Man pages for BGmisc
An R Package for Extended Behavior Genetics Analysis
| addParentRow | Create a properly formatted parent row for the pedigree |
| addPersonToPed | addPersonToTree A function to add a new person to an existing... |
| addRowlessParents | Add addRowlessParents |
| adjustKidsPerCouple | Generate or Adjust Number of Kids per Couple Based on Mating... |
| applyTagMappings | Apply Tag Mappings to a Line |
| ASOIAF | A pedigree of ice and fire |
| assignCoupleIDs | Assign Couple IDs |
| BGmisc-package | BGmisc: An R Package for Extended Behavior Genetics Analysis |
| buildBetweenGenerations | Process Generation Connections |
| buildTreeGrid | Parse Tree |
| buildWithinGenerations | Process Generations for Pedigree Simulation |
| calcAllGens | calcAllGens A function to calculate the number of individuals... |
| calcFamilySize | calcFamilySize A function to calculate the total number of... |
| calcFamilySizeByGen | calcFamilySizeByGen An internal supporting function for... |
| calculateCIs | Calculate Confidence Intervals for Correlation Coefficients |
| calculateH | Falconer's Formula |
| calculateRelatedness | Calculate Relatedness Coefficient |
| calculateSummaryDT | Function to calculate summary statistics for all numeric... |
| checkIDs | Validates and Optionally Repairs Unique IDs in a Pedigree... |
| checkIDuniqueness | Check for duplicated individual IDs |
| checkParentIDs | Validates and Optionally Repairs Parent IDs in a Pedigree... |
| checkParentSex | Check Parental Role Sex Consistency |
| checkPedigreeNetwork | Validate Pedigree Network Structure |
| checkSex | Validates and Optionally Repairs Sex Coding in a Pedigree... |
| checkWithinRowDuplicates | Check for within-row duplicates (self-parents, same mom/dad) |
| collapseNames | collapse Names |
| com2links | Convert Sparse Relationship Matrices to Kinship Links |
| combine_columns | Combine Columns |
| comp2vech | comp2vech Turn a variance component relatedness matrix into... |
| computeParentAdjacency | Compute Parent Adjacency Matrix with Multiple Approaches |
| convertGrid2LongTree | Make Long Tree |
| countPatternRows | Count GEDCOM Pattern Rows |
| createGenDataFrame | Create Data Frame for Generation |
| deduplicatePairs | Deduplicate pairs of IDs in a data frame |
| determineSex | Determine Sex of Offspring |
| dot-assignParentValue | Assign parent values based on component type |
| dot-collapseNames.legacy | collapse Names |
| dot-com2links.legacy | Convert Sparse Relationship Matrices to Kinship Links |
| dot-com2links.og | Convert Pedigree Matrices to Related Pairs File (Legacy) |
| dot-combine_columns.legacy | Combine Columns |
| dot-computeTranspose | Compute the transpose multiplication for the relatedness... |
| dot-countPatternRows.legacy | Check for Pattern Rows |
| dot-extract_info.legacy | Extract Information from Line |
| dot-fisherz | Fisher's r to z transformation and back |
| dot-fisherz2r | Fisher's r to z transformation and back |
| dot-getModalValue | Get the Modal Value of a Vector |
| dot-loadOrComputeInverseDiagonal | Load or compute the inverse diagonal matrix |
| dot-loadOrComputeIsChild | Load or compute the isChild matrix |
| dot-loadOrComputeIsPar | Load or compute the isPar matrix |
| dot-loadOrComputeParList | parent-child adjacency data |
| dot-mapFAMC2parents.legacy | Assign momID and dadID based on family mapping |
| dot-mapFAMS2parents.legacy | Create a mapping of family IDs to parent IDs |
| dot-postProcessGedcom.legacy | Post-process GEDCOM Data Frame |
| dot-processParents.legacy | Process parents information |
| dot-process_tag.legacy | Process a GEDCOM Tag |
| dot-readGedcom.legacy | Read a GEDCOM File |
| dropLink | dropLink A function to drop a person from his/her parents in... |
| efunc | Error Function |
| extract_info | Extract Information from Line |
| extractMemberTable | Match Members |
| findBiggest | This function finds the biggest families in a pedigree. It is... |
| findFounder | Function to find the originating member for each line |
| findOldest | This function finds the oldest families in a pedigree. It is... |
| fitComponentModel | fitComponentModel Fit the estimated variance components of a... |
| getGridNeighbors | Build adjacency list (4-way neighbors) |
| getWikiTreeSummary | Extract Summary Text |
| hazard | Simulated pedigree with two extended families and an... |
| identifyComponentModel | identifyComponentModel Determine if a variance components... |
| inbreeding | Artificial pedigree data on eight families with inbreeding |
| inferRelatedness | Infer Relatedness Coefficient |
| initializeCheckpoint | Initialize checkpoint files |
| initialize_empty_df | initialize_empty_df |
| initializeRecord | Initialize an Empty Individual Record |
| insertEven | evenInsert A function to insert m elements evenly into a... |
| isChild | Determine isChild Status, isChild is the 'S' matrix from RAM |
| loadOrComputeCheckpoint | Load or compute a checkpoint |
| makeInbreeding | makeInbreeding A function to create inbred mates in the... |
| makeTwins | makeTwins A function to impute twins in the simulated... |
| mapFAMC2parents | Assign momID and dadID based on family mapping |
| mapFAMS2parents | Create a Mapping from Family IDs to Parent IDs |
| markPotentialChildren | Mark and Assign children |
| Null | Compute the null space of a matrix |
| null2NA | nullToNA |
| parseIndividualBlock | Parse a GEDCOM Individual Block |
| parseNameLine | Parse a Full Name Line |
| parseTreeRelationships | infer relationship from tree template |
| ped2add | Take a pedigree and turn it into an additive genetics... |
| ped2ce | Take a pedigree and turn it into an extended environmental... |
| ped2cn | Take a pedigree and turn it into a common nuclear... |
| 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... |
| ped2paternal | Add a paternal line ID variable to a pedigree |
| populateParents | Assign Parent |
| postProcessGedcom | Post-process GEDCOM Data Frame |
| potter | Fictional pedigree data on a wizarding family |
| processEventLine | Process Event Lines (Birth or Death) |
| process_one | Convert Sparse Relationship Matrices to Kinship Links for one... |
| processParents | Process Parents Information from GEDCOM Data |
| process_tag | Process a GEDCOM Tag |
| 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 |
| resample | Resample Elements of a Vector |
| rmvn | rmvn |
| royal92 | Royal pedigree data from 1992 |
| simulatePedigree | Simulate Pedigrees This function simulates "balanced"... |
| splitIndividuals | Split GEDCOM Lines into Individual Blocks |
| standardizeColnames | Standardize Column Names in a Dataframe (Internal) |
| summarizeFamilies | Summarize the families in a pedigree |
| summarizeFounder | Function to summarize the originating members for each line |
| 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 |
| tryNA | modified tryCatch function |
| validate_and_convert_matrix | validate_and_convert_matrix |
| vech | vech Create the half-vectorization of a matrix |
