An R Package for Extended Behavior Genetics Analysis

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Documentation for package ‘BGmisc’ version 1.3.5

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.computeTranspose Compute the transpose multiplication for the relatedness matrix
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'.
ASOIAF A song of ice and fire pedigree data
assignCoupleIds Assign Couple IDs
buildBetweenGenerations Process Generation Connections
buildWithinGenerations Process Generations for Pedigree Simulation
calculateH Falconer's Formula
calculateRelatedness Calculate Relatedness Coefficient
checkIDs Validates and Optionally Repairs Unique IDs in a Pedigree Dataframe
checkPedigreeNetwork Validate Pedigree Network Structure
checkSex Validates and Optionally Repairs Sex Coding in a Pedigree Dataframe
com2links Convert Sparse Relationship Matrices to Kinship Links
comp2vech comp2vech Turn a variance component relatedness matrix into its half-vectorization
compute_parent_adjacency Compute Parent Adjacency Matrix with Multiple Approaches
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 Segment Pedigree into Extended Families
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
readGedcom Read a GEDCOM File
readWikifamilytree Read Wiki Family Tree
recodeSex Recodes Sex Variable in a Pedigree Dataframe
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
royal92 Royal pedigree data from 1992
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'.
summarizeFamilies Summarize the families in a pedigree
summarizeMatrilines Summarize the maternal lines in a pedigree
summarizePatrilines Summarize the paternal lines in a pedigree
summarizePedigrees Summarize Pedigree Data
vech vech Create the half-vectorization of a matrix