Package: nprcgenekeepr 2.0.0.9000

nprcgenekeepr: Genetic Tools for Colony Management

Provides genetic tools for colony management and implements 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 these main 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. Further tabs cover mate pair analysis, genetic diversity, marker genetics, potential parents, cross-center identity mapping, de-identified export, and genetic-health trends.

Authors:Michael Raboin [aut], Terry Therneau [aut], Amanda Vinson [aut, dtc], R. Mark Sharp [aut, cre, cph, dtc], Matthew Schultz [aut], Southwest National Primate Research Center [fnd], Oregon National Primate Research Center [fnd]