Files in rmsharp/nprcmanager

Genetic Tools for Colony Management

20200415_cran-comments.md 20200510_cran-comments.md 20200517_cran-comments.md 20201107_cran-comments.md 20210324_cran-comments.md 20210330_cran-comments.md 20241220_cran-comments.md CODE_OF_CONDUCT.md LICENSE.md NEWS.Rmd NEWS.md R/addAnimalsWithNoRelative.R R/addBackSecondParents.R R/addErrTxt.R R/addGenotype.R R/addGroupOfUnusedAnimals.R R/addIdRecords.R R/addKinshipValueCount.R R/addParents.R R/addSexAndAgeToGroup.R R/addUIds.R R/agePyramidPlot.R R/allTrueNoNA.R R/alleleFreq.R R/assignAlleles.R R/calcA.R R/calcAge.R R/calcFE.R R/calcFEFG.R R/calcFG.R R/calcGU.R R/calcRetention.R R/calculateSexRatio.R R/checkChangedColAndErrorLst.R R/checkChangedColsLst.R R/checkErrorLst.R R/checkGenotypeFile.R R/checkParentAge.R R/checkRequiredCols.R R/chooseAlleles.R R/chooseAllelesChar.R R/chooseDate.R R/colChange.R R/convertAncestry.R R/convertDate.R R/convertFromCenter.R R/convertRelationships.R R/convertSexCodes.R R/convertStatusCodes.R R/correctParentSex.R R/countFirstOrder.R R/countKinshipValues.R R/countLoops.R R/createExampleFiles.R R/createPedOne.R R/createPedSix.R R/createPedTree.R R/createSimKinships.R R/create_wkbk.R R/cumulateSimKinships.R R/data.R R/dataframe2string.R R/fillBins.R R/fillGroupMembers.R R/fillGroupMembersWithSexRatio.R R/filterAge.R R/filterKinMatrix.R R/filterPairs.R R/filterReport.R R/filterThreshold.R R/findGeneration.R R/findLoops.R R/findOffspring.R R/findPedigreeNumber.R R/fixColumnNames.R R/fixGenotypeCols.R R/geneDrop.R R/getAncestors.R R/getAnimalsWithHighKinship.R R/getChangedColsTab.R R/getConfigFileName.R R/getCurrentAge.R R/getDateColNames.R R/getDateErrorsAndConvertDatesInPed.R R/getDatedFileName.R R/getDemographics.R R/getEmptyErrorLst.R R/getErrorTab.R R/getFocalAnimalPed.R R/getGVGenotype.R R/getGVPopulation.R R/getGenoDefinedParentGenotypes.R R/getGenotypes.R R/getIdsWithOneParent.R R/getIncludeColumns.R R/getIndianOriginStatus.R R/getLkDirectAncestors.R R/getLkDirectRelatives.R R/getLogo.R R/getMaxAx.R R/getMinParentAge.R R/getOffspring.R R/getParamDef.R R/getParents.R R/getPedDirectRelatives.R R/getPedMaxAge.R R/getPedigree.R R/getPossibleCols.R R/getPotentialParents.R R/getPotentialSires.R R/getProbandPedigree.R R/getProductionStatus.R R/getProportionLow.R R/getPyramidAgeDist.R R/getPyramidPlot.R R/getRecordStatusIndex.R R/getRequiredCols.R R/getSexRatioWithAdditions.R R/getSimSires.R R/getSiteInfo.R R/getTokenList.R R/getVersion.R R/get_and_or_list.R R/get_elapsed_time_str.R R/groupAddAssign.R R/groupMembersReturn.R R/hasBothParents.R R/hasGenotype.R R/headerDisplayNames.R R/initializeHaremGroups.R R/insertChangedColsTab.R R/insertErrorTab.R R/insertSeparators.R R/isEmpty.R R/is_valid_date_str.R R/kinMatrix2LongForm.R R/kinship.R R/kinshipMatricesToKValues.R R/kinshipMatrixToKValues.R R/makeAvailable.R R/makeCEPH.R R/makeExamplePedigreeFile.R R/makeGeneticDiversityDashboard.R R/makeGroupMembers.R R/makeGrpNum.R R/makeRelationsClassesTable.R R/makeRoundUp.R R/makeSimPed.R R/makesLoop.R R/mapIdsToObfuscated.R R/meanKinship.R R/nprcgenekeeper.R R/nprcgenekeepr-package.R R/obfuscateDate.R R/obfuscateId.R R/obfuscatePed.R R/offspringCounts.R R/orderReport.R R/print.summary.nprcgenekeeprErr.R R/qcStudbook.R R/rankSubjects.R R/rbindFill.R R/readExcelPOSIXToCharacter.R R/removeAutoGenIds.R R/removeDuplicates.R R/removeEarlyDates.R R/removeGroupIfNoAvailableAnimals.R R/removePotentialSires.R R/removeSelectedAnimalFromAvailableAnimals.R R/removeUninformativeFounders.R R/removeUnknownAnimals.R R/reportGV.R R/resetGroup.R R/runGenekeepr.R R/saveDataframesAsFiles.R R/setExit.R R/setPopulation.R R/set_seed.R R/str_detect_fixed_all.R R/summarizeKinshipValues.R R/summary.nprcgenekeeprErr.R