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 |