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Changelog

Source: NEWS.md

nprcgenekeepr 1.0.6 (20241215)

  • Minor changes
    • Update version in preparation for CRAN submission
    • Added article demonstrating Simulated Kinships with Partial Parentage
    • Added use of CICD pipeline as GitHub Actions
      • lintr pipeline
      • R CMD check pipeline with multiple R environments and versions
      • pkgdown pipeline
    • Added several unit tests
    • Cleaned up code based on lintr feedback
    • Added example deidentified pedigree data 2022-05-02_Deidentified_Pedigree.xlsx, 2022-05-02_Deidentified_Pedigree_focal_animals.csv, deidentified_jmac_ped.csv (text, except for dates, are in double quotes), deidentified_jmac_ped_edited.csv (edited to remove double quotes).
    • Made getVersion() more robust.
    • Abstracted out removal of auto generated Ids in preparation of allowing the user to define how auto generated Ids will be formed.
    • Added some quality assurance badges to README.
    • Added CRAN status badge to README.
    • Added Rhub.yaml file for checking on Rhub.

nprcgenekeepr 1.0.5.9004 (20221213)

  • Minor changes
    • Changed method used to test class of object to use inherits().
    • Corrected getPedDirectRelative() so that all direct relatives are found. Supplemented unit tests for more direct relative types.
    • Added unit tests for trimPedigree().
    • Changed call as.character(date_object) to format(date_object) in getDatedFileName.R to prepare for newer code in development version of
    • Technical edits of R code based on lintr::lint_dir(“R”)

nprcgenekeepr 1.0.5.9003 (20220625)

  • Minor changes
    • Removed dependency on gdata.
    • Removed getMinParentAge as it was never used.
    • Starting to replace rbind() with rbindlist() from data.table were possible.

nprcgenekeepr 1.0.5.9002 (20220425)

  • Minor changes
    • Added use of data.table in an effort to reduce memory use and CPU use for estimation of kinship values.
    • Functions were refactored and the ability to handle larger simulations resulted.

nprcgenekeepr 1.0.5.9001 (20210830)

  • Major changes
    • Added ability to use simulation to estimate the kinship values of animals with incomplete parental information that are known to have been born within the colony. These animals may have 0 or 1 known parents but have a value in the pedigree file or database for the fromcenter or fromCenter field of “Y”, “YES”, “T”, or “TRUE”.
  • Minor changes
    • Increase unit test coverage primarily to include more rare events and events that should not happen and are trapped and result in errors.
    • Changed to travis-ci.com

nprcgenekeepr 1.0.5 (20210328)

CRAN release: 2021-03-31

  • Major changes – none
  • Minor changes
    • CRAN submission primarily in response to a change in shiny 1.6 that removed an internal shiny function (shiny:::%OR%) and replaced it with rlang::%||%
    • Stale URL in historical documentation that were causing notes to be generated in automated tests have been removed.
    • A URL referring to Terry Therneau’s page was updated from “http” to “https”.
    • I have incremented the version from 1.0.4 (github.com only version) to 1.0.5, updated NEWS to reflect the changes, and updated all documentation to reflect the version change.

nprcgenekeepr 1.0.4.9003 (20210318)

  • Major changes – none
  • Minor changes
    • Testing .travis.yml code change to get textshaping to build on all systems..
    • Cleaned up .travis.yml in response to syntax checking on travis.org.
    • Added markdown to suggest due to new changes in knitr.

nprcgenekeepr 1.0.4 (20210318)

  • Major changes – none
  • Minor changes
    • Added suppression of warnings from DT at beginning of server.R since it is unlikely for anyone to call affected functions in the controlled environment.
    • Changed call to shiny:::%OR% to rlang::%||% in server.R since the update to 1.6 of shiny broke the code. Thanks to Dan Metzger of Wisconsin National Primate Research Center.

nprcgenekeepr 1.0.3 (20200526)

CRAN release: 2020-06-02

  • Major changes – none
  • Minor changes
    • CRAN re-submission: responded to the two requests provided by reviewer
      • I have removed the capitalization from “Genetic Tools for Colony Management” and “Genetic Value Analysis Reports” within DESCRIPTION.
      • I have removed the conditional installation of DT from the ui.R file.
    • I have incremented the version from 1.0.2 to 1.0.3, updated NEWS to reflect the changes, and updated all documentation to reflect the version change.

nprcgenekeepr 1.0.2 (20200517)

