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Changelog

Source: NEWS.md

nprcgenekeepr 2.0.0.9000 (development version)

Package

  • CRAN accepted the 2.0.0 submission (tagged v2.0.0); published 2026-07-26. Development continues here on top of it.

Pedigree Diagram

  • The Pedigree Browser tab gained an interactive Diagram view: click any animal to re-center the diagram on it. Pedigrees above 750 animals show an informative message instead of rendering, to keep diagrams readable (issue #129).
  • The Diagram tab includes an in-app legend explaining what each shape means for an animal’s sex (issue #132).
  • The Diagram tab includes hover tooltips and a search/highlight box for finding an animal by id (issue #135).
  • The Diagram tab’s layout follows the standard kinship2 convention used in published pedigree charts: a mated pair is joined by a mate line, and an individual with more than one mate is drawn once per mating rather than once total. makePedigreeMatingLayout() builds this layout; makePedigreeDiagramData() is unrelated to it.
  • The Diagram tab includes a Diagram Edge Style toggle: choose between a default “Direct” straight-line connector style and an alternative “Rectilinear (kinship2-style)” right-angle style (issue #142).
  • The Diagram tab can shade individuals as affected by a condition, using an optional affected column, matching a kinship2 shading convention (issue #133).
  • The Diagram tab can show each animal’s name next to its id, via an optional name column and a Show Names on Diagram toggle; de-identified exports automatically remove names (issue #136).
  • The Diagram tab can show twin connectors (identical, fraternal, or unknown zygosity), using the same twin-code convention as kinship2 (issue #137).
  • The Diagram tab places the male parent on the left within a mated pair by default, matching the convention most pedigree readers expect (issue #145).
  • Unaffected and unknown-status individuals are shown unshaded (open) rather than filled, matching kinship2’s own shading convention.
  • The Diagram tab draws a mate line thicker and in a distinct color for a consanguineous mating (parents who are blood relatives), matching kinship2’s convention – detected automatically from the pedigree, no extra column needed. Applies to the “Direct” edge style; “Rectilinear” support follows below.
  • The Rectilinear edge style correctly avoids an unnecessary extra bend in unrelated mate lines even when a pedigree has one parent recorded but missing their own row.
  • The consanguineous-mating marker above also survives a “Rectilinear” reroute (a mate line that needs to bend around an obstacle).
  • When a pedigree has no affected column at all, animals default to unshaded (open) rather than shaded as affected, matching kinship2’s convention – including the package’s own bundled example pedigree.
  • Every pair of animals at the same generation keeps at least a consistent minimum gap apart, so nearby unrelated animals are never drawn closer together than directly-related ones.
  • When a mated pair’s two parents are recorded at different generations, their shared mating symbol is placed on the correct row by construction. A visible consequence: a parent who anchors matings at more than one generation appears as a duplicate node more often than a naive single-row placement would produce (22 individuals in the bundled example pedigree).
  • The Diagram tab defaults to the “Rectilinear (kinship2-style)” edge style; with no style chosen, the display limit is 400 animals (switching to “Direct” raises it to 750).
  • In the Rectilinear edge style, a sibling group’s connecting bar avoids visually crossing an unrelated animal’s own row in the common case – most importantly when a sibling also anchors her own mating at the same generation (issue #160). Two rarer related cases remain open, disclosed follow-ups for a future pass.
  • In the Rectilinear edge style, the layout detects when a straight connector line would visually pass through an unrelated animal – most often in large, many-founder colony pedigrees – and reroutes around the obstacle. A small number of curved duplicate-animal connectors get only a partial correction and remain a disclosed residual.
  • A mating symbol is always kept within the range spanned by its own two parents, matching kinship2’s convention – most notably for a mating with only one child, which would otherwise have no other children to center between. This is a disclosed trade-off, not a free improvement: for the matings it affects, the symbol can sit further from where its children are actually centered, and two unrelated sibling groups’ bars can somewhat more often overlap visually – both accepted costs of the correct parent-centered placement.
  • For one specific pattern (a sibling-consanguineous mating), the trade-off above is partially mitigated – though in the one test case built to exercise this, the visual change is too small to see on screen at normal zoom, so don’t expect a visible difference in today’s example pedigrees.
  • Which parent a mating symbol anchors to is consistent across computers and regional settings: the anchor tie-break uses a locale-independent comparison (issue #162).
  • Pedigree diagram positioning centers children accurately over their parents and produces fewer overlapping lines, especially in large or tangled families (issue #141). makePedigreeMatingLayout() has no orderBySex argument – the male-left/female-right convention is always applied. ## Kinship & Pedigree Calculations
  • Declaring a pair of animals as identical (MZ) twins now corrects their computed relatedness to genetic identity, and that correction flows through to every other relative reached through either twin – not just the pair itself. A twin/zygosity file uploaded on the Diagram tab now applies this correction everywhere relatedness is used in the app – Summary Statistics, Breeding Groups, and Genetic Value Analysis – regardless of which tab is opened first. Script users: kinship(), reportGV(), gvaConvergence(), createSimKinships(), and cumulateSimKinships() all gained a matching twinRelations argument.
  • New: kinship() can now compute X-chromosome relatedness (instead of the usual whole-genome average) via a new chrtype = "x" option – useful for traits carried on the X chromosome. The default behavior (chrtype = "autosome") is unchanged; every existing use of kinship() keeps working exactly as before. Script-callable only; no Shiny screen yet.
  • New shrinkPedigree() trims a large pedigree down to just the animals needed to keep it genetically informative within a genotyping budget, given which animals are already genotyped and, optionally, which are affected by a condition of interest. Ties are broken in a fixed, repeatable order (kinship2’s own equivalent function breaks ties randomly, so the same input there can give a different answer from one run to the next). Script-callable only; no Shiny screen yet.

