatrilines summarizePatrilines summarizePedigrees traceTreePaths trimPedigree vech

Dependencies:cli cpp11 data.table glue igraph lattice lifecycle magrittr Matrix pkgconfig rlang stringi stringr vctrs

ASOIAF: How related are Jon and Danny?

Rendered fromv5_ASOIAF.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-02-19
Started: 2025-05-29

Fitting Pedigree-Based Variance Component Models

Rendered fromv60_pedigree_model_fitting.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-06-02
Started: 2026-03-31

Modeling variance components

Rendered fromv1_modelingvariancecomponents.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-04-01
Started: 2025-05-29

Network tools for finding extended pedigrees and path tracing

Rendered fromv0_network.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-02-19
Started: 2025-05-29

Pedigree Simulation and Visualization with BGmisc

Rendered fromv2_pedigree.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-05-27
Started: 2025-05-29

Understanding and Computing Relatedness from Pedigree Data

Rendered fromv3_analyticrelatedness.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-04-01
Started: 2025-05-29

Validating and Repairing Pedigree Data with BGmisc

Rendered fromv4_validation.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-01-08
Started: 2025-05-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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.	.adjBeta
Construct Adjacency Matrix for Parent-Child Relationships Using Direct Method	.adjDirect
Construct Adjacency Matrix for Parent-Child Relationships Using Indexed Method	.adjIndexed
Assign parent values based on component type	.assignParentValue
Compute the transpose multiplication for the relatedness matrix	.computeTranspose
Load or compute the isChild matrix	.loadOrComputeIsChild
Post-process GEDCOM Data Frame	.postProcessGedcom.legacy
Create a properly formatted parent row for the pedigree	addParentRow
addPersonToPed	addPersonToPed
Add addRowlessParents	addRowlessParents
Align Phenotype Vector to Matrix Format for OpenMx	alignPhenToMatrix
Apply Tag Mappings to a Line	applyTagMappings
Process Generation Connections	buildBtwnGenerations
Build family group models	buildFamilyGroups
Build one family group model	buildOneFamilyGroup
Create an mxModel for a pedigree	buildPedigreeModelCovariance
Build Pedigree mxModel	buildPedigreeMx
Process Generations for Pedigree Simulation	buildWithinGenerations
calcAllGens A function to calculate the number of individuals in each generation. This is a supporting function for 'simulatePedigree'.	allGens calcAllGens
calcFamilySize A function to calculate the total number of individuals in a pedigree given parameters. This is a supporting function for function 'simulatePedigree'	calcFamilySize famSizeCal
calcFamilySizeByGen An internal supporting function for 'simulatePedigree'.	calcFamilySizeByGen sizeAllGens
Confidence Intervals for Correlations with Optional Design-Effect Adjustment	calculateCIs
Falconer's Formula	calculateH
Calculate Relatedness Coefficient	calculateRelatedness related_coef
Validates and Optionally Repairs Unique IDs in a Pedigree Dataframe	checkIDs
Check for duplicated individual IDs	checkIDuniqueness
Validates and Optionally Repairs Parent IDs in a Pedigree Dataframe	checkParentIDs
Check Parental Role Sex Consistency	checkParentSex
Validate Pedigree Network Structure	checkPedigreeNetwork
Validates and Optionally Repairs Sex Coding in a Pedigree Dataframe	checkSex
Check for within-row duplicates (self-parents, same mom/dad)	checkWithinRowDuplicates
collapse Names	collapseNames
Convert Sparse Relationship Matrices to Kinship Links	com2links
comp2vech Turn a variance component relatedness matrix into its half-vectorization	comp2vech
Compute Parent Adjacency Matrix with Multiple Approaches	computeParentAdjacency
Condense Matrix Slots in an OpenMx Model	condenseMatrixSlots
Count GEDCOM Pattern Rows	countPatternRows
Create Data Frame for Generation	createGenDataFrame createGenDataFrame_beta
