SeqParSib

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

internal

Multi-generational pedigree inference from incomplete data on
hundreds of SNPs, including parentage assignment and sibship clustering.
See Huisman (2017) (<DOI:10.1111/1755-0998.12665>) for more information.

Jisca Huisman

sequoia

Pedigree Inference from SNPs

SeqParSib function

<dl><dt>ParSib</dt>
<dd>either "par" to call parentage assignment, or "sib" to call the
rest of the algorithm.</dd>
<dt>GenoM</dt>
<dd>matrix with genotype data, size nInd x nSnp.</dd>
<dt>LhIN</dt>
<dd>life history data: ID - sex - birth year.</dd>
<dt>AgePriors</dt>
<dd>matrix with agepriors, size Specs["nAgeClasses"] by 8.</dd>
<dt>Parents</dt>
<dd>matrix with rownumbers of assigned parents, size nInd by 2.</dd>
<dt>quiet</dt>
<dd>suppress messages.</dd>
<dt>Specs</dt>
<dd>a named vector with parameter values, as generated by
<code>ParamToSpecs</code>.</dd>
<dt>ErrM</dt>
<dd>3x3 matrix with genotyping error probabilities; rows=actual,
columns=observed.</dd></dl>

Arguments

Fortran Wrapper for Pedigree Reconstruction — SeqParSib

<dl>

<dt>ParSib</dt>
<dd>either "par" to call parentage assignment, or "sib" to call the
rest of the algorithm.</dd>


<dt>GenoM</dt>
<dd>matrix with genotype data, size nInd x nSnp.</dd>


<dt>LhIN</dt>
<dd>life history data: ID - sex - birth year.</dd>


<dt>AgePriors</dt>
<dd>matrix with agepriors, size Specs["nAgeClasses"] by 8.</dd>


<dt>Parents</dt>
<dd>matrix with rownumbers of assigned parents, size nInd by 2.</dd>


<dt>quiet</dt>
<dd>suppress messages.</dd>


<dt>Specs</dt>
<dd>a named vector with parameter values, as generated by
<code>ParamToSpecs</code>.</dd>


<dt>ErrM</dt>
<dd>3x3 matrix with genotyping error probabilities; rows=actual,
columns=observed.</dd>

</dl>

SeqParSib: Fortran Wrapper for Pedigree Reconstruction

Description

Usage

Value

Arguments