An R Package for Extended Behavior Genetics Analysis

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Documentation for package ‘BGmisc’ version 1.2.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

adjustKidsPerCouple	Generate or Adjust Number of Kids per Couple Based on Mating Rate
allGens	allGens A function to calculate the number of individuals in each generation. This is a supporting function for 'simulatePedigree'.
assignCoupleIds	Assign Couple IDs
buildBetweenGenerations	Process Generation Connections
buildWithinGenerations	Process Generations for Pedigree Simulation
calculateRelatedness	Calculate Relatedness Coefficient
checkIDs	Validates and Optionally Repairs Unique IDs in a Pedigree Dataframe
checkSex	Validates and Optionally Repairs Sex Coding in a Pedigree Dataframe
comp2vech	comp2vech Turn a variance component relatedness matrix into its half-vectorization
createGenDataFrame	Create Data Frame for Generation
determineSex	Determine Sex of Offspring
dropLink	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'.
evenInsert	evenInsert A function to insert m elements evenly into a length n vector.
famSizeCal	famSizeCal A function to calculate the total number of individuals in a pedigree given parameters. This is a supporting function for function 'simulatePedigree'
fitComponentModel	fitComponentModel Fit the estimated variance components of a model to covariance data
hazard	Simulated pedigree with two extended families and an age-related hazard
identifyComponentModel	identifyComponentModel Determine if a variance components model is identified
inbreeding	Artificial pedigree data on eight families with inbreeding
inferRelatedness	Infer Relatedness Coefficient
makeInbreeding	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'.
makeTwins	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'.
markPotentialChildren	Mark and Assign children
ped2add	Take a pedigree and turn it into an additive genetics relatedness matrix
ped2ce	Take a pedigree and turn it into an extended environmental relatedness matrix
ped2cn	Take a pedigree and turn it into a common nuclear environmental relatedness matrix
ped2com	Take a pedigree and turn it into a relatedness matrix
ped2fam	Add an extended family ID variable to a pedigree
ped2graph	Turn a pedigree into a graph
ped2maternal	Add a maternal line ID variable to a pedigree
ped2mit	Take a pedigree and turn it into a mitochondrial relatedness matrix
ped2mt	Take a pedigree and turn it into a mitochondrial relatedness matrix
ped2paternal	Add a paternal line ID variable to a pedigree
plotPedigree	plotPedigree A wrapped function to plot simulated pedigree from function 'simulatePedigree'. This function require the installation of package 'kinship2'.
potter	Fictional pedigree data on a wizarding family
relatedness	relatedness (Deprecated)
related_coef	related_coef (Deprecated)
repairIDs	Repair Missing IDs
repairSex	Repairs Sex Coding in a Pedigree Dataframe
resample	Resample Elements of a Vector
SimPed	SimPed (Deprecated)
simulatePedigree	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.
sizeAllGens	sizeAllGens An internal supporting function for 'simulatePedigree'.
vech	vech Create the half-vectorization of a matrix