getSpeciesGestation

Maps each supplied species name to a conservative upper bound on the number
of days from conception to birth, using the <code>speciesGestation</code>
lookup table (or a supplied <code>gestationTable</code>). Matching is case- and
whitespace-insensitive. Any species that is missing, <code>NA</code>, an empty
string, or not present in the table falls back to <code>default</code> (210 days,
the conservative rhesus bound). Used by <code>getPotentialParents</code> to
key its gestation window on the first-class <code>species</code> pedigree column.

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 

getSpeciesGestation function

<dl><dt>species</dt>
<dd>character vector of species names (may contain <code>NA</code>).</dd>
<dt>gestationTable</dt>
<dd>optional data.frame with a character column
<code>species</code> and an integer column <code>gestation</code> to use instead of the
bundled <code>speciesGestation</code> table. Defaults to <code>NULL</code>, which
uses the bundled table.</dd>
<dt>default</dt>
<dd>integer fallback returned for species that are missing,
<code>NA</code>, empty, or not found in the table. Defaults to <code>210L</code>.</dd></dl>

Arguments

Look up the maximum gestation period (days) for one or more species — getSpeciesGestation

<dl>

<dt>species</dt>
<dd>character vector of species names (may contain <code>NA</code>).</dd>


<dt>gestationTable</dt>
<dd>optional data.frame with a character column
<code>species</code> and an integer column <code>gestation</code> to use instead of the
bundled <code>speciesGestation</code> table. Defaults to <code>NULL</code>, which
uses the bundled table.</dd>


<dt>default</dt>
<dd>integer fallback returned for species that are missing,
<code>NA</code>, empty, or not found in the table. Defaults to <code>210L</code>.</dd>

</dl>

getSpeciesGestation: Look up the maximum gestation period (days) for one or more species

Description

Usage

Value

Arguments

Examples