obfuscatePed

User provides a pedigree object (<code>ped</code>), the number of characters to be
used for alias IDs (<code>size</code>), and the maximum number of days that the
birthdate can be shifted (<code>maxDelta</code>).

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 

obfuscatePed function

<dl><dt>ped</dt>
<dd>pedigree object</dd>
<dt>size</dt>
<dd>integer value indicating number of characters in alias IDs</dd>
<dt>maxDelta</dt>
<dd>integer value indicating maximum number of days that
the birthdate can be shifted</dd>
<dt>existingIds</dt>
<dd>character vector of existing aliases to avoid duplication.</dd>
<dt>map</dt>
<dd>logical if <code>TRUE</code> a list object is returned with the new
pedigree and a named character vector with the names being the original IDs
and the values being the new alias values. Defaults to <code>FALSE</code>.</dd></dl>

Arguments

obfuscatePed takes a pedigree object and creates aliases for all IDs and
adjusts all date within a specified amount. — obfuscatePed

<dl>

<dt>ped</dt>
<dd>pedigree object</dd>


<dt>size</dt>
<dd>integer value indicating number of characters in alias IDs</dd>


<dt>maxDelta</dt>
<dd>integer value indicating maximum number of days that
the birthdate can be shifted</dd>


<dt>existingIds</dt>
<dd>character vector of existing aliases to avoid duplication.</dd>


<dt>map</dt>
<dd>logical if <code>TRUE</code> a list object is returned with the new
pedigree and a named character vector with the names being the original IDs
and the values being the new alias values. Defaults to <code>FALSE</code>.</dd>

</dl>

obfuscatePed: obfuscatePed takes a pedigree object and creates aliases for all IDs and adjusts all date within a specified amount.

Description

Usage

Value

Arguments

Examples