getSpeciesMinBreedingAge

Maps each supplied (species, sex) pair to the minimum age in years at which
an animal of that species and sex can produce offspring, using the
<code>speciesGestation</code> lookup table (or a supplied
<code>breedingTable</code>). Matching is case- and whitespace-insensitive on both
species and sex. Any species that is missing, <code>NA</code>, an empty string, or
not present in the table -- and any sex that is not <code>"M"</code> or <code>"F"</code>
-- falls back to <code>default</code> (2 years, the legacy package-wide minimum
parent age). Used by the Genetic Value Analysis unknown-parent mean-kinship
correction to form a focal animal's contemporaneous breeding-age peer
cohort. The bundled table is populated for the common colony NHP species;
the user-configurable override path is a separate feature.

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 

getSpeciesMinBreedingAge function

<dl><dt>species</dt>
<dd>character vector of species names (may contain <code>NA</code>).</dd>
<dt>sex</dt>
<dd>character vector of sexes (<code>"M"</code> or <code>"F"</code>); recycled to
the length of <code>species</code> (or vice versa).</dd>
<dt>breedingTable</dt>
<dd>optional data.frame with a character column
<code>species</code> and numeric columns <code>minMaleBreedingAge</code> and
<code>minFemaleBreedingAge</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>numeric fallback returned for species that are missing,
<code>NA</code>, empty, or not found, and for a sex that is not
<code>"M"</code>/<code>"F"</code>. Defaults to <code>2</code>.</dd></dl>

Arguments

Look up the minimum breeding age (years) for one or more species and sexes — getSpeciesMinBreedingAge

<dl>

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


<dt>sex</dt>
<dd>character vector of sexes (<code>"M"</code> or <code>"F"</code>); recycled to
the length of <code>species</code> (or vice versa).</dd>


<dt>breedingTable</dt>
<dd>optional data.frame with a character column
<code>species</code> and numeric columns <code>minMaleBreedingAge</code> and
<code>minFemaleBreedingAge</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>numeric fallback returned for species that are missing,
<code>NA</code>, empty, or not found, and for a sex that is not
<code>"M"</code>/<code>"F"</code>. Defaults to <code>2</code>.</dd>

</dl>

getSpeciesMinBreedingAge: Look up the minimum breeding age (years) for one or more species and sexes

Description

Usage

Value

Arguments

Examples