qcPed

<dl>
<dt>id</dt>
<dd>character column of animal IDs</dd><dt>sire</dt>
<dd>the male parent of the animal indicated by the <code>id</code> column.</dd><dt>dam</dt>
<dd>the female parent of the animal indicated by the <code>id</code>
column.</dd><dt>sex</dt>
<dd>sex of the animal indicated by the <code>id</code> column.</dd><dt>gen</dt>
<dd>generation number (integers beginning with 0 for the founder
generation) of the animal indicated by the <code>id</code> column.</dd><dt>birth</dt>
<dd>birth date in <code>Date</code> format of the animal indicated by the
<code>id</code> column.</dd><dt>exit</dt>
<dd>exit date in <code>Date</code> format of the animal indicated by the
<code>id</code> column.</dd><dt>age</dt>
<dd>age in year (numeric) of the animal indicated by the <code>id</code>
column.</dd>
</dl>

datasets

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 

qcPed function

An object of class <code>data.frame</code> with 280 rows and 8 columns.

Format

<dl>
<dt>id</dt>
<dd>character column of animal IDs</dd>

<dt>sire</dt>
<dd>the male parent of the animal indicated by the <code>id</code> column.</dd>

<dt>dam</dt>
<dd>the female parent of the animal indicated by the <code>id</code>
column.</dd>

<dt>sex</dt>
<dd>sex of the animal indicated by the <code>id</code> column.</dd>

<dt>gen</dt>
<dd>generation number (integers beginning with 0 for the founder
generation) of the animal indicated by the <code>id</code> column.</dd>

<dt>birth</dt>
<dd>birth date in <code>Date</code> format of the animal indicated by the
<code>id</code> column.</dd>

<dt>exit</dt>
<dd>exit date in <code>Date</code> format of the animal indicated by the
<code>id</code> column.</dd>

<dt>age</dt>
<dd>age in year (numeric) of the animal indicated by the <code>id</code>
column.</dd>


</dl>

qcPed: qcPed is a dataframe with 277 rows and 6 columns

Description

Usage

Arguments

Format