Package index • BGmisc

All functions

addParentRow(): Create a properly formatted parent row for the pedigree

addPersonToPed(): addPersonToPed

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

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

makeTwins(): makeTwins

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