Files in nprcgenekeepr

Genetic Tools for Colony Management

MD5

NEWS.md README.md

NAMESPACE

DESCRIPTION

LICENSE

R/gvaConvergence.R R/kinshipMatricesToKValues.R R/getGenoDefinedParentGenotypes.R R/readExcelPOSIXToCharacter.R R/normalizeGvReport.R R/get_and_or_list.R R/getFocalAnimalPedFromFile.R R/assertRequiredColsPresent.R R/muffleIncompleteFinalLine.R R/modGeneticDiversity.R R/calcGUSE.R R/assignAlleles.R R/addGroupOfUnusedAnimals.R R/chooseAllelesChar.R R/defaultSiteParams.R R/calcFG.R R/hasBothParents.R R/print.summary.nprcgenekeeprErr.R R/chooseDate.R R/hasInvalidIdChar.R R/classifyParentage.R R/findGeneration.R R/convertDate.R R/getConfigFileName.R R/unknown2NA.R R/getPotentialSires.R R/correctParentSex.R R/obfuscateDate.R R/getSpeciesGestation.R R/checkGenotypeFile.R R/getPyramidAgeDist.R R/getGVPopulation.R R/getAnimalsWithHighKinship.R R/summarizeKinshipValues.R R/makeGroupNum.R R/addParents.R R/createSimKinships.R R/withinIntegerRange.R R/calcGU.R R/setExit.R R/mapIdsToObfuscated.R R/getFounders.R R/convertStatusCodes.R R/insertChangedColsTab.R R/getPossibleCols.R R/getPedMaxAge.R R/makeCEPH.R R/headerDisplayNames.R R/runQcStudbook.R R/getRecordStatusIndex.R R/removeDuplicates.R R/modGvAndBgDesc.R R/getChangedColsTab.R R/removeAutoGenIds.R R/getLivingBreeders.R R/resetGroup.R R/shouldShowChangedColsTab.R R/saveDataframesAsFiles.R R/calcRetention.R R/getPedDirectRelatives.R R/isEmpty.R R/orderReport.R R/checkChangedColAndErrorLst.R R/findPedigreeNumber.R R/getProductionStatus.R R/modPyramid.R R/makeFounderStatsTable.R R/getOffspring.R R/getSpeciesOverridesPath.R R/getLkDirectRelatives.R R/findLoops.R R/filterKinMatrix.R R/makesLoop.R R/hasNetrc.R R/kinMatrix2LongForm.R R/get_elapsed_time_str.R R/createPedSix.R R/fillGroupMembers.R R/filterPairs.R R/colChange.R R/safeExecute.R R/calcFE.R R/sexCodes.R R/chooseAlleles.R R/getDatedFileName.R R/data.R R/calcA.R R/alleleFreq.R R/flagOverriddenRelationships.R R/modORIPReporting.R R/getIncludeColumns.R R/getPedigree.R R/getGenotypes.R R/convertSexCodes.R R/getBoxWhiskerDescription.R R/makeGeneticDiversityHeatmap.R R/appServer.R R/loadSpeciesOverrides.R R/makeAvailable.R R/getGVGenotype.R R/removeUninformativeFounders.R R/removeEarlyDates.R R/initializeHaremGroups.R R/rankSubjects.R R/logModuleEvent.R R/isFounder.R R/kinship.R R/readFocalAnimalIds.R R/getPotentialParents.R R/calcNeVariance.R R/addBackSecondParents.R R/filterReport.R R/makeRelationClassesTable.R R/getEmptyErrorLst.R R/filterAge.R