Genetic Tools for Colony Management

Provides genetic tools for colony management and is a derivation of the work in Amanda Vinson and Michael J Raboin (2015) <> "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.


Reference manual

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1.0.5 by R. Mark Sharp, 7 months ago,

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Authors: Michael Raboin [aut] , Terry Therneau [aut] , Amanda Vinson [aut, dtc] , R. Mark Sharp [aut, cre, cph, dtc] , Southwest National Primate Research Center NIH grant P51 RR13986 [fnd] , Oregon National Primate Research Center grant P51 OD011092 [fnd]

Documentation:   PDF Manual  

MIT + file LICENSE license

Imports anytime, futile.logger, htmlTable, lubridate, Matrix, plotrix, readxl, Rlabkey, rlang, shiny, stringi, utils, WriteXLS

Suggests covr, dplyr, ggplot2, grid, kableExtra, knitr, markdown, pkgdown, png, rmarkdown, roxygen2, shinyBS, shinyWidgets, testthat

See at CRAN