nprcgenekeepr: 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) <https://www.ncbi.nlm.nih.gov/pmc/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.

Version: 1.0.5
Depends: R (≥ 3.6.0)
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 (≥ 7.0.0), shinyBS, shinyWidgets, testthat
Published: 2021-03-31
Author: Michael Raboin [aut], Terry Therneau [aut], Amanda Vinson [aut, dtc], R. Mark Sharp ORCID iD [aut, cre, cph, dtc], Southwest National Primate Research Center NIH grant P51 RR13986 [fnd], Oregon National Primate Research Center grant P51 OD011092 [fnd]
Maintainer: R. Mark Sharp <rmsharp at me.com>
BugReports: https://github.com/rmsharp/nprcgenekeepr/issues
License: MIT + file LICENSE
URL: https://rmsharp.github.io/nprcgenekeepr/, https://github.com/rmsharp/nprcgenekeepr
NeedsCompilation: no
Language: en-US
Materials: README NEWS
CRAN checks: nprcgenekeepr results

Documentation:

Reference manual: nprcgenekeepr.pdf
Vignettes: Genetic Management Tools Manual
Interactive Use of nprcgenekeepr

Downloads:

Package source: nprcgenekeepr_1.0.5.tar.gz
Windows binaries: r-devel: nprcgenekeepr_1.0.5.zip, r-release: nprcgenekeepr_1.0.5.zip, r-oldrel: nprcgenekeepr_1.0.5.zip
macOS binaries: r-release (arm64): nprcgenekeepr_1.0.5.tgz, r-release (x86_64): nprcgenekeepr_1.0.5.tgz, r-oldrel: nprcgenekeepr_1.0.5.tgz
Old sources: nprcgenekeepr archive

Linking:

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