R/getConfigApiKey.R R/modGeneticValue.R R/fillGroupMembersWithSexRatio.R R/calcFEFG.R R/savePlotToFile.R R/obfuscatePed.R R/makeRoundUp.R R/create_wkbk.R R/removePotentialSires.R R/columnSchema.R R/makeExamplePedigreeFile.R R/getProportionLow.R R/getDescendantPedigree.R R/addIdRecords.R R/loadSiteConfig.R R/getErrorTab.R R/fillBins.R R/getIndianOriginStatus.R R/countLoops.R R/checkKinshipOverrides.R R/rbindFill.R R/makeGeneticSummaryTable.R R/getPedigreeSource.R R/summary.nprcgenekeeprErr.R R/checkFgDegeneracy.R R/toCharacter.R R/convertFromCenter.R R/checkParentAge.R R/addSexAndAgeToGroup.R R/applyKinshipOverrides.R R/getPyramidPlot.R R/readKinshipOverrides.R R/getIdsWithOneParent.R R/kinshipMatrixToKValues.R R/insertErrorTab.R R/appUI.R R/getKinshipWithMaleStatus.R R/meanKinship.R R/getGeneticDiversityStats.R R/runModularApp.R R/allTrueNoNA.R R/createExampleFiles.R R/groupMembersReturn.R R/convertAncestry.R R/cumulateSimKinships.R R/addGenotype.R R/findOffspring.R R/getDateErrorsAndConvertDatesInPed.R R/createPedOne.R R/createPedTree.R R/getProbandPedigree.R R/getLkDirectAncestors.R R/modSummaryStats.R R/resolveBreedingAge.R R/is_valid_date_str.R R/getSiteInfo.R R/runGenekeepr.R R/addErrTxt.R R/modInput.R R/modPotentialParents.R R/applyKinshipOverridesToMatrix.R R/getSpeciesMinBreedingAge.R R/calcGeneDiversity.R R/insertSeparators.R R/getParents.R R/offspringCounts.R R/reportGV.R R/addKinshipValueCount.R R/addAnimalsWithNoRelative.R R/nprcgenekeepr-package.R R/addUIds.R R/str_detect_fixed_all.R R/shouldShowOripTab.R R/calcNeSexRatio.R R/modBreedingGroups.R R/getVersion.R R/checkChangedColsLst.R R/setLabKeyDefaults.R R/removeUnknownAnimals.R R/trimPedigree.R R/modPedigree.R R/groupAddAssign.R R/getDateColNames.R R/calcFGSE.R R/filterThreshold.R R/checkErrorLst.R R/calcAge.R R/getRequiredCols.R R/getSexRatioWithAdditions.R R/correctUnknownParentMeanKinship.R R/calcFounderContributions.R R/getFileDirectRelatives.R R/getTokenList.R R/getDemographics.R R/hasGenotype.R R/makeGroupMembers.R R/checkRequiredCols.R R/set_seed.R R/getParamDef.R R/removeGroupIfNoAvailableAnimals.R R/getCurrentAge.R R/prepareKinshipOverrides.R R/countFirstOrder.R R/getAncestors.R R/obfuscateId.R R/setPopulation.R R/makeSimPed.R R/removeSelectedAnimalFromAvailableAnimals.R R/autoIdFormat.R R/countKinshipValues.R R/calculateSexRatio.R R/getMaxAx.R R/getFocalAnimalPed.R R/qcStudbook.R R/processQcStudbookResult.R R/geneDrop.R R/fixColumnNames.R R/convertRelationships.R R/dataframe2string.R