Marker Genetics

  • New Marker Genetics tab, starting with a Kinship Comparison sub-tab: compares DNA-based relatedness (from marker genotypes) side by side with pedigree-based relatedness (issue #130).
  • The Marker Genetics tab includes a Heterozygosity sub-tab: compares each animal’s own genetic diversity to what’s expected for the population (issue #130).
  • The Marker Genetics tab includes a Parentage Exclusion sub-tab: flags a pedigree-recorded parent that the DNA evidence contradicts (issue #130).
  • The Marker Genetics tab includes a Cross-Center sub-tab comparing genetic diversity between two centers’ populations (issue #130) – not to be confused with the separate Cross-Center Identity tab described below, which matches and merges individual animal records rather than comparing population-level diversity.
  • New Candidate Parent Assignment sub-tab: for a flagged animal, ranks which other genotyped animals could be the real parent instead, based on DNA evidence. Report-only. New markerParentageLikelihood() (issue #147).
  • The Candidate Parent Assignment sub-tab’s automatic suggestion covers the common case where a flagged animal’s recorded parent is present in the data but simply wrong (issue #155).
  • New locus-metadata check (checkLocusMetadata()): reports, for each marker locus, whether its chromosome/position data is complete, partial, or missing – PLINK-style. New example files included. No Shiny screen yet (issue #153).
  • New checkLinkageMarkerGenotypeFile() validates marker panels with more than 2 alleles per locus (e.g. STR/microsatellite markers), alongside the existing 2-allele check. No Shiny screen yet (issue #153).
  • New markerRealizedRelatednessVariance() estimates how much a pair’s actual DNA-based relatedness can vary around what the pedigree alone would predict. No Shiny screen yet (issue #153).
  • New markerLdBlock() reports which nearby markers on the same chromosome tend to be inherited together, with a matching obfuscateLdBlocks() for de-identified export. No Shiny screen yet (issue #153).
  • The Marker Genetics tab includes a Linkage and LD Block Metrics sub-tab, combining the locus-coverage, relatedness-variance, and linkage-block reports above in one place, with de-identified export (issue #153).
  • New sequence-scale marker genotype check (checkSequenceGenotypeFile()), for genotype files with far more markers than a standard panel. No Shiny screen yet (issue #152).
  • The DNA-relatedness and candidate-parent calculations (markerKinship()/markerParentageLikelihood()) are optimized to handle large marker panels efficiently (issue #152).
  • New: computes each animal’s inbreeding level directly from large-scale sequence data (runs of homozygosity), not just from the pedigree. No Shiny screen yet. New computeGenomicROH() (issue #152).
  • New obfuscateGenotypeMatrix() de-identifies a sequence-scale genotype file’s animal ids. No Shiny screen yet (issue #152).
  • The Marker Genetics tab includes a Genomic ROH (F_ROH) tab: the sequence-based inbreeding calculation above, with de-identified export (new obfuscateGenomicROH()) (issue #152). ## Cross-Center Identity Matching
  • New resolveCrossCenterIds() merges pedigree records for the same animals held by two different centers, using a curator-confirmed id-matching table.
  • New checkCrossCenterMapping() reports every problem with a cross-center id-matching table at once, instead of stopping at the first one found. Merging preserves every one of an animal’s own data columns (issue #149).
  • New Cross-Center Identity tab: walks a curator through matching and merging records from two centers, with a preview and downloadable results behind a confirmation step (issue #149). ## Genetic Value Analysis
  • The Genetic Value Analysis tab gained a configurable Ranking Scheme control: choose a priority-tier ranking alongside the existing combined kinship/uniqueness score (issue #125). Script users: reportGV() gained matching guCutoff/zScoreCutoff/axisPriority arguments.
  • The Genetic Value Analysis Summary Statistics table gained Skewness and Kurtosis columns, describing the shape of the genetic-value distribution (issue #126). Script users: new calcSkewness()/ calcKurtosis().
  • The Genetic Value Analysis rankings table gained a flagged column marking animals whose ranking correction couldn’t be applied for lack of a comparable peer group (issue #127).

