Package: nprcgenekeepr
Type: Package
Title: Genetic Tools for Colony Management
Version: 1.0.7
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' '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.
URL: https://rmsharp.github.io/nprcgenekeepr/,
        https://github.com/rmsharp/nprcgenekeepr
BugReports: https://github.com/rmsharp/nprcgenekeepr/issues
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
Language: en-US
Encoding: UTF-8
License: MIT + file LICENSE
RoxygenNote: 7.3.2
LazyData: TRUE
VignetteBuilder: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2025-04-22 19:08:14 UTC; rmsharp
Author: Michael Raboin [aut],
  Terry Therneau [aut],
  Amanda Vinson [aut, dtc],
  R. Mark Sharp [aut, cre, cph, dtc]
    (<https://orcid.org/0000-0002-6170-6942>),
  Matthew Schultz [aut] (<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: 2025-04-24 17:20:05 UTC
Built: R 4.3.3; ; 2025-04-24 18:22:59 UTC; unix
