CalcBYprobs | Birth year probabilities |
CalcMaxMismatch | Maximum Number of Mismatches |
CalcOHLLR | Calculate OH and LLR for a pedigree |
CalcPairLL | Calculate Likelihoods for Alternative Relationships |
CalcRped | Calculate Pedigree Relatedness |
CheckGeno | Check Genotype Matrix |
ComparePairs | Compare Pairwise Relationships |
Conf_griffin | Example output from estimating confidence probabilities: griffins |
DyadCompare | Compare Dyads (DEPRECATED) |
ErrToM | Generate Genotyping Error Matrix |
EstConf | Confidence Probabilities |
EstEr | Estimate genotyping error rate (REMOVED; will be re-implemented) |
FieldMums_griffin | Example field-observed mothers: griffins |
FindFamilies | Assign Family IDs |
GenoConvert | Convert Genotype Data |
Geno_griffin | Example genotype file: Griffins |
Geno_HSg5 | Example genotype file: 'HSg5' |
GetAncestors | Get ancestors |
getAssignCat | Assignability of Reference Pedigree |
GetDescendants | Get descendants |
getGenerations | Count Generations |
GetLLRAge | LLR-age from Ageprior Matrix |
GetMaybeRel | Find Putative Relatives |
GetRelM | Matrix with Pairwise Relationships |
Inherit_patterns | Inheritance patterns |
LHConvert | Extract Sex and Birth Year from PLINK File |
LH_griffin | Example life history data: griffins |
LH_HSg5 | Example life history file: 'HSg5' |
MakeAgePrior | Age Priors |
MaybeRel_griffin | Example output from check for relatives: griffins |
MkGenoErrors | Simulate Genotyping Errors |
PedCompare | Compare Two Pedigrees |
PedPolish | Fix Pedigree |
PedStripFID | Back-transform IDs |
Ped_griffin | Example pedigree: griffins |
Ped_HSg5 | Example pedigree: 'HSg5' |
PlotAgePrior | Plot Age Priors |
PlotPairLL | Plot Pair Log10-Likelihoods |
PlotPedComp | Visualise PedCompare Output |
PlotRelPairs | Plot Pairwise Relationships |
PlotSeqSum | Plot Summary Overview of sequoia Output |
SeqOUT_griffin | Example output from pedigree inference: griffins |
SeqOUT_HSg5 | Example output from pedigree inference: 'HSg5' |
sequoia | Pedigree Reconstruction |
SimGeno | Simulate Genotypes |
SimGeno_example | Example genotype file: 'HSg5' |
SnpStats | SNP Summary Statistics |
SummarySeq | Summarise Sequoia Output or Pedigree |
writeColumns | Write Data to a File Column-wise |
writeSeq | Write Sequoia Output to File |