Package: nprcgenekeepr
Type: Package
Title: Genetic Tools for Colony Management
Version: 2.0.0.9000
Authors@R: c(
    person("Michael", "Raboin", role = c("aut")),
    person("Terry", "Therneau", role = c("aut")),
    person("Amanda", "Vinson", role = c("aut", "dtc")),
    person("R. Mark", "Sharp", email = "rmsharp@me.com", 
    comment = c(ORCID = "0000-0002-6170-6942"), 
    role = c("aut", "cre", "cph", "dtc")),
    person("Matthew", "Schultz", role = c("aut"),
    comment = c(ORCID = "0000-0001-5103-4305")), 
    person("Southwest National Primate Research Center", role = "fnd",
    comment = "NIH grant P51 RR13986, work up to and including version 1.0"),
    person("Oregon National Primate Research Center", role = "fnd",
    comment = "NIH grant P51 OD011092, work up to and including version 1.0"))
Description: 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.
URL: https://rmsharp.github.io/nprcgenekeepr/,
        https://github.com/rmsharp/nprcgenekeepr
BugReports: https://github.com/rmsharp/nprcgenekeepr/issues
Depends: R (>= 4.1.0)
Imports: anytime, bslib, data.table, DT, futile.logger, ggplot2,
        htmlTable, lifecycle, lubridate, Matrix, openxlsx, plotrix,
        quadprog, readxl, Rlabkey (>= 3.2.0), sessioninfo, shiny,
        stringi, utils, visNetwork
Suggests: chromote, dplyr, shinytest2, htmltools, htmlwidgets,
        kableExtra, kinship2, knitr, markdown, mockery, pkgdown,
        rmarkdown, shinyBS, spelling, testthat, withr, yaml
Language: en-US
Encoding: UTF-8
License: MIT + file LICENSE
LazyData: TRUE
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Config/renv/profiles/dev/dependencies: checkhelper, devtools, httpuv,
        qpdf, markdown, pak, roxygen2, spelling, usethis
Config/Needs/website: quarto
Config/Needs/coverage: covr
Config/Needs/dev: devtools, roxygen2
Config/roxygen2/version: 8.0.0
Repository: https://rmsharp.r-universe.dev
Date/Publication: 2026-10-11 19:14:17 UTC
RemoteUrl: https://github.com/rmsharp/nprcgenekeepr
RemoteRef: HEAD
RemoteSha: 5a41dbbdd427e682bb403bd60ff06fb777ac981f
NeedsCompilation: no
Packaged: 2026-10-11 23:53:07 UTC; root
Author: Michael Raboin [aut],
  Terry Therneau [aut],
  Amanda Vinson [aut, dtc],
  R. Mark Sharp [aut, cre, cph, dtc] (ORCID:
    <https://orcid.org/0000-0002-6170-6942>),
  Matthew Schultz [aut] (ORCID: <https://orcid.org/0000-0001-5103-4305>),
  Southwest National Primate Research Center [fnd] (NIH grant P51
    RR13986, work up to and including version 1.0),
  Oregon National Primate Research Center [fnd] (NIH grant P51 OD011092,
    work up to and including version 1.0)
Maintainer: R. Mark Sharp <rmsharp@me.com>