API for nprcgenekeepr
Genetic Tools for Colony Management
| Global functions | |
|---|---|
| R_version | Source code |
| addAnimalsWithNoRelative | Man page Source code |
| addBackSecondParents | Man page Source code |
| addErrTxt | Source code |
| addGenotype | Man page Source code |
| addGroupOfUnusedAnimals | Source code |
| addIdRecords | Man page Source code |
| addKinshipValueCount | Source code |
| addParents | Man page Source code |
| addSexAndAgeToGroup | Man page Source code |
| addUIds | Man page Source code |
| allTrueNoNA | Source code |
| alleleFreq | Man page Source code |
| appServer | Man page Source code |
| appUI | Man page Source code |
| applyKinshipOverrides | Man page Source code |
| applyKinshipOverridesToMatrix | Source code |
| assertRequiredColsPresent | Source code |
| assignAlleles | Man page Source code |
| calcA | Man page Source code |
| calcAge | Man page Source code |
| calcFE | Man page Source code |
| calcFEFG | Man page Source code |
| calcFG | Man page Source code |
| calcFGSE | Man page Source code |
| calcFounderContributions | Source code |
| calcGU | Man page Source code |
| calcGUSE | Man page Source code |
| calcGeneDiversity | Man page Source code |
| calcNeSexRatio | Man page Source code |
| calcNeVariance | Man page Source code |
| calcRetention | Man page Source code |
| calculateSexRatio | Man page Source code |
| checkChangedColAndErrorLst | Source code |
| checkChangedColsLst | Man page Source code |
| checkErrorLst | Man page Source code |
| checkFgDegeneracy | Source code |
| checkGenotypeFile | Man page Source code |
| checkKinshipOverrides | Man page Source code |
| checkParentAge | Man page Source code |
| checkRequiredCols | Man page Source code |
| chooseAlleles | Man page Source code |
| chooseAllelesChar | Source code |
| chooseDate | Man page Source code |
| classifyParentage | Source code |
| colChange | Source code |
| convertAncestry | Man page Source code |
| convertDate | Man page Source code |
| convertFromCenter | Man page Source code |
| convertRelationships | Man page Source code |
| convertSexCodes | Man page Source code |
| convertStatusCodes | Man page Source code |
| correctParentSex | Man page Source code |
| correctUnknownParentMeanKinship | Source code |
| countFirstOrder | Man page Source code |
| countKinshipValues | Man page Source code |
| countLoops | Man page Source code |
| createExampleFiles | Man page Source code |
| createPedOne | Source code |
| createPedSix | Source code |
| createPedTree | Man page Source code |
| createSimKinships | Man page Source code |
| create_wkbk | Man page Source code |
| cumulateSimKinships | Man page Source code |
| dataframe2string | Man page Source code |
| defaultSiteParams | Source code |
| exampleNprcgenekeeprConfig | Man page |
| examplePedigree | Man page |
| fillBins | Source code |
| fillGroupMembers | Source code |
| fillGroupMembersWithSexRatio | Man page Source code |
| filterAge | Source code |
| filterKinMatrix | Man page Source code |
| filterPairs | Man page Source code |
| filterReport | Man page Source code |
| filterThreshold | Man page Source code |
| finalRpt | Man page |
| findGeneration | Man page Source code |
| findLoops | Man page Source code |
| findOffspring | Man page Source code |
| findPedigreeNumber | Man page Source code |
| firstPedigreeSpecies | Source code |
| fixColumnNames | Man page Source code |
| flagOverriddenRelationships | Source code |
| flattenPotentialParents | Source code |
| focalAnimals | Man page |
| gatedSeed | Source code |
| geneDrop | Man page Source code |
| getAncestors | Man page Source code |
| getAnimalsWithHighKinship | Man page Source code |
| getAutoIdFormat | Man page Source code |
| getAutoIdPrefix | Source code |
| getBoxWhiskerDescription | Man page Source code |
| getBreedingPeerCohort | Source code |
| getChangedColsTab | Man page Source code |
| getConfigApiKey | Source code |
