filterAge

a dataframe with columns <code>id1</code>, <code>id2</code>, and
<code>kinship</code>. This is the kinship data reformatted from a matrix,
to a long-format table.

dataframe of pedigree information including the IDs listed
in "candidates".

numeric value representing minimum years of age of
animals to retain.

minAge

Provides genetic tools for colony management and is a derivation
of the work in Amanda Vinson and Michael J Raboin (2015)
<https://www.ncbi.nlm.nih.gov/pmc/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

filterAge: Removes kinship values where an animal is less than the minAge

Description

Usage

Arguments