Breeding Group Formation

  • The Breeding Group Formation tab now shows up to 5 candidate groupings per run, with a selector and comparison table (issue #125). Script users: groupAddAssign() gained a matching candidates field in its return value.
  • The Breeding Group Formation tab gained an Include animals by control: an alternative genetic-value-floor option alongside the existing top-N cutoff (issue #128).
  • The Breeding Group Formation tab gained a Candidates to retain control, replacing a fixed cap of 5. Script users: groupAddAssign() gained a matching maxCandidates argument (issue #146).
  • The Breeding Group Formation tab gained an Exhaustive enumeration mode checkbox: checks every possible single-group split instead of sampling, for the simplest case. Script users: groupAddAssign() gained a matching exhaustive argument (issue #146).

Mate Pair Analysis

  • New reportMatePairs() reports individual mate-pair candidates with their relatedness and genetic-value context. Report-only (issue #151).
  • New Mate Pair Analysis tab: a curator view built on the report above, kept separate from Breeding Group Formation (issue #151).

De-Identified Export

  • obfuscatePed() gained a linkedDateShift argument (default TRUE): shifts all of one animal’s dates by the same offset when de-identifying, so the gaps between its own dates stay realistic instead of possibly ending up out of order (issue #150).
  • New De-Identified Export tab: a curator workflow with a live preview and 3 downloadable files (the de-identified pedigree, a record of what was changed, and a private key to re-identify records later) behind a confirmation step (issue #150).

General Fixes

  • Fixed: the sort order in a few tables (the Genetic Value Analysis tiers, the main pedigree table, and the Breeding Group member table) could vary depending on the server’s own regional settings, purely from how ids happened to sort – not from any real difference in the data. All three now sort in a fixed, consistent order everywhere.

nprcgenekeepr 2.0.0 (20260708)