inst/WORDLIST

inst/doc/simulatedKValues.html

inst/doc/gvaConvergence.html

inst/doc/a2interactive.Rmd

inst/doc/a2interactive.html

inst/doc/a3manual.R inst/doc/a3manual.Rmd inst/doc/simulatedKValues.Rmd

inst/doc/a3manual.html

inst/doc/gvaConvergence.Rmd

inst/www/js/data-ready.js

inst/testdata/qcPed.txt

inst/testdata/qcPed.xlsx

inst/testdata/qcPed.csv

inst/testdata/qcPedEmpty.txt

inst/extdata/2022-05-02_Deidentified_Pedigree_focal_animals.csv

inst/extdata/ExamplePedigree_bad_dates.txt

inst/extdata/pedTwo.csv

inst/extdata/pedThree.csv

inst/extdata/jsslogo.jpg

inst/extdata/no_animals.csv

inst/extdata/obfuscated_rhesus_mhc_ped.csv

inst/extdata/pedOne.csv

inst/extdata/ExamplePedigree.txt

inst/extdata/rhesusPedigree_fromCenter.csv

inst/extdata/2022-05-02_Deidentified_Pedigree.xlsx

inst/extdata/focalAnimalsShortList.csv

inst/extdata/pedFive.csv

inst/extdata/create_nprcgenekeepr_hexbadge.R

inst/extdata/focalAnimals.csv

inst/extdata/emptyFocalAnimals.csv

inst/extdata/obfuscated_rhesus_mhc_breeder_genotypes.csv

inst/extdata/deidentified_jmac_ped_edited.csv

inst/extdata/ExamplePedigree.csv

inst/extdata/example_nprcgenekeepr_config

inst/extdata/pedSix.csv

inst/extdata/deidentified_jmac_ped.csv

inst/extdata/pedFour.csv

inst/extdata/ui_guidance/gvAndBgDesc.html

inst/extdata/ui_guidance/pyramidPlot.html

inst/extdata/ui_guidance/input_format.html

inst/extdata/ui_guidance/genetic_value.html

inst/extdata/ui_guidance/population_genetics_terms.html

inst/extdata/ui_guidance/summary_stats.html

inst/extdata/ui_guidance/group_formation.html

inst/extdata/ui_guidance/pedigree_browser.html

inst/shinytest/app.R

build/vignette.rds

tests/testthat.R tests/spelling.R tests/testthat/test_resetGroup.R tests/testthat/test_makeGeneticSummaryTable.R tests/testthat/test-e2e-boundary-conditions.R tests/testthat/test_getSpeciesMinBreedingAge.R tests/testthat/test_checkParentAge.R tests/testthat/test_sexCodes.R tests/testthat/test_getPyramidAgeDist.R tests/testthat/test_species_first_class.R tests/testthat/test_modInput.R tests/testthat/test_getPedigreeSource.R tests/testthat/test_makeExamplePedigreeFile.R tests/testthat/test-e2e-workflow-integration.R tests/testthat/test_shouldShowOripTab.R tests/testthat/test_gvaConvergence.R tests/testthat/test_getDatedFilename.R tests/testthat/helper-vignette-minParentAge-scan.R tests/testthat/test_appServer_dynamicTabs.R tests/testthat/test_withinIntegerRange.R tests/testthat/test_effectivePopulationSizeDocs.R tests/testthat/test_calcFounderContributions.R tests/testthat/test_getPedMaxAge.R tests/testthat/test_is_valid_date_str.R tests/testthat/test_countKinshipValues.R tests/testthat/test_addErrTxt.R tests/testthat/test_helper_shinytest2.R tests/testthat/test_makeSimPed.R tests/testthat/test_loadSiteConfig.R tests/testthat/test_getVersion.R tests/testthat/test_getTokenList.R tests/testthat/test-e2e-pedigree-module.R tests/testthat/test_print.summary.nprcgenekeeprErr.R tests/testthat/test_getFocalAnimalPed.R tests/testthat/test_modSummaryStats_relationships.R tests/testthat/test_checkKinshipOverrides.R