| getConfigFileName | Man page Source code |
| getCurrentAge | Man page Source code |
| getDateColNames | Source code |
| getDateErrorsAndConvertDatesInPed | Man page Source code |
| getDatedFilename | Man page Source code |
| getDemographics | Man page Source code |
| getDescendantPedigree | Man page Source code |
| getEmptyErrorLst | Man page Source code |
| getErrorTab | Man page Source code |
| getFileDirectRelatives | Man page Source code |
| getFocalAnimalPed | Man page Source code |
| getFocalAnimalPedFromFile | Man page Source code |
| getFounders | Man page Source code |
| getGVGenotype | Man page Source code |
| getGVPopulation | Man page Source code |
| getGeneticDiversityStats | Man page Source code |
| getGenoDefinedParentGenotypes | Source code |
| getGenotypes | Man page Source code |
| getIdsWithOneParent | Man page Source code |
| getIncludeColumns | Man page Source code |
| getIndianOriginStatus | Source code |
| getKinshipWithMaleStatus | Source code |
| getLivingBreeders | Source code |
| getLkDirectAncestors | Man page Source code |
| getLkDirectRelatives | Man page Source code |
| getMaxAx | Source code |
| getOffspring | Man page Source code |
| getOptionalConfigToken | Source code |
| getParamDef | Source code |
| getParents | Man page Source code |
| getPedDirectRelatives | Man page Source code |
| getPedMaxAge | Man page Source code |
| getPedigree | Man page Source code |
| getPedigreeSource | Source code |
| getPossibleCols | Man page Source code |
| getPotentialParents | Man page Source code |
| getPotentialSires | Man page Source code |
| getProbandPedigree | Man page Source code |
| getProductionStatus | Source code |
| getProportionLow | Source code |
| getPyramidAgeDist | Man page Source code |
| getPyramidPlot | Man page Source code |
| getRecordStatusIndex | Source code |
| getRequiredCols | Man page Source code |
| getSexRatioWithAdditions | Source code |
| getSiteInfo | Man page Source code |
| getSpeciesGestation | Man page Source code |
| getSpeciesMinBreedingAge | Man page Source code |
| getSpeciesOverridesPath | Source code |
| getTokenList | Man page Source code |
| getVersion | Man page Source code |
| get_and_or_list | Man page Source code |
| get_elapsed_time_str | Man page Source code |
| groupAddAssign | Man page Source code |
| groupMembersReturn | Source code |
| gvaConvergence | Man page Source code |
| hasBothParents | Man page Source code |
| hasGenotype | Man page Source code |
| hasInvalidIdChar | Source code |
| hasNetrc | Source code |
| headerDisplayNames | Man page Source code |
| initializeHaremGroups | Source code |
| insertChangedColsTab | Source code |
| insertErrorTab | Source code |
| insertSeparators | Source code |
| isEmpty | Source code |
| isFounder | Man page Source code |
| isGeneratedUnknownId | Source code |
| is_valid_date_str | Man page Source code |
| kinMatrix2LongForm | Man page Source code |
| kinship | Man page Source code |
| kinshipMatricesToKValues | Man page Source code |
| kinshipMatrixToKValues | Man page Source code |
| lacy1989Ped | Man page |
| lacy1989PedAlleles | Man page |
| loadSiteConfig | Man page Source code |
| loadSpeciesOverrides | Man page Source code |
| logModuleEvent | Man page Source code |
| makeAvailable | Source code |
| makeCEPH | Man page Source code |
| makeExamplePedigreeFile | Man page Source code |
| makeFounderStatsTable | Man page Source code |
| makeGeneticDiversityHeatmap | Man page Source code |
| makeGeneticSummaryTable | Man page Source code |
| makeGroupMembers | Man page Source code |
| makeGroupNum | Man page Source code |
| makeGrpNum | Man page Source code |
| makeRelationClassesTable | Man page Source code |
| makeRoundUp | Source code |
| makeSimPed | Man page Source code |
| makesLoop | Source code |
| mapIdsToObfuscated | Man page Source code |
| meanKinship | Man page Source code |
| mergeSpeciesOverrides | Source code |