CRAN release: 2026-07-26

  • Major changes
    • (breaking) qcStudbook() and geneDrop() now reject id, sire, or dam values containing a period (offenders returned in errorLst$invalidIdChars); auto-generated IDs remain period-free.
    • (breaking) Removed the unused exports getLogo(), shouldShowErrorTab(), modMinimalTestUI(), and modMinimalTestServer(). The Shiny application was rewritten internally as a modular architecture; runGeneKeepR() remains the primary entry point (runModularApp() works as a deprecated alias). (#27, #110)
    • New Potential Parents tab listing candidate sires and dams for in-colony animals with at least one unknown parent, screened by estimated conception date (wiring in the exported getPotentialParents()); dam selection uses a gestation-derived exclusion window rather than a fixed +/- 182.5-day window. (#48, #31)
    • Gestation length and minimum breeding ages are now species-aware: the bundled speciesGestation table covers 14 common colony NHP species (previously only rhesus macaque), with numeric rather than integer breeding ages so fractional minima are represented exactly. getPotentialParents() and the Potential Parents tab derive each animal’s gestation window from its species via the new getSpeciesGestation(); the Genetic Value Analysis missing-parent correction uses per-species minimum breeding ages; and an optional configuration-file entry (speciesOverridesPath, plus minBreedingAgeDefault and gestationDefault) overrides these values via the new loadSpeciesOverrides(). Species absent from the table keep the previous defaults (a 210-day gestation and a 2-year minimum breeding age), so existing results are unchanged. Completes issue #73. (#73)
    • New sex-specific minimum breeding ages: qcStudbook(), checkParentAge(), runQcStudbook(), and getPotentialParents() now accept minSireAge and minDamAge in place of a single minParentAge (kept as a deprecated alias that sets both). The Shiny app’s single “Minimum Parent Age” field is replaced by separate “Minimum Sire Age” and “Minimum Dam Age” fields. (#119)
    • New ORIP Reporting tab with ONPRC colony summaries for the NIH Office of Research Infrastructure Programs (site information, a colony table with founder counts, genetic-diversity metrics, and CSV exports); shown only at ONPRC. (#47, #49)
    • The Pedigree Browser “trim based on focal animals” option now includes descendants as well as ancestors, via the new exported getDescendantPedigree(). (#35)
    • Added the exported founder helpers isFounder() and getFounders().
    • Added the exported getAutoIdFormat() and setAutoIdFormat(), making the auto-generated placeholder-ID format configurable (default "U%04d"). (#44, #38)
    • Genetic Value Analysis tab parity: the genome-uniqueness threshold is now a user control (default 4), a subset filter and “Export Subset” download were added, the default gene-drop iterations changed to 1000 (matched at the function level: reportGV() and geneDrop() now also default to 1000, down from 5000), and an inert “Minimum breeding age” slider was removed.
    • Improved visualizations: educational box-plot popovers (getBoxWhiskerDescription()), plot export to PNG, PDF, and SVG (savePlotToFile()), and an enhanced age-sex pyramid (getPyramidPlot()).
    • The Genetic Value Analysis now reports three additional population-genetic summaries: gene diversity (GD = 1 - 1 / (2 * FG)) and – over the current living breeders – a sex-ratio effective population size (4 * Nm * Nf / (Nm + Nf)) and a variance effective population size (the Crow & Kimura (1970) form), via the new exported calcGeneDiversity(), calcNeSexRatio(), and calcNeVariance(); each is defined, with its idealizing assumptions, in the in-app Population Genetics Terms panel. (#118)
    • The Genetic Value Analysis now reports the sampling precision of each animal’s genome uniqueness: a new guSE column (the gene-drop Monte Carlo standard error, via the new calcGUSE()) and a “Genome Uniqueness SE (max)” summary row. The new gvaConvergence() gives evidence-based advice on how many gene-drop iterations a pedigree needs for a stable ranking, by comparing rankings from split halves of one gene drop; it also accepts a kinshipOverrides argument.
    • The Genetic Value Analysis now corrects the mean kinship of animals missing one parent, which previously understated their relatedness and let them rank as more genetically valuable than they should. A new parentage column labels each animal “known”, “one unknown parent”, or “both unknown”; animals with both parents unknown and no recorded origin (“Undetermined”) are now ranked last, with genome uniqueness reported as 0 rather than the inflated gene-drop-founder artifact value. Animals recorded as genuine imports (an origin) are unaffected. (Changes reported rankings and genome-uniqueness numbers for affected animals.)
    • reportGV() and the Genetic Value Analysis tab now accept an optional kinshipOverrides argument (or file upload) of outside-information kinship coefficients (id1, id2, kinship) that replace the pedigree-derived kinship for the named pairs before ranking; applies across the Genetic Value Analysis, breeding-group formation, and summary-statistics tabs, and the summary-statistics relationship table gains an overridden flag column. New exported applyKinshipOverrides(), checkKinshipOverrides(), and readKinshipOverrides(); gvaConvergence() also accepts overrides. The unknown-parent mean-kinship correction is kept even when an override is supplied. Leaving no override reproduces previous results exactly. (#13, #95)
    • getLkDirectRelatives() now returns the full connected pedigree component (ancestors, descendants, and collaterals such as siblings and mates) instead of only the strict ancestor/descendant lineage; the new file-sourced getFileDirectRelatives() provides the same for file pedigrees. The new getFocalAnimalPedFromFile() and setLabKeyDefaults() let the focal-animal workflow run fully offline from files, and the Shiny input module offers an optional pedigree-file input alongside the LabKey/EHR path.
  • Minor changes
