| .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 |
| addParentRow |
Create a properly formatted parent row for the pedigree |
| addRowlessParents |
Add addRowlessParents |
| adjustKidsPerCouple |
Generate or Adjust Number of Kids per Couple Based on Mating Rate |
| 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 |
| ASOIAF |
A song of ice and fire pedigree data |
| assignCoupleIDs |
Assign Couple IDs |
| assignCoupleIds |
Assign Couple IDs |
| buildBetweenGenerations |
Process Generation Connections |
| buildWithinGenerations |
Process Generations for Pedigree Simulation |
| 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 |
| 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 |
calcFamilySize A function to calculate the total number of individuals in a pedigree given parameters. This is a supporting function for function 'simulatePedigree' |
| findBiggest |
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. |
| 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 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 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'. |
| postProcessGedcom |
Post-process GEDCOM Data Frame |
| potter |
Fictional pedigree data on a wizarding family |
| processEventLine |
Process Event Lines (Birth or Death) |
| processParents |
Process Parents Information from GEDCOM Data |
| 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 |
| resample |
Resample Elements of a Vector |
| royal92 |
Royal pedigree data from 1992 |
| 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'. |
| splitIndividuals |
Split GEDCOM Lines into Individual Blocks |
| standardizeColnames |
Standardize Column Names in a Dataframe (Internal) |
| summariseFamilies |
Summarize the families in a pedigree |
| summariseMatrilines |
Summarize the maternal lines in a pedigree |
| summarisePatrilines |
Summarize the paternal lines in a pedigree |
| summarisePedigrees |
Summarize Pedigree Data |
| 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 |
| 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 |
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