An R Package for Extended Behavior Genetics Analysis

Documentation for package ‘BGmisc’ version 1.5.0

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-- A --

addParentRow	Create a properly formatted parent row for the pedigree
addPersonToPed	addPersonToTree A function to add a new person to an existing pedigree 'data.frame'.
addRowlessParents	Add addRowlessParents
allGens	calcAllGens A function to calculate the number of individuals in each generation. This is a supporting function for 'simulatePedigree'.
applyTagMappings	Apply Tag Mappings to a Line

-- B --

buildBetweenGenerations	Process Generation Connections
buildWithinGenerations	Process Generations for Pedigree Simulation

-- C --

calcAllGens	calcAllGens A function to calculate the number of individuals in each generation. This is a supporting function for 'simulatePedigree'.
calcFamilySize	calcFamilySize A function to calculate the total number of individuals in a pedigree given parameters. This is a supporting function for function 'simulatePedigree'
calcFamilySizeByGen	calcFamilySizeByGen An internal supporting function for 'simulatePedigree'.
calculateCIs	Calculate Confidence Intervals for Correlation Coefficients
calculateH	Falconer's Formula
calculateRelatedness	Calculate Relatedness Coefficient
checkIDs	Validates and Optionally Repairs Unique IDs in a Pedigree Dataframe
checkIDuniqueness	Check for duplicated individual IDs
checkParentIDs	Validates and Optionally Repairs Parent IDs in a Pedigree Dataframe
checkParentSex	Check Parental Role Sex Consistency
checkPedigreeNetwork	Validate Pedigree Network Structure
checkSex	Validates and Optionally Repairs Sex Coding in a Pedigree Dataframe
checkWithinRowDuplicates	Check for within-row duplicates (self-parents, same mom/dad)
collapseNames	collapse Names
com2links	Convert Sparse Relationship Matrices to Kinship Links
comp2vech	comp2vech Turn a variance component relatedness matrix into its half-vectorization
computeParentAdjacency	Compute Parent Adjacency Matrix with Multiple Approaches
countPatternRows	Count GEDCOM Pattern Rows
createGenDataFrame	Create Data Frame for Generation

-- D --

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'.

-- E --

evenInsert

evenInsert A function to insert m elements evenly into a length n vector.

-- F --

famSizeCal	calcFamilySize A function to calculate the total number of individuals in a pedigree given parameters. This is a supporting function for function 'simulatePedigree'
findBiggest	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	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.
findOldest	This function finds the oldest families in a pedigree. It is supposed to be used internally by the 'summarize_pedigree' function.
findoldest	This function finds the oldest families in a pedigree. It is supposed to be used internally by the 'summarize_pedigree' function.
fitComponentModel	fitComponentModel Fit the estimated variance components of a model to covariance data

-- H --

hazard

Simulated pedigree with two extended families and an age-related hazard

-- I --

identifyComponentModel	identifyComponentModel Determine if a variance components model is identified
inbreeding	Artificial pedigree data on eight families with inbreeding
initializeRecord	Initialize an Empty Individual Record
insertEven	evenInsert A function to insert m elements evenly into a length n vector.
isChild	Determine isChild Status, isChild is the 'S' matrix from RAM

-- M --

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'.
mapFAMS2parents	Create a Mapping from Family IDs to Parent IDs
markPotentialChildren	Mark and Assign children

-- P --

parseNameLine	Parse a Full Name Line
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 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
postProcessGedcom	Post-process GEDCOM Data Frame
potter	Fictional pedigree data on a wizarding family
prepSummarizePedigrees	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.
processEventLine	Process Event Lines (Birth or Death)
processParents	Process Parents Information from GEDCOM Data

-- R --

readGed	Read a GEDCOM File
readGedcom	Read a GEDCOM File
readgedcom	Read a GEDCOM File
readWikifamilytree	Read Wiki Family Tree
recodeSex	Recodes Sex Variable in a Pedigree Dataframe
related_coef	Calculate Relatedness Coefficient
repairIDs	Repair Missing IDs
repairParentIDs	Repair Parent IDs
repairSex	Repairs Sex Coding in a Pedigree Dataframe
royal92	Royal pedigree data from 1992

-- S --

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	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	calcFamilySizeByGen An internal supporting function for 'simulatePedigree'.
sliceFamilies	sliceFamilies
splitIndividuals	Split GEDCOM Lines into Individual Blocks
standardizeColnames	Standardize Column Names in a Dataframe (Internal)
summariseFamilies	Summarize the families in a pedigree
summarisefamilies	Summarize the families in a pedigree
summariseMatrilines	Summarize the maternal lines in a pedigree
summarisematrilines	Summarize the maternal lines in a pedigree
summarisePatrilines	Summarize the paternal lines in a pedigree
summarisepatrilines	Summarize the paternal lines in a pedigree
summarisePedigrees	Summarize Pedigree Data
summarisepedigrees	Summarize Pedigree Data
summarizeFamilies	Summarize the families in a pedigree
summarizefamilies	Summarize the families in a pedigree
summarizeMatrilines	Summarize the maternal lines in a pedigree
summarizematrilines	Summarize the maternal lines in a pedigree
summarizePatrilines	Summarize the paternal lines in a pedigree
summarizepatrilines	Summarize the paternal lines in a pedigree
summarizePedigrees	Summarize Pedigree Data
summarizepedigrees	Summarize Pedigree Data

-- T --

traceTreePaths

Trace paths between individuals in a family tree grid

-- V --

validate_and_convert_matrix	validate_and_convert_matrix
vech	vech Create the half-vectorization of a matrix

-- misc --

.adjBeta	Construct Adjacency Matrix for Parent-Child Relationships Using Beta Method This function constructs an adjacency matrix for parent-child relationships using a beta method. It identifies parent-child pairs based on the specified component of relatedness.
.adjDirect	Construct Adjacency Matrix for Parent-Child Relationships Using Direct Method
.adjIndexed	Construct Adjacency Matrix for Parent-Child Relationships Using Indexed Method
.adjLoop	Construct Adjacency Matrix for Parent-Child Relationships
.assignParentValue	Assign parent values based on component type
.computeTranspose	Compute the transpose multiplication for the relatedness matrix
.loadOrComputeIsChild	Load or compute the isChild matrix
.postProcessGedcom.legacy	Post-process GEDCOM Data Frame