tests/testthat/test_insertErrorTab.R tests/testthat/helper-fgSEValidation.R tests/testthat/test_dataframe2string.R tests/testthat/test_pkgdown_reference_config.R tests/testthat/test_kinshipOverrideDocs.R tests/testthat/test_modBreedingGroups_groupAddAssign.R tests/testthat/test_addParents.R tests/testthat/test_getConfigApiKey.R tests/testthat/test_countLoops.R tests/testthat/test_shouldShowChangedColsTab.R tests/testthat/test_modPotentialParents_coverage.R tests/testthat/test_makeGroupNum.R tests/testthat/test_getProbandPedigree.R tests/testthat/test-e2e-data-ready.R tests/testthat/test-e2e-input-detailed.R tests/testthat/test-e2e-potential-parents-module.R tests/testthat/test_rhesusGenotypes.R tests/testthat/test_fillGroupMembers.R tests/testthat/test_convertFromCenter.R tests/testthat/test_runQcStudbook.R tests/testthat/test_modBreedingGroups_kinshipOverrides.R tests/testthat/test-e2e-home-navigation.R tests/testthat/test_vignettes_no_deprecated_minParentAge.R tests/testthat/test_modInput_qcStudbook.R tests/testthat/test-e2e-genetic-value-tutorial.R tests/testthat/test_checkErrorLst.R tests/testthat/test_getPyramidPlot.R tests/testthat/test_summarizeKinshipValues.R tests/testthat/test_normalizeGvReport.R tests/testthat/test_makeRelationsClasses.R tests/testthat/test_summary.nprcgenekeeprGV.R tests/testthat/test_getPedDirectRelatives.R tests/testthat/test_prepareKinshipOverrides.R tests/testthat/test_obfuscatePed.R tests/testthat/test_obfuscateId.R tests/testthat/test_orderReport.R tests/testthat/test_convertDate.R tests/testthat/test_calcFEFG.R tests/testthat/test_addSexAndAgeToGroup.R tests/testthat/helper-fgSEFixtures.R tests/testthat/test_correctParentSex.R tests/testthat/test_appUI_version.R tests/testthat/test_getFileDirectRelatives.R tests/testthat/test_print.summary.nprcgenekeeprGV.R tests/testthat/test_modInput_incomplete_final_line.R tests/testthat/test_rhesusPedigree.R tests/testthat/test-e2e-error-states.R tests/testthat/test-app-navigation.R tests/testthat/test_calcA.R tests/testthat/test_getPossibleCols.R tests/testthat/test_convertSexCodes.R tests/testthat/test_filterThreshold.R tests/testthat/test_examplePedigree.R tests/testthat/test_findGeneration.R tests/testthat/test-shinytest2-debug.R tests/testthat/test_getParents.R tests/testthat/test_makeRoundup.R tests/testthat/test_modErrorHandling.R tests/testthat/test_classifyParentage.R tests/testthat/test_removeEarlyDates.R tests/testthat/test_modSummaryStats_ggplots.R tests/testthat/test_getIncludeColumns.R tests/testthat/test_calcGUSE.R tests/testthat/test_checkGenotypeFile.R tests/testthat/test_create_test_app.R tests/testthat/test_summary.nprcgenekeeprErr.R tests/testthat/test_getPotentialParents.R tests/testthat/test_modSummaryStats.R tests/testthat/test_getMaxAx.R tests/testthat/test_moduleContract.R tests/testthat/test_calcRetention.R tests/testthat/test_modSummaryStats_kinshipOverrides.R tests/testthat/test_examples_invoke_documented_fn.R tests/testthat/test_modFounderStats.R tests/testthat/test_get_elapsed_time_str.R tests/testthat/test_kinship.R