| modBreedingGroupsServer | Man page Source code |
| modBreedingGroupsUI | Man page Source code |
| modGeneticDiversityServer | Man page Source code |
| modGeneticDiversityUI | Man page Source code |
| modGeneticValueServer | Man page Source code |
| modGeneticValueUI | Man page Source code |
| modGvAndBgDescServer | Man page Source code |
| modGvAndBgDescUI | Man page Source code |
| modInputServer | Man page Source code |
| modInputUI | Man page Source code |
| modORIPReportingServer | Man page Source code |
| modORIPReportingUI | Man page Source code |
| modPedigreeServer | Man page Source code |
| modPedigreeUI | Man page Source code |
| modPotentialParentsServer | Man page Source code |
| modPotentialParentsUI | Man page Source code |
| modPyramidServer | Man page Source code |
| modPyramidUI | Man page Source code |
| modSummaryStatsServer | Man page Source code |
| modSummaryStatsUI | Man page Source code |
| muffleCannotOpenFile | Source code |
| muffleIncompleteFinalLine | Source code |
| normalizeGvReport | Source code |
| nprcgenekeepr | Man page |
| nprcgenekeepr-package | Man page |
| nprcgenekeeprFileErr | Source code |
| obfuscateDate | Man page Source code |
| obfuscateId | Man page Source code |
| obfuscatePed | Man page Source code |
| offspringCounts | Man page Source code |
| orderReport | Source code |
| parseOptionalAge | Source code |
| ped1Alleles | Man page |
| pedDuplicateIds | Man page |
| pedFemaleSireMaleDam | Man page |
| pedGood | Man page |
| pedInvalidDates | Man page |
| pedMissingBirth | Man page |
| pedOne | Man page |
| pedSameMaleIsSireAndDam | Man page |
| pedSix | Man page |
| pedWithGenotype | Man page |
| pedWithGenotypeReport | Man page |
| pedigreeGestationDefault | Source code |
| pedigreeReadReason | Source code |
| prefillGuardAllows | Source code |
| prepareKinshipOverrides | Source code |
| print.summary.nprcgenekeeprErr | Man page Source code |
| print.summary.nprcgenekeeprGV | Man page Source code |
| processQcStudbookResult | Man page Source code |
| qcBreeders | Man page |
| qcPed | Man page |
| qcPedGvReport | Man page |
| qcStudbook | Man page Source code |
| rankSubjects | Man page Source code |
| rbindFill | Source code |
| readAndMergeSpeciesOverrides | Source code |
| readExcelPOSIXToCharacter | Source code |
| readFocalAnimalIds | Source code |
| readKinshipOverrides | Man page Source code |
| removeAutoGenIds | Man page Source code |
| removeDuplicates | Man page Source code |
| removeEarlyDates | Man page Source code |
| removeGroupIfNoAvailableAnimals | Source code |
| removePotentialSires | Man page Source code |
| removeSelectedAnimalFromAvailableAnimals | Source code |
| removeUninformativeFounders | Man page Source code |
| removeUnknownAnimals | Man page Source code |
| reportGV | Man page Source code |
| resetGroup | Source code |
| resolveBreedingAge | Source code |
| rhesusGenotypes | Man page |
| rhesusPedigree | Man page |
| runGeneKeepR | Man page Source code |
| runModularApp | Man page Source code |
| runQcStudbook | Man page Source code |
| safeExecute | Man page Source code |
| saveDataframesAsFiles | Man page Source code |
| savePlotToFile | Man page Source code |
| setAutoIdFormat | Man page Source code |
| setExit | Man page Source code |
| setLabKeyDefaults | Man page Source code |
| setPopulation | Man page Source code |
| set_seed | Man page Source code |
| shouldShowChangedColsTab | Man page Source code |
| shouldShowOripTab | Man page Source code |
| smallPed | Man page |
| smallPedTree | Man page |
| speciesGestation | Man page |
| str_detect_fixed_all | Source code |
| summarizeKinshipValues | Man page Source code |
| summary.nprcgenekeeprErr | Man page Source code |
| summary.nprcgenekeeprGV | Man page Source code |
| toCharacter | Man page Source code |
| trimPedigree | Man page Source code |
| unknown2NA | Source code |
| withinIntegerRange | Man page Source code |
