# Pedigree Inference from SNPs

## Documentation for package ‘sequoia’ version 2.3.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

CalcBYprobs | Birth year probabilities
CalcMaxMismatch | Maximum Number of Mismatches
CalcOHLLR | Calculate OH and LLR
CalcPairLL | Calculate Likelihoods for Alternative Relationships
CalcRped | Calculate Pedigree Relatedness
CheckGeno | Check Genotype Matrix
ComparePairs | Compare Pairwise Relationships
DyadCompare | Compare Dyads
ErrToM | Generate Genotyping Error Matrix
EstConf | Confidence Probabilities
FieldMums_griffin | Example field-observed mothers: griffins
FindFamilies | Assign Family IDs
GenoConvert | Convert Genotype Data
getAssignCat | Assignability of Reference Pedigree
getGenerations | Count Generations
GetLLRAge | LLR-age from Ageprior Matrix
GetMaybeRel | Find Putative Relatives
GetRelM | Matrix with Pairwise Relationships
Inherit | Inheritance patterns
LHConvert | Extract Sex and Birth Year from PLINK File
LH_griffin | Example lifehistory data: griffins
LH_HSg5 | Example life history file
MakeAgePrior | Age Priors
MkGenoErrors | Simulate Genotyping Errors
PedCompare | Compare Two Pedigrees
PedPolish | Fix Pedigree
PedStripFID | Back-transform IDs
Ped_griffin | Example pedigree: griffins
Ped_HSg5 | Example pedigree
PlotAgePrior | Plot Age Priors
PlotPairLL | Plot Pair Log10-Likelihoods
PlotPedComp | Visualise PedCompare Output
PlotRelPairs | Plot Pairwise Relationships
SeqOUT_griffin | Example sequoia output (griffins)
sequoia | Pedigree Reconstruction
SimGeno | Simulate Genotypes
SimGeno_example | Example genotype file
SnpStats | SNP Summary Statistics
SummarySeq | Summarise Sequoia Output or Pedigree
tryCatch.W.E | tryCatch both warnings (with value) and errors
writeColumns | Write Data to a File Column-wise
writeSeq | Write Sequoia Output to File