nprcgenekeepr-package {nprcgenekeepr}R Documentation

Genetic Management Functions

Description

Primary Data Structure — Pedigree

Contains studbook information for a number of individuals. ASSUME: All IDs listed in the sire or dam columns must have a row entry in the id column

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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.

Author(s)

Maintainer: R. Mark Sharp rmsharp@me.com (ORCID) [copyright holder, data contributor]

Authors:

Other contributors:

See Also

getIncludeColumns to get set of columns that can be used in a pedigree file

A Pedigree is a data frame within the R environment with the following possible columns:

Pedigree File Testing Functions

Gene Dropping Function

Genetic Value Analysis Functions

Contains functions to calculate the kinship coefficient and genome uniqueness for animals listed in a Pedigree table.

Plotting Functions

Breeding Group Formation Functions

Useful links:


[Package nprcgenekeepr version 1.0.7 Index]