View source: R/Sequoia_F90wrappers.R
SeqParSib | R Documentation |
Call main Fortran part of sequoia, and convert its output to a list with dataframes.
SeqParSib(
ParSib,
FortPARAM,
GenoM,
LhIN,
AgePriors,
Parents,
mtDif,
DumPfx,
quiet
)
ParSib |
either "par" to call parentage assignment, or "sib" to call the rest of the algorithm. |
FortPARAM |
a named vector with parameter values, as generated by
|
GenoM |
matrix with genotype data, size nInd x nSnp. |
LhIN |
life history data: ID - sex - birth year. |
AgePriors |
matrix with agepriors, size 'FortPARAM["nAgeClasses"]' by 8. |
Parents |
matrix with rownumbers of assigned parents, size nInd by 2. |
mtDif |
matrix indicating whether individuals have definitely a different mitochondrial haplotype (1), or (possibly) the same (0). Size nInd x nInd. |
DumPfx |
dummy prefixes |
quiet |
suppress messages. |
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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