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://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.
| Version: | 1.0.7 |
| Depends: | R (≥ 3.6.0) |
| Imports: | anytime, data.table, futile.logger, htmlTable, lifecycle, lubridate, Matrix, plotrix, readxl, Rlabkey, sessioninfo, shiny, stringi, utils, WriteXLS |
| Suggests: | covr, dplyr, ggplot2, grid, kableExtra, knitr, markdown, pkgdown, png, rmarkdown, roxygen2 (≥ 7.3.2), shinyBS, shinyWidgets, spelling, testthat |
| Published: | 2025-04-24 |
| DOI: | 10.32614/CRAN.package.nprcgenekeepr |
| Author: | 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 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 (source, R code) Interactive Use of nprcgenekeepr (source) Simulated Kinships with Partial Parentage (source) |
Downloads:
| Package source: | nprcgenekeepr_1.0.7.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): nprcgenekeepr_1.0.7.tgz, r-oldrel (arm64): nprcgenekeepr_1.0.7.tgz, r-release (x86_64): nprcgenekeepr_1.0.7.tgz, r-oldrel (x86_64): nprcgenekeepr_1.0.7.tgz |
| Old sources: | nprcgenekeepr archive |
Linking:
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