NEWS

R. Mark Sharp, Ph.D.

nprcgenekeepr 3.0.0 (20261030)

This release expands nprcgenekeepr beyond pedigree management and genetic value analysis. It adds interactive pedigree diagrams, marker-based genetic analysis, MHC haplotype reporting, cross-center identity matching, ancestry-aware breeding safeguards, de-identified export workflows, and longitudinal monitoring of colony genetic health.

Each app tab in these notes is explained in the Colony Manager’s Guide. To reach it from the app, open the Help tab, follow Online Documentation, and under Articles choose “Purpose, Approach, and a Colony Manager’s Guide to Practice”. The guide is on the website only; for working from a script, the installed tutorial is vignette("a2interactive", package = "nprcgenekeepr").

Input

• New: the Input tab now warns when animals in the uploaded pedigree have no birth date. The Warnings tab counts them and says that age-based checks and counts cannot use them. The pedigree can still be used.
• New: the Input tab now warns when an animal’s death or departure date is earlier than its birth date, and names the first five such animals. The pedigree can still be used. runQcStudbook(reportChanges = TRUE) returns this warning and the one above.
• New placeholder column: the pedigree check records which animals are stand-ins. Enter FALSE for a real animal whose id looks like one (such as U1234) and it is kept as real throughout.
• New: with “Pedigree(s) and genotypes in one file”, the Input tab now reads genotypes from columns named allele_1 and allele_2 or first_name and second_name as well as first and second, accepts text labels as well as whole numbers, and says under the QC Summary which columns it read or why it read none. A file with text in first and second now has its genotypes used, so its Genetic Value results can change.
• Fixed: The Input tab lists every invalid date by row.
• Fixed: A fromCenter value that is not a whole yes or no stops the load and names its rows, in convertFromCenter() and qcStudbook() too.
• Fixed: The Changed Columns tab reports only real renames, including a lowercase geographicorigin, recordstatus or fromcenter header, and a column named NA no longer stops checkRequiredCols() or fixColumnNames().
• Fixed: The count boxes of the QC Summary (Records Processed, Errors and Warnings) are colored by what the check found.
• Fixed: An id that merely starts with a capital U is no longer taken for a stand-in, so “Display Unknown IDs” hides only ids shaped like U0001, and a generated stand-in id never repeats a real one (addUIds()).
• Fixed: A sire or dam with an unreadable sex is no longer reported as a “female sire” or “male dam”.
• Fixed: An empty cell in a CSV or text file is read as missing, so a blank ancestry no longer counts as OTHER instead of UNKNOWN.
• Fixed: On Linux computers with ARM processors, a small file whose last value is in quotes and that has no final line break now loads.
• Fixed: With “Pedigree(s) and genotypes in separate files”, a genotype file the app cannot use is reported on the QC Summary (“The genotype file was not used, so no genotypes are used.”, with the reason) and the app keeps running.

Pedigree Diagram

• The Pedigree Browser has a new interactive Diagram view that follows most kinship2 drawing conventions. The comparison article checks by code that the same individuals and relationships appear as in kinship2; the layouts are not identical.
• Click an animal to re-center the diagram. You can also pan and zoom, hover for details, search for an id, and save an image. Connectors can be right-angle, as in kinship2, or straight.
• Optional pedigree columns shade affected animals and show names. Deceased animals, twins and consanguineous matings are marked in the drawing, and a legend explains the symbols.
• A pedigree too large to draw shows a message instead, saying what to do.
• Script users: makePedigreeDiagramData(), makePedigreeMatingLayout() and drawPedigreeDiagram() draw the Diagram from a script. Save it as a web page or put it in an R Markdown report.
• Five small example pedigrees show classic mating structures; the Pedigree Diagram article walks through them.

Kinship & Pedigree Calculations

Major

• Animals declared as identical (MZ) twins now have their relatedness corrected to genetic identity, and the correction passes to relatives of either twin.
• A twin/zygosity file uploaded on the Diagram tab applies this throughout the app.
• Script users: kinship(), reportGV(), gvaConvergence(), createSimKinships() and cumulateSimKinships() take twinRelations. readTwinRelations(), checkTwinRelations() and obfuscateTwinRelations() read, validate and de-identify the file.
• New shrinkPedigree() trims a large pedigree to the animals needed to stay informative within a genotyping budget. Script only.

Minor

• kinship() computes X-chromosome relatedness with chrtype = "x" (needs sex); the default is unchanged. Script only.

