Package: BGmisc 1.3.5

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. (2024) <doi:10.1101/2024.12.19.629449>]. For a full overview, see Garrison et al. (2024) <doi:10.21105/joss.06203>.

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]

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

Datasets:

ASOIAF - A song of ice and fire pedigree data
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

6.71 score 1 stars 35 scripts 738 downloads 42 exports 21 dependencies

Last updated 2 hours agofrom:f42eea26b8. Checks:9 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Apr 03 2025
R-4.5-win	OK	Apr 03 2025
R-4.5-mac	OK	Apr 03 2025
R-4.5-linux	OK	Apr 03 2025
R-4.4-win	OK	Apr 03 2025
R-4.4-mac	OK	Apr 03 2025
R-4.4-linux	OK	Apr 03 2025
R-4.3-win	OK	Apr 03 2025
R-4.3-mac	OK	Apr 03 2025

Exports:allGens calculateRelatedness checkIDs checkPedigreeNetwork checkSex com2links comp2vech createGenDataFrame dropLink evenInsert extractSummaryText famSizeCal fitComponentModel identifyComponentModel inferRelatedness makeInbreeding makeTwins parseTree ped2add ped2ce ped2cn ped2com ped2fam ped2graph ped2maternal ped2mit ped2paternal plotPedigree readGedcom readWikifamilytree recodeSex related_coef relatedness repairSex resample SimPed simulatePedigree summarizeFamilies summarizeMatrilines summarizePatrilines summarizePedigrees vech

Dependencies:cli cpp11 data.table evaluate glue highr igraph kinship2 knitr lattice lifecycle magrittr Matrix pkgconfig quadprog rlang stringi stringr vctrs xfun yaml

Adjacency matrix methods

Rendered frompartial.Rmdusingknitr::rmarkdownon Apr 03 2025.

Last update: 2025-04-02
Started: 2025-04-02

Modeling variance components

Rendered frommodelingrelatedness.Rmdusingknitr::rmarkdownon Apr 03 2025.

Last update: 2025-04-02
Started: 2023-09-10

Network tools for finding extended pedigrees and path tracing

Rendered fromnetwork.Rmdusingknitr::rmarkdownon Apr 03 2025.

Last update: 2024-06-10
Started: 2023-09-10

Pedigree Simulation and Visualization with BGmisc

Rendered frompedigree.Rmdusingknitr::rmarkdownon Apr 03 2025.

Last update: 2024-06-10
Started: 2023-09-10

Calculating and Inferring Relatedness Coefficients with BGmisc

Rendered fromanalyticrelatedness.Rmdusingknitr::rmarkdownon Apr 03 2025.

Last update: 2025-04-02
Started: 2023-09-11

Validating and Repairing Pedigree Data with BGmisc

Rendered fromvalidation.Rmdusingknitr::rmarkdownon Apr 03 2025.

Last update: 2025-04-02
Started: 2024-06-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compute the transpose multiplication for the relatedness matrix	.computeTranspose
Generate or Adjust Number of Kids per Couple Based on Mating Rate	adjustKidsPerCouple
allGens A function to calculate the number of individuals in each generation. This is a supporting function for 'simulatePedigree'.	allGens
A song of ice and fire pedigree data	ASOIAF
Assign Couple IDs	assignCoupleIds
Process Generation Connections	buildBetweenGenerations
Process Generations for Pedigree Simulation	buildWithinGenerations
Falconer's Formula	calculateH
Calculate Relatedness Coefficient	calculateRelatedness
Validates and Optionally Repairs Unique IDs in a Pedigree Dataframe	checkIDs
Validate Pedigree Network Structure	checkPedigreeNetwork
Validates and Optionally Repairs Sex Coding in a Pedigree Dataframe	checkSex
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	compute_parent_adjacency
Create Data Frame for Generation	createGenDataFrame
Determine Sex of Offspring	determineSex
dropLink A function to drop a person from his/her parents in the simulated pedigree 'data.frame'. The person can be dropped by specifying his/her ID or by specifying the generation which the randomly to-be-dropped person is in. The function can separate one pedigree into two pedigrees. Separating into small pieces should be done by running the function multiple times. This is a supplementary function for 'simulatePedigree'.	dropLink
evenInsert A function to insert m elements evenly into a length n vector.	evenInsert
famSizeCal A function to calculate the total number of individuals in a pedigree given parameters. This is a supporting function for function 'simulatePedigree'	famSizeCal
fitComponentModel Fit the estimated variance components of a model to covariance data	fitComponentModel
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
Infer Relatedness Coefficient	inferRelatedness
makeInbreeding A function to create inbred mates in the simulated pedigree 'data.frame'. Inbred mates can be created by specifying their IDs or the generation the inbred mate should be created. When specifying the generation, inbreeding between siblings or 1st cousin needs to be specified. This is a supplementary function for 'simulatePedigree'.	makeInbreeding
makeTwins A function to impute twins in the simulated pedigree 'data.frame'. Twins can be imputed by specifying their IDs or by specifying the generation the twin should be imputed. This is a supplementary function for 'simulatePedigree'.	makeTwins
Mark and Assign children	markPotentialChildren
Take a pedigree and turn it into an additive genetics relatedness matrix	ped2add
Take a pedigree and turn it into an extended environmental relatedness matrix	ped2ce
Take a pedigree and turn it into a common nuclear environmental relatedness matrix	ped2cn
Take a pedigree and turn it into a relatedness matrix	ped2com
Segment Pedigree into Extended Families	ped2fam
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 paternal line ID variable to a pedigree	ped2paternal
plotPedigree A wrapped function to plot simulated pedigree from function 'simulatePedigree'. This function require the installation of package 'kinship2'.	plotPedigree
Fictional pedigree data on a wizarding family	potter
Read a GEDCOM File	readGedcom
Read Wiki Family Tree	readWikifamilytree
Recodes Sex Variable in a Pedigree Dataframe	recodeSex
related_coef (Deprecated)	related_coef
relatedness (Deprecated)	relatedness
Repair Missing IDs	repairIDs
Repairs Sex Coding in a Pedigree Dataframe	repairSex
Resample Elements of a Vector	resample
Royal pedigree data from 1992	royal92
SimPed (Deprecated)	SimPed
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.	simulatePedigree
sizeAllGens An internal supporting function for 'simulatePedigree'.	sizeAllGens
Summarize the families in a pedigree	summarizeFamilies
Summarize the maternal lines in a pedigree	summarizeMatrilines
Summarize the paternal lines in a pedigree	summarizePatrilines
Summarize Pedigree Data	summarizePedigrees
vech Create the half-vectorization of a matrix	vech