filterThreshold

Part of Group Formation
Filters kinship values less than the specified threshold from a long-format
table of 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 

filterThreshold function

<dl><dt>kin</dt>
<dd>a dataframe with columns <code>id1</code>, <code>id2</code>, and
<code>kinship</code>. This is the kinship data reformatted from a matrix,
to a long-format table.</dd>
<dt>threshold</dt>
<dd>numeric value representing the minimum kinship level to be
considered in group formation. Pairwise kinship below this level will be
ignored.</dd></dl>

Arguments

Filters kinship to remove rows with kinship values less than the specified
threshold — filterThreshold

<dl>

<dt>kin</dt>
<dd>a dataframe with columns <code>id1</code>, <code>id2</code>, and
<code>kinship</code>. This is the kinship data reformatted from a matrix,
to a long-format table.</dd>


<dt>threshold</dt>
<dd>numeric value representing the minimum kinship level to be
considered in group formation. Pairwise kinship below this level will be
ignored.</dd>

</dl>

filterThreshold: Filters kinship to remove rows with kinship values less than the specified threshold

Description

Usage

Value

Arguments

Examples