Determine Sex of Offspring	determineSex determineSex_beta
Drop Identical Duplicate IDs from Pedigree Data Frame	dropIdenticalDuplicateIDs
dropLink	dropLink
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.	findBiggest findbiggest
Find Leaf Nodes in a Pedigree	findLeaves
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.	findOldest findoldest
fitComponentModel Fit the estimated variance components of a model to covariance data	fitComponentModel
Fit an OpenMx pedigree model to observed data	fitPedigreeModel
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.	fuseTwins
Compute the generational distance between two individuals	getGenDist
Simulated pedigree with two extended families and an age-related hazard	hazard
identifyComponentModel Determine if a variance components model is identified	identifyComponentModel
Artificial pedigree data on eight families with inbreeding	inbreeding
Initialize an Empty Individual Record	initializeRecord
evenInsert A function to insert m elements evenly into a length n vector.	evenInsert insertEven
makeInbreeding	makeInbreeding
makeTwins	makeTwins
Create a Mapping from Family IDs to Parent IDs	mapFAMS2parents
Mark and Assign children	markPotentialChildren markPotentialChildren_beta
Parse Name Line	parseNameLine
Take a pedigree and turn it into an additive genetics relatedness matrix	ped2add
Add a focal-person additive relatedness column to a pedigree	ped2addFocal
Take a pedigree and turn it into an extended environmental relatedness matrix	ped2ce
Take a pedigree and turn it into a common nuclear environmental matrix	ped2cn
Add a focal-person common nuclear relatedness column to a pedigree	ped2cnFocal
Take a pedigree and turn it into a relatedness matrix	ped2com
Segment Pedigree into Extended Families	ped2fam
Compute relatedness between all individuals and a focal person	ped2focal
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	ped2gen
Compute a full pairwise generational distance matrix	ped2genDist
Compute generational distances from a focal individual to all others	ped2genDistFocal
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	ped2genFocal
Turn a pedigree into a graph	ped2graph
Add a maternal line ID variable to a pedigree	ped2maternal
Take a pedigree and turn it into a mitochondrial relatedness matrix	ped2mit ped2mt
Add a focal-person mitochondrial relatedness column to a pedigree	ped2mitFocal ped2mtFocal
Add a paternal line ID variable to a pedigree	ped2paternal
Post-process GEDCOM Data Frame	postProcessGedcom
Fictional pedigree data on a wizarding family	potter
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.	prepSummarizePedigrees
Process Event Lines (Birth or Death)	processEventLine
Process Parents Information from GEDCOM Data	processParents
Read a GEDCOM File	readGed readGedcom readgedcom
Read Wiki Family Tree	readWikifamilytree
Recodes Sex Variable in a Pedigree Dataframe	recodeSex
Repair Missing IDs	repairIDs
Repair Parent IDs	repairParentIDs
Repairs Sex Coding in a Pedigree Dataframe	repairSex
Restore Original Column Names in a Pedigree Dataframe	restorePedColnames
Royal pedigree data from 1992	royal92
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.	SimPed simulatePedigree
Simulate Multiple Pedigrees	simulatePedigrees
sliceFamilies	sliceFamilies
Summarize the families in a pedigree	summariseFamilies summarisefamilies summarizeFamilies summarizefamilies
Summarize the maternal lines in a pedigree	summariseMatrilines summarisematrilines summarizeMatrilines summarizematrilines
Summarize the paternal lines in a pedigree	summarisePatrilines summarisepatrilines summarizePatrilines summarizepatrilines
Summarize Pedigree Data	summarisePedigrees summarisepedigrees summarizePedigrees summarizepedigrees
Trace paths between individuals in a family tree grid	traceTreePaths
Iteratively Trim Leaf Nodes from a Pedigree	trimPedigree
validate_and_convert_matrix	validate_and_convert_matrix
vech Create the half-vectorization of a matrix	vech