SeqParSib: Fortran Wrapper for Pedigree Reconstruction

In sequoia: Pedigree Inference from SNPs

Fortran Wrapper for Pedigree Reconstruction

Description

Call main Fortran part of sequoia, and convert its output to a list with dataframes.

Usage

SeqParSib(
  ParSib,
  FortPARAM,
  GenoM,
  LhIN,
  AgePriors,
  Parents,
  mtDif,
  DumPfx,
  quiet
)

Arguments

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 ParamToSpecs.
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.

Value

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.

sequoia documentation built on Sept. 8, 2023, 5:29 p.m.