getPyramidPlot

The pedigree provided must have the following columns: <code>sex</code> and
<code>age</code>. This needs to be augmented to allow pedigrees structures that
are provided by the nprcgenekeepr package.

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' 'mulatta')".
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 

getPyramidPlot function

<dl><dt>ped</dt>
<dd>The pedigree information in data.frame format</dd>
<dt>binWidth</dt>
<dd>numeric bin width for age groups (default 2).</dd>
<dt>ageUnit</dt>
<dd>character either "years" (default) or "months".</dd>
<dt>colorScheme</dt>
<dd>character color scheme: "default" (blue/pink) or
"viridis" (colorblind-friendly).</dd>
<dt>showCounts</dt>
<dd>logical whether to show count values on bars
(default TRUE).</dd>
<dt>ageLabelCex</dt>
<dd>numeric expansion factor for age labels (default 1.0).</dd></dl>

Arguments

Create an age-sex pyramid plot of a pedigree — getPyramidPlot

<dl>

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


<dt>binWidth</dt>
<dd>numeric bin width for age groups (default 2).</dd>


<dt>ageUnit</dt>
<dd>character either "years" (default) or "months".</dd>


<dt>colorScheme</dt>
<dd>character color scheme: "default" (blue/pink) or
"viridis" (colorblind-friendly).</dd>


<dt>showCounts</dt>
<dd>logical whether to show count values on bars
(default TRUE).</dd>


<dt>ageLabelCex</dt>
<dd>numeric expansion factor for age labels (default 1.0).</dd>

</dl>

getPyramidPlot: Create an age-sex pyramid plot of a pedigree

Description

Usage

Value

Arguments

Examples