appUI

Main Application UI for nprcgenekeepr

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 

appUI function

<dl><dt>siteInfo</dt>
<dd>Named list of site configuration as returned by
<code>getSiteInfo</code>; defaults to <code>NULL</code>, in which case it is
resolved internally via <code>getSiteInfo(expectConfigFile = FALSE)</code>. A
present-but-malformed site-config file makes that call fail; the failure
is caught and logged (<code>futile.logger::flog.warn</code>) rather than
propagating, and the UI falls back to hiding the ORIP Reporting tab. Its
<code>center</code> and <code>configFile</code> elements gate the Oregon
(ONPRC)-specific ORIP Reporting tab, which is shown only for an actual
ONPRC configuration (see <code>shouldShowOripTab</code>).</dd></dl>

Arguments

Main Application UI for nprcgenekeepr — appUI

<dl>

<dt>siteInfo</dt>
<dd>Named list of site configuration as returned by
<code>getSiteInfo</code>; defaults to <code>NULL</code>, in which case it is
resolved internally via <code>getSiteInfo(expectConfigFile = FALSE)</code>. A
present-but-malformed site-config file makes that call fail; the failure
is caught and logged (<code>futile.logger::flog.warn</code>) rather than
propagating, and the UI falls back to hiding the ORIP Reporting tab. Its
<code>center</code> and <code>configFile</code> elements gate the Oregon
(ONPRC)-specific ORIP Reporting tab, which is shown only for an actual
ONPRC configuration (see <code>shouldShowOripTab</code>).</dd>

</dl>

appUI: Main Application UI for nprcgenekeepr

Description

Usage

Value

Arguments