    • Fixed a startup crash that occurred when a documented-format site configuration file was present, via the new tolerant loadSiteConfig(). (#50)
    • The About panel now shows the installed package version dynamically (it previously displayed a hard-coded “Version 1.0.8”).
    • geneDrop() now reports duplicate animal IDs with a clear error instead of the base-R duplicate 'row.names' are not allowed message.
    • Reading a file whose final line lacks a trailing newline no longer emits the spurious “incomplete final line” warning. (#4)
    • addGenotype() now coerces its allele columns to character, so the integer allele encoding is consistent whether they are supplied as character or factor.
    • Re-exported the bundled rhesusPedigree and rhesusGenotypes data sets with canonical column types (character id, sire, and dam and Date birth and exit in rhesusPedigree; all-character columns in rhesusGenotypes), preserving every value.
    • summarizeKinshipValues() now reports the secondQuartile column as the lower hinge (fivenum()[2]) instead of duplicating min.
    • New dependencies: bslib, DT, and ggplot2 (Imports); shinytest2 (Suggests).
    • create_wkbk() now writes .xlsx files with openxlsx instead of WriteXLS, removing the package’s Perl requirement (WriteXLS shelled out to a bundled Perl script). Output and behavior are otherwise unchanged.
    • Replaced the magrittr pipe (%>%) with the base R native pipe (|>) in vignettes and examples; magrittr is no longer used.
    • getPedMaxAge() now returns NA instead of -Inf when a pedigree has no non-missing ages, so the age-sex pyramid plot renders cleanly instead of deriving a spurious -Inf axis bound. (#121)
    • makeSimPed() now preserves a known parent instead of overwriting it with a random candidate, correcting createSimKinships() and cumulateSimKinships() for animals with one known and one unknown parent. (Changes simulated-kinship values for affected pedigrees.)
    • The exported makeGrpNum() has been renamed to makeGroupNum() for naming consistency with the sibling export makeGroupMembers(); the old name is kept as a deprecated alias.
    • The Genetic Value Analysis report and both of its CSV exports (the full ranked report and the genetic-value subset) now include sire and dam columns, showing which animals have an unknown parent.
    • File-based pedigree ingestion now treats species as a first-class column: it is recognized and placed immediately after sex in the canonical column order, and typed as character, rather than surviving as an untyped trailing column.
    • In the Pedigree Browser tab, “Clear Focal Animals” now also clears a focal-animals list uploaded via the file browser (and its displayed file name) and any focal Ids typed into the text box, so neither is silently re-read on the next “Update Focal Animals”.
    • getPedDirectRelatives(unrelatedParents = TRUE) now returns a placeholder ego record for a referenced parent with no record of its own, instead of erroring; previously dormant since no caller exercised the TRUE branch. (#114)
    • The offline focal-animal path no longer prints a benign cannot open file ... console warning when the focal-id list file is missing or unreadable; the classed error it already reported is unchanged.
    • Documentation: extensive help-page and dataset-documentation corrections, including the genetic-value @return and parameter descriptions, dataset titles and descriptions, and the @examples for getPedDirectRelatives(), cumulateSimKinships(), and getIdsWithOneParent().
    • Documentation: the example configuration file (inst/extdata/example_nprcgenekeepr_config) now documents that lkPedColumns is center-specific: SNPRC uses the flat dam/sire columns (direct columns) while ONPRC uses the Id/parents/dam lookup-traversal form (curated parentage).
    • Fixed a CRAN Policy violation: the Shiny application no longer writes a debug log file to the user’s home directory unconditionally at startup. The log file is now created only after a user explicitly enables the Input tab’s “Debug on” checkbox, matching the documented behavior.
    • Fixed a data-corruption bug: uploading a pedigree as an Excel workbook via the Input tab silently converted every alphanumeric sire/dam ID to a missing value, collapsing the pedigree to near-all-founders with no error or warning shown to the user. CSV and tab/comma-delimited text uploads were unaffected.
    • Fixed the Breeding Groups tab’s “Custom” sex ratio option: selecting it previously had no numeric input to specify the ratio and silently behaved identically to “None”. A numeric “Custom ratio (F per M)” field now appears when “Custom” is selected, and its value is used when forming groups.
    • Fixed the Breeding Groups tab’s “Number of top animals” field: it never appeared regardless of the selected animal source, including the default “Top ranked” selection where it is supposed to be visible on page load.
    • data(examplePedigree) now includes a fromCenter (colony-origin) column, derived from its existing origin/recordStatus fields, so the Potential Parents tab can show a populated result (1,587 candidates) against the package’s own example data instead of only its graceful-degradation message.

nprcgenekeepr 1.0.8 (20250723)

CRAN release: 2025-07-26

  • Minor changes
    • Added returned value descriptions for all functions within R directory where formerly missing.
    • Changed unit test for get_elapsed_time_str() to use a mocked version of proc.time()

nprcgenekeepr 1.0.7 (20250506)

CRAN release: 2025-04-24

  • Minor changes
    • Added returned value descriptions for all functions where formerly missing.
    • Removed extraneous spaces from DESCRIPTION file.
    • Exposed all examples in roxygen2 comments by removing and and . The example with runGeneKeepR() is protected with if (interactive()) {}.

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.
    • Stopped using travis-ci and started using GitHub Actions with 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:

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 \arguments 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