tests/testthat/test_cumulateSimKinships.R tests/testthat/test-e2e-summary-statistics-module.R tests/testthat/test_applyKinshipOverrides.R tests/testthat/test-e2e-genetic-value-module.R tests/testthat/test_modGvAndBgDesc.R tests/testthat/test_groupAddAssign.R tests/testthat/test_addSecondParents.R tests/testthat/test_calcGU.R tests/testthat/test_getDemographics.R tests/testthat/test_modGeneticValue.R tests/testthat/test_kinshipMatricesToKValues.R tests/testthat/test-e2e-breeding-groups-module.R tests/testthat/test_allTrueNoNA.R tests/testthat/test_assertRequiredColsPresent.R tests/testthat/test_qcStudbook.R tests/testthat/test_calculatetSexRatio.R tests/testthat/test_createPedSix.R tests/testthat/test_appServer_server.R tests/testthat/test_addBackSecondParents.R tests/testthat/test_modBreedingGroups.R tests/testthat/test_geneDrop.R tests/testthat/test_addGenotype.R tests/testthat/test-e2e-breeding-groups-tutorial.R tests/testthat/test_modSiteConfig.R tests/testthat/test_headerDisplayNames.R tests/testthat/test_getRecordStatusIndex.R tests/testthat/test_getChangedColsTab.R tests/testthat/test-e2e-settings-about.R tests/testthat/test_modPotentialParents.R tests/testthat/test_modPotentialParents_sexSpecificAge.R tests/testthat/test_makeGroupMembers.R tests/testthat/test_removeUninformativeFounders.R tests/testthat/test_hasInvalidIdChar.R tests/testthat/test_calcNeSexRatio.R tests/testthat/test-e2e-pedigree-detailed.R tests/testthat/test_convertStatusCodes.R tests/testthat/test_kinMatrix2LongForm.R tests/testthat/test-e2e-pedigree-tutorial.R tests/testthat/test_modORIPReporting.R tests/testthat/test_findPedigreeNumber.R tests/testthat/test_filterKinMatrix.R tests/testthat/test-e2e-input-incomplete-final-line.R tests/testthat/test_addIdRecords.R tests/testthat/test_getFounders.R tests/testthat/test_monolith_removed.R tests/testthat/test_getFocalAnimalPedFromFile.R tests/testthat/test_getLkDirectAncestors.R tests/testthat/test_addUIds.R tests/testthat/test_removeAutoGenIds.R tests/testthat/test-e2e-pyramid-module.R tests/testthat/test_trimPedigree.R tests/testthat/test_modPyramid.R tests/testthat/test_fixColumnNames.R tests/testthat/test_modInput_sexSpecificAge.R tests/testthat/test_getLkDirectRelatives.R tests/testthat/test_readKinshipOverrides.R tests/testthat/test_modBreedingGroups_sharedKinship.R tests/testthat/test-e2e-input-module.R tests/testthat/test_resolveBreedingAge.R tests/testthat/test_modInput_coverage.R tests/testthat/test_modGeneticValue_kinshipOverrides.R tests/testthat/test_getPedigree.R tests/testthat/test_makeFounderStatsTable.R tests/testthat/test_hasGenotype.R tests/testthat/test_findLoops.R tests/testthat/test_modSummaryStats_popovers.R tests/testthat/test_convertAncestry.R tests/testthat/test_exampleData_columnNames.R tests/testthat/test_getIndianOriginStatus.R tests/testthat/test_getSiteInfo.R tests/testthat/test_checkRequiredCols.R tests/testthat/test_isFounder.R tests/testthat/test_modGeneticDiversity.R tests/testthat/test_calcFE.R tests/testthat/test_checkChangedColsLst.R tests/testthat/test_correctUnknownParentMeanKinship.R