  • Major changes – none
  • Minor changes
    • CRAN re-submission: responded to all requests provided by reviewer
      • I have not changed the capitalization of Shiny in the description section of the DESCRIPTION file as it is the name of the type of application and is not being used as the name of the package. The use of the capitalization is consistent with the capitalization used within the documentation for the shiny package (?shiny, See the Details section, first sentence where it is used as the type of tutorial.) and all documentation and tutorials provided by the author and RStudio where it is capitalized everywhere except when referring to the package.
      • I have continued to use dontrun for the following examples:
        • runGeneKeepr(), which starts the Shiny application
        • getFocalAnimalPed(), which is dependent on a valid LabKey instance, a proper configuration file, and a .netrc or _netrc authentication file.
      • I have exchanged dontrun for donttest for the following examples:
        • create_wkbk()
        • createPedTree()
        • findLoops()
        • countLoops()
        • All 11 examples in data.R
        • makeExamplePedigreeFile

nprcgenekeepr 1.0.1 (20200510)

  • Major changes – none
  • Minor changes
    • CRAN re-submission: responded to all requests provided by reviewer
      • Reduced the time required for unit test from over 12 minutes to 21.6 seconds by skipping those test dependent on stochastic creation of simulated pedigrees and breeding groups when not running on my system.
      • Reduced the time to run examples and create vignettes by reducing the number of stochastic modeling iterations by orders of magnitude without reducing the examples provided for user-facing functions.
      • Checking (–as-cran –run-donttest) Duration: 2m 21.8s on my system.
      • The files with the Rd-tag of missing do not take arguments.
      • Corrected private referencing (:::) for exported functions.
      • Exported all functions used in examples to remove private referencing (:::).
      • Removed all single quotes on names, abbreviations, initialisms, and, acronyms.
      • The phrase Electronic Health Records (EHR) is the name of a module within LabKey, which this software can use as a source of pedigree information so the capitalization is appropriate.
      • Two exported functions used by server.R to call tabpanel() do not have examples.

nprcgenekeepr 1.0 (20200415)

  • Major changes – none
  • Minor changes
    • CRAN submission

nprcgenekeepr 0.5.43 (20200414)

  • Major changes – none
  • Minor changes
    • Final preparation for CRAN submission

nprcgenekeepr 0.5.42.9012 (20200412)

  • Major changes – none
  • Minor changes
    • Updated unit test for dataframe2string to account for change in age of a sire from 8.67 to 8.66 years.
    • Renamed tutorials.

nprcgenekeepr 0.5.42.9011 (20200409)

  • Major changes – none
  • Minor changes
    • Build failed on Travis-ci due to unit test failure but the test has never failed and does not fail on other builds. Removed set_seed() to see if that helps.
    • Fixed GitHub issue 3
    • Added additional explanatory text from Matt Schultz edits for the Colony Manager version of the Shiny tutorial.

nprcgenekeepr 0.5.42.9010 (20200405)

  • Major changes – none
  • Minor changes
    • Added code to address issue 1 (GitHub). See comment 1 for details, but more should be done.
    • Refreshed Shiny_app_use.Rmd to reflect changes since November 2019.

nprcgenekeepr 0.5.42.9009 (20200402)

  • Major changes – none
  • Minor changes
    • Wrapped example for makeExamplePedigreeFile with \dontrun{} because R 4.0.0 alpha was leaving the side effect of the dataframe stored in a CSV file named as the text of the next line.

nprcgenekeepr 0.5.42.9008 (20200321)

  • Major changes – none
  • Minor changes
    • Changed dependency to R >= 3.6 since caTools is not available for R < 3.6.

nprcgenekeepr 0.5.42.9007 (20200319)

  • Major changes – none
  • Minor changes
    • Changed warnings unit test for getLkDirectAncestors to work with Windows.

nprcgenekeepr 0.5.42.9006 (20200319)

  • Major changes – none
  • Minor changes
    • Completed examples in function documentation
    • Corrected spelling of several word throughout found with spelling::spell_check_package(".").

nprcgenekeepr 0.5.42.9005 (20200201)

  • Major changes – none
  • Minor changes
    • Added examples to function documentation
    • Added ColonyManagerTutorial.Rmd initial draft, which is copy of shiny_app_use.Rmd. It is to be converted for use by colony managers.

nprcgenekeepr 0.5.42.9004 (20200201)

  • Major changes – none
  • Minor changes
    • Added examples to function documentation
    • Added obfuscated rhesus pedigree and rhesus haplotypes to use in examples

nprcgenekeepr 0.5.42.9003

  • Major changes – none
  • Minor changes
    • Renamed local and remote repositories from nprcmanager to nprcgenekeepr.

nprcgenekeepr 0.5.42.9002

  • Major changes
    • Changed name of package to nprcgenekeepr. This required changing of many of the supporting files and functions. Having good unit test coverage of the functions (739 test with > 90 percent coverage) made this possible.
    • This is the last version under the nprcmanager repository name.
    • Conversion worked
      • Running the build check had OK: 739; Failed: 0; Warnings: 0; Skipped: 0
  • Minor changes – none