Age-Sex Pyramid

• Fixed: Download Plot saves nothing until a pedigree is loaded.

Genetic Value Analysis

Major

• With no focal animals entered, the Pedigree Browser now takes the living animals as the population instead of every animal ever recorded, so the default Genetic Value rankings and founder measures describe the living colony. A pedigree with no living animal still uses every animal. Script users: setPopulation() still flags every animal when given no IDs.
• Fixed: unchecking “Display Unknown IDs” in the Pedigree Browser no longer stops the Genetic Value Analysis with a “logic error”. The box hides rows only in the Pedigree Browser table; every other tab uses the full pedigree (“Trim pedigree based on focal animals” still narrows it).
• Configurable Ranking Scheme: a priority-tier ranking alongside the combined kinship/uniqueness score (issue #125).
• Script users: reportGV() takes guCutoff, zScoreCutoff and axisPriority.

Minor

• The rankings table gained a flagged column for animals whose ranking correction could not be applied for lack of a comparable peer group (issue #127).
• The rankings table starts with the animal ID. It used to start with an unlabeled column of leftover row numbers (such as 4, 5, 6, 9, 10) that were not the rank; the rank column, last in the table, still gives each animal’s rank.
• The Genetic Value Analysis tab no longer shows the “Calculate Genome Uniqueness” and “Calculate Mean Kinship” check boxes. They did nothing: the analysis works out both numbers whether or not they were ticked.
• Fixed: Founder genome equivalents, their standard error and gene diversity are worked out from the pedigree alone, so genotypes no longer make them NA.
• Fixed: An Excel file of kinship overrides works as a CSV of the same table does, in the app and in readKinshipOverrides().
• Fixed: Genetic Value tiers and the pedigree and group tables sort the same way whatever the server’s regional settings.

Summary Statistics

• New: Skewness and Kurtosis (issue #126; script: calcSkewness(), calcKurtosis()).
• Fixed: The twelve Export pop-ups show only their sentence, with no character(0) title bar.

Breeding Group Formation

Major

• Groups are formed from living animals only, whatever the Source, so the default Top ranked 20 are animals that can breed. An animal counts as alive when its Status is ALIVE (or, in a pedigree with no Status column, when it has no exit date). If none is alive, the tab says so and forms no groups.
• Several candidate groupings are shown per run, with a selector and comparison table (issue #125). Script users: groupAddAssign() returns a candidates field and takes maxCandidates (issue #146).
• Formation can follow your center’s ancestry rules (issue #168). Upload a rules file in the new Ancestry Guardrails section to block or flag mixing of ancestry groups. A block rule can be overridden with a written reason, and an audit record can be downloaded. Without a rules file, formation is unchanged. Script users: readAncestryRules(), checkAncestryRules(), the ancestryRules argument of groupAddAssign(), and reportAncestryViolations().
• A harem’s automatically chosen sire is now kept apart from his relatives like every other animal. An animal at or above the Max kinship threshold to him, or one an ancestry block rule bars from him, stays out of his harem; if that leaves no one, the harem is the sire alone. Results for a given random seed differ from earlier versions.
• With a Custom sex ratio, a male under the Minimum breeding age, or with no birth date, is left out of the groups and listed under Unused animals. A group stops filling when no breeding-age male is left for it, so it can end with fewer females than the ratio asks for. groupAddAssign() and fillGroupMembersWithSexRatio() follow the same rule. On a pedigree with such males, results for a given random seed differ from earlier versions.

Minor

• New Include animals by control: a genetic-value floor as an alternative to the top-N cutoff (issue #128).
• New Exhaustive enumeration mode: lists every maximal group that can be housed together, for the simplest case only. Script users: the exhaustive argument of groupAddAssign() (issue #146).
• The Source choice “Upload list”, which had no place to give it a list, is now “My own list”. Paste the animal IDs into the box that appears. Groups are formed from those that are alive; an ID that is not in the pedigree stops the run and is named, and an animal that is not alive is left out and named.
• The last box on the Groups tab, which holds the animals that fit no group, is headed Unused animals instead of the next group number. The Statistics table, the Group Detail list and the Genetic Diversity heat map use the same name.
• Fixed: With Harem selected, seeding a male in some groups but not all no longer stops the run with “subscript out of bounds”. A group with a seeded male keeps him as its sire; a group with no seeded male is given a sire chosen at random.
• Fixed: A script that passes harem = TRUE and a non-zero sexRatio to groupAddAssign() now stops with a message naming both settings, instead of returning groups of one or two animals; use one or the other.
• Fixed: A box that holds exactly one animal is headed “(1 animal)” on the Groups tab, not “(1 animals)”.
• Fixed: After you read a different pedigree or trim it on the Pedigree Browser, a group holding an animal that is not loaded no longer shows old group sizes over empty tables and a red error. The Groups, Statistics and Group Detail pages say so in one sentence and ask you to form the groups again or bring back the earlier pedigree. Group Detail shows no tables or Export buttons until then. The groups are kept, so bringing that pedigree back shows them again.
• Fixed: Forming groups that include animals with no birth date no longer ends the session after a genetic value analysis.

