NEWS

R. Mark Sharp 03/28/2021

nprcgenekeepr 1.0.5 (20210328)

• 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)

• 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

nprcmanager 0.5.42.9001

• Major changes – none
• Minor changes
  • Adding small executable examples in roxygen2 comments that will go into the Rd-files. Since I have tests, I am wrapping the examples in .
  • Added code prior to changing par() in getPyramidPlot.R to reset par() with
    opar <- par(no.readonly =TRUE)
on.exit(par(opar))
    
  • Removed the word “Implements” from the title.
  • Reworded the first sentence of the Description element and therein removing “implements” and “nprcmanager” as unnecessary words.
  • Added single quotes around all package, software, and API names within the Description element of the DESCRIPTION file.

nprcmanager 0.5.42.9000

• Major changes
  • Added ability to export genetic summary statistic plots
• Minor changes – none

nprcmanager 0.5.42 (20191208)

• CRAN submission
• Move output of suspicious parent list from the user’s home directory to the result of tempdir().

nprcmanager 0.5.41 (20191130)

• CRAN submission.

nprcmanager 0.5.40.9002 (20191119)

• Tried to get vignette for shiny application to find images on all building platforms by adding “./” to relative path.

nprcmanager 0.5.40.9001 (20191115)

• Added unit test for create_wkbk from github.com/rmsharp/rmsutilityr
• Fixed bug in Genetic Value Analysis tab were failure to remove all white space in Filter View Id window did not clear filter.
• Changed minimum parent age default from 4 to 2 years.
• Added ability to download founders in a maleFounders.csv file and a femaleFounders.csv file.
• Added createExampleFiles and saveDataframesAsFiles to allow the user to generate all of the example pedigrees and other files used in testing and in tutorials.
• Removed Development_Plans.Rmd from build because it has has been replaced by adding issues on our GitHub issue tracker.

nprcmanager 0.5.40.9000 (20191115)

• Corrected bug in addIdRecords to handle NA characters; amended its unit tests to check for correct behavior
• Changed name of sexRatioWithAddions to getSexRatioWithAdditions

nprcmanager 0.5.39 (20191115)

• Moved vignettes to expose them in GitHub Pages.
• Removed more unneeded files from package.

nprcmanager 0.5.38 (20191113)

• Changed getBreederPed function to getFocalAnimalPed and animals read in by that function from breeders to focalAnimals

nprcmanager 0.5.37 (20191108)

• Working on updating documentation

nprcmanager 0.5.36 (20191106)

• Added colorIndex to list returned by getIndianOriginStatus(), getProductionStatus(), and getProportionLow(). Updated related unit tests
• Changed getSiteInfo() to reflect ONPRC’s query structure
• Changed .Rbuildignore to leave out .png image files needed for Shiny tutorial.

nprcmanager 0.5.35 (20191013)

• Corrected calculateSexRatio and updated unit test
• Modified getProductionStatus to match new definition and added unit tests

nprcmanager 0.5.34 (20191006)

• Added code to filter out animals no longer at institution and without birth date.

nprcmanager 0.5.33 (20191006)

• Broke up LICENSE contents into LICENSE and LICENSE.md for CRAN compliance

nprcmanager 0.5.32 (20191004)

• Corrected ancestry to sexCodes in test_convertSexCodes()

nprcmanager 0.5.31 (20191003)

• Added more tutorial notes
• Removed undefined elements in DESCRIPTION file including Displaymode: Showcase, which is recommended in a Shiny example by RStudio. This was removed based on RHUB feedback.
• Added more code for genetic diversity dashboard.

nprcmanager 0.5.30 (20190829)

• Began adding code for the genetic diversity dashboard. This includes the functions getIndianOriginStatus and getProportionLow, and a rudimentary makeGeneticDiversityDashboard function.
• Added another obfuscation function mapIdsToObfuscated to further facilitate creation of obfuscated data. This was specifically used to obfuscate haplotype data Ids.

nprcmanager 0.5.29 (20190810)

