makeGroupMembers

Convenience function to make the initial groupMembers animal list

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 

makeGroupMembers function

<dl><dt>numGp</dt>
<dd>integer value indicating the number of groups that should be
formed from the list of IDs. Default is 1.</dd>
<dt>currentGroups</dt>
<dd>list of character vectors of IDs of animals currently
assigned to the group. Defaults to character(0) assuming no groups are
existent.</dd>
<dt>candidates</dt>
<dd>character vector of IDs of the animals available for
use in the group.</dd>
<dt>ped</dt>
<dd>dataframe that is the <code>Pedigree</code>. It contains pedigree
information including the IDs listed in <code>candidates</code>.</dd>
<dt>harem</dt>
<dd>logical variable when set to <code>TRUE</code>, the formed groups
have a single male at least <code>minAge</code> old.</dd>
<dt>minAge</dt>
<dd>integer value indicating the minimum age to consider in group
formation. Pairwise kinships involving an animal of this age or younger will
be ignored. Default is 1 year.</dd></dl>

Arguments

Convenience function to make the initial groupMembers animal list — makeGroupMembers

<dl>

<dt>numGp</dt>
<dd>integer value indicating the number of groups that should be
formed from the list of IDs. Default is 1.</dd>


<dt>currentGroups</dt>
<dd>list of character vectors of IDs of animals currently
assigned to the group. Defaults to character(0) assuming no groups are
existent.</dd>


<dt>candidates</dt>
<dd>character vector of IDs of the animals available for
use in the group.</dd>


<dt>ped</dt>
<dd>dataframe that is the <code>Pedigree</code>. It contains pedigree
information including the IDs listed in <code>candidates</code>.</dd>


<dt>harem</dt>
<dd>logical variable when set to <code>TRUE</code>, the formed groups
have a single male at least <code>minAge</code> old.</dd>


<dt>minAge</dt>
<dd>integer value indicating the minimum age to consider in group
formation. Pairwise kinships involving an animal of this age or younger will
be ignored. Default is 1 year.</dd>

</dl>

makeGroupMembers: Convenience function to make the initial groupMembers animal list

Description

Usage

Value

Arguments