Package: nprcgenekeepr
Type: Package
Title: Genetic Tools for Colony Management
Version: 2.0.0
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 NIH grant P51 RR13986", 
    role = "fnd"),
    person("Oregon National Primate Research Center grant P51 OD011092",
    role = "fnd"))
Description: 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' 'mulatta')".
    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.
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,
        readxl, Rlabkey (>= 3.2.0), sessioninfo, shiny, stringi, utils
Suggests: covr, dplyr, grid, shinytest2, kableExtra, knitr, markdown,
        mockery, pkgdown, png, rmarkdown, roxygen2 (>= 8.0.0), shinyBS,
        shinyWidgets, spelling, testthat, withr
Language: en-US
Encoding: UTF-8
License: MIT + file LICENSE
LazyData: TRUE
VignetteBuilder: knitr
Config/renv/profiles/dev/dependencies: checkhelper, devtools, httpuv,
        qpdf, markdown, pak, roxygen2, spelling, usethis
Config/Needs/website: quarto
Config/roxygen2/version: 8.0.0
NeedsCompilation: no
Packaged: 2026-07-17 14:50:56 UTC; rmsharp
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 NIH grant P51 RR13986 [fnd],
  Oregon National Primate Research Center grant P51 OD011092 [fnd]
Maintainer: R. Mark Sharp <rmsharp@me.com>
Repository: CRAN
Date/Publication: 2026-07-26 10:50:02 UTC
Built: R 4.5.3; ; 2026-08-05 13:49:45 UTC; windows
