Fortran Wrapper for Pedigree Reconstruction
Call main Fortran part of sequoia, and convert its output to a list with dataframes.
SeqParSib(ParSib, FortPARAM, GenoM, LhIN, AgePriors, Parents, DumPfx, quiet)
ParSib |
either "par" to call parentage assignment, or "sib" to call the rest of the algorithm. |
GenoM |
matrix with genotype data, size nInd x nSnp. |
LhIN |
life history data: ID - sex - birth year. |
AgePriors |
matrix with agepriors, size Specs["nAgeClasses"] by 8. |
Parents |
matrix with rownumbers of assigned parents, size nInd by 2. |
quiet |
suppress messages. |
Specs |
a named vector with parameter values, as generated by
|
ErrM |
3x3 matrix with genotyping error probabilities; rows=actual, columns=observed. |
A list with
PedigreePar or Pedigree |
the pedigree |
DummyIDs |
Info on dummies (not included if parentage-only) |
TotLikParents or TotLikSib |
Total log-likelihood per iteration |
AgePriorExtra |
Ageprior including columns for grandparental and avuncular relationships |
LifeHistPar or LifeHistSib |
Includes sex and birthyear estimate inferred from the pedigree for individuals with initially unknown sex and/or birthyear |
.
For a detailed description of the output see sequoia.
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