createSimKinships

<code>createSimKinships</code> uses <code>makeSimPed</code> with the <code>ped</code> object
and the <code>allSimParents</code> object to create a set of kinship matrices to
be used in forming the Monte Carlo estimates for the kinship values.

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 

createSimKinships function

<dl><dt>ped</dt>
<dd>The pedigree information in data.frame format</dd>
<dt>allSimParents</dt>
<dd>list made up of lists where the internal list
has the offspring ID, <code>id</code>, a vector of representative sires
(<code>sires</code>), and a vector of representative dams (<code>dams</code>).</dd>
<dt>pop</dt>
<dd>Character vector with animal IDs to consider as the population of
interest. This allows you to provide a pedigree in <code>ped</code> that
has more animals than you want to use in the simulation by defining
<code>pop</code> with the subset of interest. The default is NULL.</dd>
<dt>n</dt>
<dd>integer value of the number of simulated pedigrees to generate.</dd>
<dt>verbose</dt>
<dd>logical vector of length one that indicates whether or not
to print out when an animal is missing a sire or a dam.</dd></dl>

Arguments

Makes a list object of kinship matrices from simulated pedigrees of possible
parents for animals with unknown parents — createSimKinships

<dl>

<dt>ped</dt>
<dd>The pedigree information in data.frame format</dd>


<dt>allSimParents</dt>
<dd>list made up of lists where the internal list
has the offspring ID, <code>id</code>, a vector of representative sires
(<code>sires</code>), and a vector of representative dams (<code>dams</code>).</dd>


<dt>pop</dt>
<dd>Character vector with animal IDs to consider as the population of
interest. This allows you to provide a pedigree in <code>ped</code> that
has more animals than you want to use in the simulation by defining
<code>pop</code> with the subset of interest. The default is NULL.</dd>


<dt>n</dt>
<dd>integer value of the number of simulated pedigrees to generate.</dd>


<dt>verbose</dt>
<dd>logical vector of length one that indicates whether or not
to print out when an animal is missing a sire or a dam.</dd>

</dl>

createSimKinships: Makes a list object of kinship matrices from simulated pedigrees of possible parents for animals with unknown parents

Description

Usage

Value

Arguments

Examples