tests/testthat/exampleFile.txt

tests/testthat/test_mapIdsToObfuscated.R tests/testthat/test_createSimKinships.R tests/testthat/test_modSummaryStats_parity.R tests/testthat/test_fillBins.R tests/testthat/test_flagOverriddenRelationships.R tests/testthat/test_fillGroupMembersWithSexRatio.R tests/testthat/test_loadSpeciesOverrides.R tests/testthat/test_modPlotDownload.R tests/testthat/test-e2e-pyramid-detailed.R tests/testthat/test_createPedTree.R tests/testthat/test_rankSubjects.R tests/testthat/test_addAnimalsWithNoRelative.R tests/testthat/helper-shinytest2.R tests/testthat/test_modPedigree_processing.R tests/testthat/test_filterReport.R tests/testthat/test_getSpeciesGestation.R tests/testthat/test_kinshipMatrixToKValues.R tests/testthat/test_getKinshipWithMaleStatus.R tests/testthat/test_modGeneticValue_coverage.R tests/testthat/test_createExampleFiles.R tests/testthat/test_resetPopulation.R tests/testthat/test_modInput_excelSireDam.R tests/testthat/test_filterPairs.R tests/testthat/test_chooseAllelesChar.R tests/testthat/test_getConfigFileName.R tests/testthat/test_modSummaryStats_coverage.R tests/testthat/test_getLivingBreeders.R tests/testthat/test_getErrorTab.R tests/testthat/test_calcFGSE.R tests/testthat/test_calcGeneDiversity.R tests/testthat/test_appUI_siteinfo.R tests/testthat/test_alleleFreq.R tests/testthat/test_getGeneticDiversityStats.R tests/testthat/test_hasNetrc.R tests/testthat/test_modORIPReporting_server.R tests/testthat/test_filterAge.R tests/testthat/test-e2e-breeding-groups-detailed.R tests/testthat/test_setExit.R tests/testthat/test_calcFG.R tests/testthat/test_saveDataframesAsFiles.R tests/testthat/test-e2e-genetic-value-detailed.R tests/testthat/test_makeGeneticDiversityHeatmap.R tests/testthat/test-set_seed.R tests/testthat/test_reportGV.R tests/testthat/test_modBreedingGroups_coverage.R tests/testthat/test_insertSeparators.R tests/testthat/setup.R tests/testthat/test_convertRelationships.R tests/testthat/test_modPedigree.R tests/testthat/test_assignAlleles.R tests/testthat/test_chooseDate.R tests/testthat/test_modPedigree_coverage.R tests/testthat/test_getOffspring.R tests/testthat/test_autoIdFormat.R tests/testthat/test_meanKinship.R tests/testthat/test_calcNeVariance.R tests/testthat/test_getGVPopulation.R tests/testthat/test_appServer_logging.R tests/testthat/test_getGenotypes.R tests/testthat/test_countFirstOrder.R tests/testthat/test_calcAge.R tests/testthat/test_createPedOne.R tests/testthat/test_runModularApp_alias.R tests/testthat/test-e2e-orip-module.R tests/testthat/test_fgSEValidation.R tests/testthat/test_removeDuplicates.R tests/testthat/test_shinytest2_workflow_coverage.R tests/testthat/test_getProductionStatus.R tests/testthat/test_modPyramid_coverage.R tests/testthat/test_create_wkbk.R tests/testthat/test_getAncestors.R tests/testthat/test_muffleIncompleteFinalLine.R tests/testthat/test_defaultSiteParams.R tests/testthat/test_getDescendantPedigree.R tests/testthat/test-app-loading.R tests/testthat/test_obfuscateDate.R tests/testthat/test_getProportionLow.R tests/testthat/test_getParamDef.R tests/testthat/test_removeUnknownAnimals.R tests/testthat/test_setLabKeyDefaults.R tests/testthat/test-e2e-input-tutorial.R tests/testthat/test_gvaConvergence_kinshipOverrides.R vignettes/a2interactive.Rmd vignettes/a3manual.Rmd vignettes/simulatedKValues.Rmd vignettes/gvaConvergence.Rmd vignettes/manual_components/_database_access.Rmd vignettes/manual_components/_genome_uniqueness_algorithm.Rmd vignettes/manual_components/_introduction.Rmd vignettes/manual_components/_installation.Rmd vignettes/manual_components/_genetic_value_analysis.Rmd vignettes/manual_components/_input.Rmd vignettes/manual_components/_gv_and_bg_desc.Rmd vignettes/manual_components/_orip_reporting.Rmd vignettes/manual_components/_online_documentation.Rmd vignettes/manual_components/_summary_of_major_functions.Rmd vignettes/manual_components/_software_development.Rmd vignettes/manual_components/_breeding_group_algorithm.Rmd vignettes/manual_components/_summary_statistics.Rmd vignettes/manual_components/_breeding_group_formation.Rmd vignettes/manual_components/_pedigree_browser.Rmd vignettes/manual_components/_running_shiny_application.Rmd