Mate Pair Analysis

• New Mate Pair Analysis tab: a curator view of possible mate pairs with relatedness and genetic-value context, separate from Breeding Group Formation. Report only (issue #151).
• Mate pair reports can follow your ancestry rules (issue #169). Rules loaded on the Breeding Groups tab apply here, and a rule can be overridden with a written reason.
• Eligible and excluded pairs can be exported.
• Script users: reportMatePairs().

Genetic Diversity

• Fixed: A breeding group with no breeding-age females has a gray Production cell, because Production cannot be calculated for it.
• Fixed: An undefined Inbreeding cell is red.
• Fixed: A female with no birth date and no offspring is left out of the Production and Inbreeding cells, and a note under the heat map gives the counts.
• Fixed: The heat map’s column and group names are written level, bold and whole, at 2.5 times the old size.
• Fixed: After focal animals are chosen, the tab scores every group with the whole pedigree’s kinship instead of stopping with “kmat is missing kinship for group member(s)”.

Marker Genetics

• New Marker Genetics tab (issue #130):
  • Kinship Comparison compares DNA-based with pedigree-based relatedness.
  • Heterozygosity compares each animal’s diversity with the population expectation.
  • Parentage Exclusion flags a recorded parent that the DNA contradicts.
  • Candidate Parent Assignment ranks genotyped animals that could be a flagged animal’s real parent. Report only (issue #147).
  • Cross-Center compares diversity between two centers. It is not the Cross-Center Identity tab below, which merges individual records.
  • Linkage and LD Block Metrics reports locus coverage, relatedness variance and linked marker blocks (issue #153).
  • Genomic ROH (F_ROH) shows the sequence-based inbreeding calculation, from runs of homozygosity, with de-identified export (issue #152).
• Script users: checkMarkerGenotypeFile(), buildMarkerGenotypeMatrix(), markerKinship(), markerObservedHeterozygosity(), markerExpectedHeterozygosity(), markerParentageExclusion(), markerParentageLikelihood(), markerFst(), checkLocusMetadata(), checkLinkageMarkerGenotypeFile(), markerRealizedRelatednessVariance(), markerLdBlock(), obfuscateLdBlocks(), checkSequenceGenotypeFile(), computeGenomicROH(), obfuscateGenomicROH() and obfuscateGenotypeMatrix().

MHC Haplotype Reporting

• New MHC Haplotype Reporting tab: upload haplotype designations to see how common each haplotype is, which are rare, and which animals carry them, with de-identified downloads (issue #148).
• Script users: checkMhcHaplotypeFile(), mhcHaplotypeFrequency(), mhcHaplotypeCarriers() and obfuscateMhcHaplotypes().

Cross-Center Identity Matching

• 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).
• Script users: checkCrossCenterMapping() checks an id-matching table and resolveCrossCenterIds() merges the records.

De-Identified Export

Major

• New De-Identified Export tab: a preview on request and three downloads (the de-identified pedigree, a record of changes, and a private re-identification key) behind a confirmation step (issue #150).

Minor

• obfuscatePed() gained linkedDateShift (default TRUE): all of one animal’s dates move by the same offset, so the gaps between them stay realistic (issue #150).

Potential Parents

• Changed: Potential Parents (getPotentialParents()) lists candidates only for the missing parent: an animal with a recorded dam and no sire gets candidate sires, and the reverse.
• New: each Potential Parents result (getPotentialParents()) now says where its dam list came from, in damBasis.
• Fixed: A female who gave birth too close in time to have carried the animal is left out as dam.

