getPotentialParents

Provides genetic tools for colony management and is a derivation
of the work in Amanda Vinson and Michael J Raboin (2015)
<https://pmc.ncbi.nlm.nih.gov/articles/PMC4671785/> "A Practical
Approach for Designing Breeding Groups to Maximize Genetic Diversity in a
Large Colony of Captive Rhesus Macaques ('Macaca' 'mulatto')".
It provides a 'Shiny' application with an exposed API.
The application supports five groups of functions:
(1) Quality control of studbooks contained in text files or 'Excel'
workbooks and of pedigrees within 'LabKey' Electronic Health Records
(EHR);
(2) Creation of pedigrees from a list of animals using the 'LabKey' EHR
integration;
(3) Creation and display of an age by sex pyramid plot of the living
animals within the designated pedigree;
(4) Generation of genetic value analysis reports; and
(5) Creation of potential breeding groups with and without proscribed sex
ratios and defined maximum kinships.

R. Mark Sharp

nprcgenekeepr

Genetic Tools for Colony Management

Michael Raboin

Terry Therneau

Amanda Vinson

Matthew Schultz

Southwest National Primate Research Center NIH grant P51 RR13986 

Oregon National Primate Research Center grant P51 OD011092 

getPotentialParents function

<dl><dt>ped</dt>
<dd>the pedigree information in data.frame format. Pedigree
(req. fields: id, sire, dam, gen, population).
This requires complete pedigree information.</dd>
<dt>minParentAge</dt>
<dd>numeric values to set the minimum age in years for
an animal to have an offspring. Defaults to 2 years. The check is not
performed for animals with missing birth dates.</dd>
<dt>maxGestationalPeriod</dt>
<dd>integer value describing the days between
conception and birth. This will be used to prevent the removal of sires
who exit the colony between date of conception and birth. Need to decide
where this will come from.</dd></dl>

Arguments

Get the lists of portential parents for all individuals born in the colony
with one or two unknown parents. — getPotentialParents

<dl>

<dt>ped</dt>
<dd>the pedigree information in data.frame format. Pedigree
(req. fields: id, sire, dam, gen, population).
This requires complete pedigree information.</dd>


<dt>minParentAge</dt>
<dd>numeric values to set the minimum age in years for
an animal to have an offspring. Defaults to 2 years. The check is not
performed for animals with missing birth dates.</dd>


<dt>maxGestationalPeriod</dt>
<dd>integer value describing the days between
conception and birth. This will be used to prevent the removal of sires
who exit the colony between date of conception and birth. Need to decide
where this will come from.</dd>

</dl>

getPotentialParents: Get the lists of portential parents for all individuals born in the colony with one or two unknown parents.

Description

Usage

Value

Arguments