data/speciesGestation.RData

data/ped1Alleles.RData

data/finalRpt.RData

data/smallPedTree.RData

data/rhesusPedigree.RData

data/lacy1989Ped.RData

data/focalAnimals.RData

data/pedSix.RData

data/exampleNprcgenekeeprConfig.RData

data/pedMissingBirth.RData

data/pedWithGenotype.RData

data/pedWithGenotypeReport.RData

data/pedDuplicateIds.RData

data/examplePedigree.RData

data/qcBreeders.RData

data/qcPedGvReport.RData

data/pedOne.RData

data/qcPed.RData

data/pedInvalidDates.RData

data/pedGood.RData

data/pedSameMaleIsSireAndDam.RData

data/lacy1989PedAlleles.RData

data/pedFemaleSireMaleDam.RData

data/rhesusGenotypes.RData

data/smallPed.RData

man/getBoxWhiskerDescription.Rd man/geneDrop.Rd man/modORIPReportingUI.Rd man/modGeneticValueServer.Rd man/savePlotToFile.Rd man/makeSimPed.Rd man/modGvAndBgDescServer.Rd man/makeFounderStatsTable.Rd man/processQcStudbookResult.Rd man/meanKinship.Rd man/createPedTree.Rd man/modGeneticValueUI.Rd man/convertDate.Rd man/ped1Alleles.Rd man/makeCEPH.Rd man/createExampleFiles.Rd man/getSpeciesMinBreedingAge.Rd man/lacy1989Ped.Rd man/getFileDirectRelatives.Rd man/makeExamplePedigreeFile.Rd man/convertFromCenter.Rd man/qcStudbook.Rd man/getPedMaxAge.Rd man/runModularApp.Rd man/modBreedingGroupsServer.Rd man/offspringCounts.Rd man/checkChangedColsLst.Rd man/modSummaryStatsUI.Rd man/getAnimalsWithHighKinship.Rd man/readKinshipOverrides.Rd man/calcFEFG.Rd man/exampleNprcgenekeeprConfig.Rd man/kinMatrix2LongForm.Rd man/pedSix.Rd man/trimPedigree.Rd man/appServer.Rd man/focalAnimals.Rd man/runGeneKeepR.Rd man/getFocalAnimalPedFromFile.Rd man/getLkDirectRelatives.Rd man/countKinshipValues.Rd man/pedMissingBirth.Rd man/correctParentSex.Rd man/summarizeKinshipValues.Rd man/getFocalAnimalPed.Rd man/modInputServer.Rd man/getIdsWithOneParent.Rd man/pedWithGenotypeReport.Rd man/checkKinshipOverrides.Rd man/groupAddAssign.Rd man/qcPedGvReport.Rd man/appUI.Rd man/create_wkbk.Rd man/getDemographics.Rd man/calcGU.Rd man/getEmptyErrorLst.Rd man/makeGeneticSummaryTable.Rd man/fixColumnNames.Rd man/kinship.Rd man/filterKinMatrix.Rd man/convertAncestry.Rd man/modPotentialParentsServer.Rd man/isFounder.Rd man/pedWithGenotype.Rd man/checkParentAge.Rd man/countLoops.Rd man/getProbandPedigree.Rd man/hasBothParents.Rd man/kinshipMatrixToKValues.Rd man/rhesusPedigree.Rd man/convertSexCodes.Rd man/dataframe2string.Rd man/filterThreshold.Rd man/modPyramidServer.Rd man/calcNeVariance.Rd man/shouldShowChangedColsTab.Rd man/makeRelationClassesTable.Rd man/makeGroupMembers.Rd man/getPedigree.Rd man/get_and_or_list.Rd man/modBreedingGroupsUI.Rd man/getConfigFileName.Rd man/applyKinshipOverrides.Rd man/hasGenotype.Rd man/getPyramidAgeDist.Rd man/modSummaryStatsServer.Rd man/getFounders.Rd man/makeGeneticDiversityHeatmap.Rd man/addIdRecords.Rd man/pedOne.Rd man/loadSpeciesOverrides.Rd man/logModuleEvent.Rd man/rankSubjects.Rd man/getVersion.Rd man/pedDuplicateIds.Rd