• Copied rmsutilityr functions into nprcmanager to make Publication on the RStudio Shiny application hosting site possible

nprcmanager 0.5.28 (20190714)

• Added to interactive tutorial
• Enhance algorithm for creating the desired sex ratio in groups.

nprcmanager 0.5.27 (20190713)

• Added to interactive tutorial
• Minor corrections of function documentation
• Moved updateProgress parameter to end of list for groupAddAssign().

nprcmanager 0.5.26 (20190707)

• Updated and corrected _software_development.Rmd
• Corrected summary statistics descriptions
• Added expectConfigFile argument to getSiteInfo() and associated unit test to allow user to avoid a warning when configuration file is not expected to be present.

nprcmanager 0.5.25 (20190701)

• Removed animals with exit dates from pyramid plots
• Added ability to retain novel column names
• Increased the number of column names understood for display in pedigree browser.

nprcmanager 0.5.24 (20190630)

• Renamed resetPopulation to setPopulation
• Added sections to interactive_use_tutorial

nprcmanager 0.5.23 (20190624)

• Added weak unit test for getGenotypes function

nprcmanager 0.5.22 (20190624)

• Corrected and augmented unit tests for print_summary_nprcmanagGV and summary.nprcmanagGV

nprcmanager 0.5.21 (20190624)

• Added unit tests for print_summary_nprcmanagGV and summary.nprcmanagGV

nprcmanager 0.5.20 (20190622)

• Added unit test for getPedigree.

nprcmanager 0.5.19 (20190622)

• Replaced examplePedigree which I an failed to obfuscate with an obfuscated version
• Added the ability to retrieve the map of original IDs to the new aliases to obfuscatePed.

nprcmanager 0.5.18 (20190622)

• Replaced actual unpublished pedigree objects with obfuscated pedigree objects so they can be shared
• Updated unit tests that were dependent on replaced pedigree objects

nprcmanager 0.5.17 (20190619)

• Removed old pedigree files in preparation for new custom built demonstration pedigrees
• Removed old, no longer used logos

nprcmanager 0.5.16 (20190615)

• Added functions used to obfuscate pedigrees. This changes the IDs, all dates and age calculations while maintaining internal relational consistency (parent IDs correspond) and date, though different are similar.

nprcmanager 0.5.15 (20190602)

• Added ability to create an example pedigree file using the examplePedigree data structure.
• Added summary.nprcmanagGV and print.summary.nprcmanagGV functions
• Added description of age-sex pyramid plot to the summary of major functions.

nprcmanager 0.5.14 (20190518)

• Added ability to use Excel files as input
  • Added getGenotypes, getPedigree, getBreederPed, readExcelPOSIXToCharacter,
  • Added selection of Excel or Text file to uitpInput.R and modified other aspects to separate out the delimiter selection logic.
  • Default file type is Excel.
  • If a user selects and Excel file and an Excel file is detected, all file type and delimiter selections are ignored and the Excel file is used and no error or warning is given.
• Improved checkRequiredCols, toCharacter and getDatedFileName functions
• Exported set_seed. This will be moved into rmsutilityr
• Removed erroneous toCharacter documentation
• Added set_seed
  • Tried unsuccessfully to use the RNGkind function and the sample.kind argument to set.seed, but found neither existed prior to R 3.6.
  • Created a R version sensitive version of set_seed that duplicates the pre-R version 3.6 set.seed function. This is only useful for creating data structures for testing purposes and should not be used to set seeds for large simulations

nprcmanager 0.5.13 (20190508)

• Updated unit tests that were using set.seed to use a R version sensitive set.seed wrapper.

nprcmanager 0.5.12 (20190507)

• Updated nprcmanager.R to add Pedigree Testing and Plotting function lists.

nprcmanager 0.5.11 (20190430)

• Changed wording and format above Suspicious Parent table in ErrorTab
• Removed row label from Suspicious Parent table
• Updated meeting notes

nprcmanager 0.5.10 (20190428)

