Package index • BGmisc

All functions

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

applyTagMappings(): Apply Tag Mappings to a Line

buildBetweenGenerations(): Process Generation Connections

buildWithinGenerations(): Process Generations for Pedigree Simulation

calcAllGens() allGens(): calcAllGens A function to calculate the number of individuals in each generation. This is a supporting function for simulatePedigree.

calcFamilySize() famSizeCal(): calcFamilySize A function to calculate the total number of individuals in a pedigree given parameters. This is a supporting function for function simulatePedigree

calcFamilySizeByGen() sizeAllGens(): calcFamilySizeByGen An internal supporting function for simulatePedigree.

calculateCIs(): Calculate Confidence Intervals for Correlation Coefficients

calculateH(): Falconer's Formula

calculateRelatedness() related_coef(): 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

determineSex(): Determine Sex of Offspring

.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

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.

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(): 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.

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

initializeRecord(): Initialize an Empty Individual Record

insertEven() evenInsert(): evenInsert A function to insert m elements evenly into a length n vector.

isChild(): Determine isChild Status, isChild is the 'S' matrix from RAM

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

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

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

readGedcom() readGed() readgedcom(): Read a GEDCOM File

readWikifamilytree(): Read Wiki Family Tree

recodeSex(): Recodes Sex Variable in a Pedigree Dataframe

repairIDs(): Repair Missing IDs

repairParentIDs(): Repair Parent IDs

repairSex(): Repairs Sex Coding in a Pedigree Dataframe

royal92: Royal pedigree data from 1992

simulatePedigree() 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.

sliceFamilies(): sliceFamilies

splitIndividuals(): Split GEDCOM Lines into Individual Blocks

standardizeColnames(): Standardize Column Names in a Dataframe (Internal)

summarizeFamilies() summariseFamilies(): Summarize the families in a pedigree

summarizeMatrilines() summariseMatrilines(): Summarize the maternal lines in a pedigree

summarizePatrilines() summarisePatrilines(): Summarize the paternal lines in a pedigree

summarizePedigrees() summarisePedigrees(): Summarize Pedigree Data

traceTreePaths(): Trace paths between individuals in a family tree grid

validate_and_convert_matrix(): validate_and_convert_matrix

vech(): vech Create the half-vectorization of a matrix