man/createSimKinships.Rd man/examplePedigree.Rd man/calcGeneDiversity.Rd man/smallPed.Rd man/makeGroupNum.Rd man/modInputUI.Rd man/getSpeciesGestation.Rd man/getChangedColsTab.Rd man/removeEarlyDates.Rd man/findPedigreeNumber.Rd man/calculateSexRatio.Rd man/getPyramidPlot.Rd man/qcPed.Rd man/addAnimalsWithNoRelative.Rd man/alleleFreq.Rd man/runQcStudbook.Rd man/getTokenList.Rd man/getDatedFilename.Rd man/pedGood.Rd man/checkGenotypeFile.Rd man/set_seed.Rd man/checkErrorLst.Rd man/getPotentialParents.Rd man/pedFemaleSireMaleDam.Rd man/calcRetention.Rd man/getErrorTab.Rd man/gvaConvergence.Rd man/getPotentialSires.Rd man/safeExecute.Rd man/toCharacter.Rd man/filterPairs.Rd man/removeUninformativeFounders.Rd man/convertStatusCodes.Rd man/findLoops.Rd man/modPedigreeUI.Rd man/findOffspring.Rd man/nprcgenekeepr-package.Rd man/getCurrentAge.Rd man/modGvAndBgDescUI.Rd man/findGeneration.Rd man/getDescendantPedigree.Rd man/filterReport.Rd man/addUIds.Rd man/mapIdsToObfuscated.Rd man/qcBreeders.Rd man/obfuscatePed.Rd man/getSiteInfo.Rd man/calcA.Rd man/pedInvalidDates.Rd man/assignAlleles.Rd man/calcGUSE.Rd man/calcFE.Rd man/addGenotype.Rd man/obfuscateId.Rd man/lacy1989PedAlleles.Rd man/kinshipMatricesToKValues.Rd man/setLabKeyDefaults.Rd man/print.Rd man/chooseDate.Rd man/saveDataframesAsFiles.Rd man/calcAge.Rd man/modGeneticDiversityUI.Rd man/getGVGenotype.Rd man/getGeneticDiversityStats.Rd man/makeGrpNum.Rd man/modPedigreeServer.Rd man/getGenotypes.Rd man/obfuscateDate.Rd man/getAncestors.Rd man/smallPedTree.Rd man/addBackSecondParents.Rd man/get_elapsed_time_str.Rd man/calcFG.Rd man/getAutoIdFormat.Rd man/getDateErrorsAndConvertDatesInPed.Rd man/getPossibleCols.Rd man/fillGroupMembersWithSexRatio.Rd man/convertRelationships.Rd man/checkRequiredCols.Rd man/removeDuplicates.Rd man/modPyramidUI.Rd man/removeUnknownAnimals.Rd man/getParents.Rd man/getOffspring.Rd man/withinIntegerRange.Rd man/is_valid_date_str.Rd man/removeAutoGenIds.Rd man/addSexAndAgeToGroup.Rd man/addParents.Rd man/removePotentialSires.Rd man/cumulateSimKinships.Rd man/setAutoIdFormat.Rd man/speciesGestation.Rd man/reportGV.Rd man/summary.Rd man/countFirstOrder.Rd man/modPotentialParentsUI.Rd man/chooseAlleles.Rd man/headerDisplayNames.Rd man/getGVPopulation.Rd man/getPedDirectRelatives.Rd man/getLkDirectAncestors.Rd man/getRequiredCols.Rd man/setPopulation.Rd man/calcFGSE.Rd man/loadSiteConfig.Rd man/rhesusGenotypes.Rd man/modGeneticDiversityServer.Rd man/finalRpt.Rd man/shouldShowOripTab.Rd man/modORIPReportingServer.Rd man/pedSameMaleIsSireAndDam.Rd man/setExit.Rd man/calcNeSexRatio.Rd man/getIncludeColumns.Rd

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man/figures/lifecycle-stable.svg

man/figures/lifecycle-superseded.svg

man/figures/logo.png

man/figures/GeneDrop.png

man/figures/lifecycle-experimental.svg

man/figures/lifecycle-deprecated.svg

nprcgenekeepr documentation built on July 26, 2026, 5:06 p.m.