CalcBYprobs | Birth year probabilities |
CalcCorners | Corner coordinates |
CalcMaxMismatch | Maximum Number of Mismatches |
CalcOHLLR | Calculate OH and LLR for a pedigree |
CalcPairLL | Calculate Likelihoods for Alternative Relationships |
CalcRped | Calculate Pedigree Relatedness |
CheckAP | check AgePrior |
CheckGeno | Check Genotype Matrix |
CheckLH | Check LifeHistData |
CheckParams | Check if input parameters are valid |
ComparePairs | Compare Pairwise Relationships |
Conf_griffin | Example output from estimating confidence probabilities:... |
CountAgeDif | Tabulate Age Differences |
DoErrors | Fortran Simulate Genotyping Errors |
DuplicateCheck | Check Data for Duplicates. |
DyadCompare | Compare Dyads (DEPRECATED) |
ErrToM | Generate Genotyping Error Matrix |
EstConf | Confidence Probabilities |
EstEr | Estimate genotyping error rate (REMOVED; will be... |
FieldMums_griffin | Example field-observed mothers: griffins |
FindFamilies | Assign Family IDs |
FoldSibGPs | Fold IDs of Sibship Grandparents |
FortifyPairs | Make Pairs Fortran Compatible |
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 |
GetDummifiable | Dummifiable IDs |
getGenerations | Count Generations |
GetLLRAge | LLR-age from Ageprior Matrix |
GetMaybeRel | Find Putative Relatives |
GetRelA | Array with Pairwise Relationships |
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' |
LLRplot | Scatter Plot of Pair LLRs |
MakeAgePrior | Age Priors |
MaybeRel_griffin | Example output from check for relatives: griffins |
MergeFill | Special Merge |
MkAPdefault | Make default 1/0 ageprior |
MkFortParams | PARAM to FortPARAM |
MkGenoErrors | Simulate Genotyping Errors |
mtSame2Dif | Check and recode mtSame matrix |
NumToID | Change Numeric Pedigree back to Character Pedigree |
OHperSNP | Estimate Genotyping Error Rate |
orderLH | Order Lifehistory Data |
ParamToSpecs | PARAM to Specs |
PedCompare | Compare Two Pedigrees |
Ped_griffin | Example pedigree: griffins |
Ped_HSg5 | Example pedigree: 'HSg5' |
PedPolish | Fix Pedigree |
PedStripFID | Back-transform IDs |
PedToNum | Turn Character Pedigree into Numeric Pedigree |
PlotAgePrior | Plot Age Priors |
PlotPairLL | Plot Pair Log10-Likelihoods |
PlotPedComp | Visualise PedCompare Output |
PlotRelPairs | Plot Pairwise Relationships |
PlotSeqSum | Plot Summary Overview of sequoia Output |
PlotSnpStats | plot SnpStats results |
rc | Find siblings |
SelectNotSampled | select non-genotyped parents |
SeqOUT_griffin | Example output from pedigree inference: griffins |
SeqOUT_HSg5 | Example output from pedigree inference: 'HSg5' |
SeqParSib | Fortran Wrapper for Pedigree Reconstruction |
sequoia | Pedigree Reconstruction |
SibMatch | Find the closest matching inferred sibship to a true sibship |
SimGeno | Simulate Genotypes |
SimGeno_example | Example genotype file: 'HSg5' |
SmoothAP | Smooth out dips in ageprior matrix |
SnpStats | SNP Summary Statistics |
SpecsToParam | Specs to PARAM |
SummarySeq | Summarise Sequoia Output or Pedigree |
tryCatch.W.E | tryCatch both warnings (with value) and errors |
Vcomp | Compare two vectors |
VennSquares | Square Venn diagram |
writeColumns | Write Data to a File Column-wise |
writeSeq | Write Sequoia Output to File |
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