Longitudinal Monitoring

• Colony managers can keep a history file of dated colony snapshots, one row of colony-level genetic-health values per date, to see whether genetic health is improving or eroding (issue #167).
• New Genetic-Health Trends tab: upload or start a history, record a snapshot from the genetic value analysis you just ran, view trend plots, and compare two dates. Snapshots recorded under different settings or software versions are flagged, so a jump is not mistaken for a real change in the colony.
• Build Earlier Snapshots on the Genetic-Health Trends tab rebuilds a yearly history from the birth and exit dates in the studbook, so a trend shows without waiting for new snapshots; rebuilt points are drawn dashed and kept apart from recorded ones (issue #170).
• Script users: readSnapshotHistory(), checkSnapshotHistory(), createColonySnapshot(), appendColonySnapshot(), plotSnapshotTrends(), calcSnapshotDeltas(), backfillColonySnapshots() and previewBackfillSupport().

Speed and Memory

• The Genetic Value analysis of the shipped example (708 animals, 1,000 iterations) takes about 0.2 seconds instead of about 3, the Summary Statistics relationship downloads of the whole example finish in under 10 seconds instead of not finishing, and 1,000 Breeding Groups trials take about 6 seconds instead of about 23 (about 5 instead of about 27 when forming harems). The app no longer keeps a kinship matrix of the whole pedigree, so it holds about 180 MB less once the example is loaded, and Summary Statistics no longer keeps the table of every pair after a relationship download (about 235 MB for the example). Results are the same as before for the same random seed.

• kinship(sparse = TRUE) takes about half a second for the whole shipped example (3,694 animals) instead of about 43 seconds.

• Loading the package takes about 0.4 seconds instead of about 0.9: it no longer loads Matrix and ggplot2, which a sparse kinship matrix or a plot loads when first needed.

General Fixes

• Configuration file
  • Fixed: A line starting with # is a comment wherever the file is read, so a site that copies the example file unedited no longer gets the API key paste-your-labkey-api-key-here in place of its .netrc file.
  • Fixed: A setting written with different capitals, such as Center, is read instead of stopping with “subscript out of bounds”.
  • Fixed: A value in double quotes is one value, so a path such as "/My Folder/EHR" is not split.
  • Fixed: A setting with nothing after its = is empty, so an empty apiKey is no key.
  • Fixed: data("exampleNprcgenekeeprConfig") is the shipped example file.
• Installation and example files
  • Fixed: The app starts after a default install, because shinyBS now installs with the package; 2.0.0 stopped with “there is no package called ‘shinyBS’” until it was installed by hand.
  • Fixed: The Japanese macaque example file deidentified_jmac_ped.csv is rebuilt from a 2018 studbook (2,590 animals, 819 with a recorded sire) and loads once Minimum Dam Age is 3.3 or lower and Minimum Sire Age is 4.3 or lower.
• Script functions
  • removeUnknownAnimals(), convertDate(), removeDuplicates() and correctParentSex() treat only animals recorded as added as stand-ins.
  • getAncestors(), findLoops() and countLoops() stop with a message naming the animals instead of an “infinite recursion” error when an animal is its own ancestor, and no longer stop with “argument is of length zero” when a parent has no row of its own.
  • getLkDirectAncestors() and getPedDirectRelatives() no longer run without end on a pedigree with an animal as its own ancestor or a row with no id.
  • reportGV() stops before any calculation, naming every missing column, when the pedigree lacks id, sire, dam, gen or sex, and reportGV() and gvaConvergence() stop with the number of animals when the population has fewer than 2.
  • convertRelationships(), makeRelationClassesTable(), filterKinMatrix(), calcGU(), calcGUSE(), calcA(), kinship(), calcFE(), calcFG(), calcFEFG() and calcFGSE() work for a single animal.
  • calcGU(), calcGUSE() and alleleFreq() return an empty table for no animals or no alleles.
  • create_wkbk(), saveDataframesAsFiles(), makeExamplePedigreeFile(), obfuscateDate(), obfuscateId(), obfuscatePed(), withinIntegerRange() and makeGeneticDiversityHeatmap() say what is wrong in their messages.
  • setExit() finds a death or departure column in any letter case.
  • makeGroupNum() and makeGrpNum() make one group when called with no number, as their help said they would.
  • convertRelationships(), makeCEPH(), groupAddAssign(), fillGroupMembersWithSexRatio() and findOffspring() take ids given as numbers or as a factor as their text; such a studbook got wrong relationship names, NA offspring counts or a stopped run.
  • get_elapsed_time_str() rounds before it writes minutes and seconds.

nprcgenekeepr 2.0.0 (20260721)

• 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 animals with an unknown parent) against the package’s own example data instead of only its graceful-degradation message.

nprcgenekeepr 1.0.8 (20250723)

• 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)

• 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 18.
  • 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)

• 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 \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

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.