• Corrected roxygen2 comment “@export” in getAnimalsWithHighKinship().
• Added unit test for fillGroupMembersWithSexRatio()

nprcmanager 0.5.09 (20190428)

• Corrected bug where parents with suspicious dates were not being reported.
• Improved display of parents with suspicious dates by outputing HTML table to the ErrorTab.

nprcmanager 0.5.08 (20190418)

• Minor rewording of option label on breeding group formation tab

nprcmanager 0.5.07 (20190408)

• Rearranged and reformatted breeding group formation tab

nprcmanager 0.5.06 (20190407)

• Changed spelling of gu.iter and gu.thresh to guIter and guThresh

nprcmanager 0.5.05 (20190406)

• Fixed all but one bug associated with having multiple dynamically generated seed animal groups.
• Added global definition of MAXGROUPS, which is current set as 10 and allows up to six seed animal groups.
• Corrected test_fillBins, which was erroneously using a current date instead of a fixed date for calculating age.

nprcmanager 0.5.04 (20190225)

• Adding ability to have up to six seed animal groups.
• Added conditional appearance of Make Groups action button that is dependent on the user having select on of the optional group formation workflows.

nprcmanager 0.5.03 (20190215)

• Adding new version of breeding group formation UI and related server code.

nprcmanager 0.5.02 (20190103)

• Added ability to specify sex ratio in increments of 0.5 (Female/Male) from 0.5 to 10 in increments of 0.5.

nprcmanager 0.5.01 (20181230)

• Correction of some bugs in harem creation and provided additional unit tests for harem creation to prevent regression.

nprcmanager 0.5.00 (20181228)

• First draft with harem group creation working.
  • Fails if more than one potential sire (male and at least of minimum age) is in the current group.
  • Fails if there are insufficient males to have one per breeding group being formed.
  • Requires the user to provide males in the candidate set that are appropriate for breeding as the current code does not check to ensure the animals are still alive. This could easily be added.
  • Males are selected for each group randomly at each iteration just as are all other members. The only difference between animal selection for harems is that sex is part of the selection process.
  • This required the creation of a few functions and modification of others. Unit tests were updated to reflect changes, but not additions. New unit tests are needed.
  • The format of the breeding group creation page must be improved.
  • The changes made and the new unit tests will serve to simplify adding the sex ratio criterion to breeding group formation.

nprcmanager 0.4.23 (20181226)

• Added code to detect LabKey connection failure and report it on an Error tab

nprcmanager 0.4.22 (20181224)

• Minor text changes to Input tab. Refactored groupAddAssign function to have a function create the return list.

nprcmanager 0.4.20 (20181222)

• Refactor of groupAddAssign function by extracting much of the function into separate functions. One such function, fillGroupMembers isolates the group formation code to allow adding the ability to satisfy sex ratio requirements and harem creation.

nprcmanager 0.4.19 (20181217)

• All minor interface changes
  • Substituted hovertext for description of minimum parental age
  • Added meeting notes for 20181210 meeting
  • Changed label on button controlling reading of pedigree information
  • Updated logo
• Added code of conduct file.
• Corrected license text

nprcmanager 0.4.18 (20181210)

• Added unit test for removing animals added to pedigree because they are unknown parents

nprcmanager 0.4.17 (20181208)

• Changed error reporting so as not to report as an error the wrong sex when animals are added into the pedigree and appear as both a sire and dam without an ego record. The error report now indicates these are both a sire and a dam. Done 20181208
• Made a combined logo for Oregon and SNPRC. Have ONPRC on top using blue and green. Done 20181208
• Additional unit tests to cover all of the new functions created to handle the PEDSYS and military formatted dates (YYYYMMDD) have been made. Done 20181112
• Corrected breeding groups formation, which was including unknown animals that had been added as placeholders for unknown parents. Done 20181119
• Hardened LabKey code by trapping a bad base URL in the configuration file with a tryCatch function and send a message to the log file. This needs to be tested with a working LabKey system.