R/toCharacter.R R/trimPedigree.R R/unknown2NA.R R/withinIntegerRange.R README.Rmd README.md cran-comments.md inst/application/global.R inst/application/server.r inst/application/ui.r inst/application/uitpBreedingGroupFormation.R inst/application/uitpGeneticValueAnalysis.R inst/application/uitpGvAndBgDesc.R inst/application/uitpInput.R inst/application/uitpOripReporting.R inst/application/uitpPedigreeBrowser.R inst/application/uitpPyramidPlot.R inst/application/uitpSummaryStatistics.R inst/extdata/code_under_development/combinerKinshipTriangles.R inst/extdata/create_nprcgenekeepr_hexbadge.R inst/extdata/meeting_notes.Rmd inst/extdata/script_used_to_look_for_gdata_dependency.R inst/extdata/trulyUnknownParents.R man/addAnimalsWithNoRelative.Rd man/addBackSecondParents.Rd man/addGenotype.Rd man/addIdRecords.Rd man/addParents.Rd man/addSexAndAgeToGroup.Rd man/addUIds.Rd man/alleleFreq.Rd man/assignAlleles.Rd man/calcA.Rd man/calcAge.Rd man/calcFE.Rd man/calcFEFG.Rd man/calcFG.Rd man/calcGU.Rd man/calcRetention.Rd man/calculateSexRatio.Rd man/checkChangedColsLst.Rd man/checkErrorLst.Rd man/checkGenotypeFile.Rd man/checkParentAge.Rd man/checkRequiredCols.Rd man/chooseAlleles.Rd man/chooseDate.Rd man/convertAncestry.Rd man/convertDate.Rd man/convertFromCenter.Rd man/convertRelationships.Rd man/convertSexCodes.Rd man/convertStatusCodes.Rd man/correctParentSex.Rd man/countFirstOrder.Rd man/countKinshipValues.Rd man/countLoops.Rd man/createExampleFiles.Rd man/createPedTree.Rd man/createSimKinships.Rd man/create_wkbk.Rd man/cumulateSimKinships.Rd man/dataframe2string.Rd man/exampleNprcgenekeeprConfig.Rd man/examplePedigree.Rd man/fillGroupMembersWithSexRatio.Rd man/filterKinMatrix.Rd man/filterPairs.Rd man/filterReport.Rd man/filterThreshold.Rd man/finalRpt.Rd man/findGeneration.Rd man/findLoops.Rd man/findOffspring.Rd man/findPedigreeNumber.Rd man/fixColumnNames.Rd man/focalAnimals.Rd man/geneDrop.Rd man/getAncestors.Rd man/getAnimalsWithHighKinship.Rd man/getChangedColsTab.Rd man/getConfigFileName.Rd man/getCurrentAge.Rd man/getDateErrorsAndConvertDatesInPed.Rd man/getDatedFilename.Rd man/getDemographics.Rd man/getEmptyErrorLst.Rd man/getErrorTab.Rd man/getFocalAnimalPed.Rd man/getGVGenotype.Rd man/getGVPopulation.Rd man/getGenotypes.Rd man/getIdsWithOneParent.Rd man/getIncludeColumns.Rd man/getLkDirectAncestors.Rd man/getLkDirectRelatives.Rd man/getLogo.Rd man/getOffspring.Rd man/getParents.Rd man/getPedDirectRelatives.Rd man/getPedMaxAge.Rd man/getPedigree.Rd man/getPossibleCols.Rd man/getPotentialParents.Rd man/getPotentialSires.Rd man/getProbandPedigree.Rd man/getPyramidAgeDist.Rd man/getPyramidPlot.Rd man/getRequiredCols.Rd man/getSiteInfo.Rd man/getTokenList.Rd man/getVersion.Rd man/get_and_or_list.Rd man/get_elapsed_time_str.Rd man/groupAddAssign.Rd man/hasBothParents.Rd man/hasGenotype.Rd man/headerDisplayNames.Rd man/is_valid_date_str.Rd man/kinMatrix2LongForm.Rd man/kinship.Rd man/kinshipMatricesToKValues.Rd man/kinshipMatrixToKValues.Rd man/lacy1989Ped.Rd man/lacy1989PedAlleles.Rd man/makeCEPH.Rd man/makeExamplePedigreeFile.Rd man/makeRelationClassesTable.Rd man/makeSimPed.Rd man/mapIdsToObfuscated.Rd man/meanKinship.Rd man/nprcgenekeepr-package.Rd man/nprcgenekeepr.Rd man/obfuscateDate.Rd man/obfuscateId.Rd man/obfuscatePed.Rd man/offspringCounts.Rd man/ped1Alleles.Rd man/pedDuplicateIds.Rd man/pedFemaleSireMaleDam.Rd man/pedGood.Rd man/pedInvalidDates.Rd man/pedMissingBirth.Rd man/pedOne.Rd man/pedSameMaleIsSireAndDam.Rd man/pedSix.Rd man/pedWithGenotype.Rd man/pedWithGenotypeReport.Rd man/print.Rd man/qcBreeders.Rd man/qcPed.Rd man/qcPedGvReport.Rd man/qcStudbook.Rd man/rankSubjects.Rd man/removeAutoGenIds.Rd man/removeDuplicates.Rd man/removeEarlyDates.Rd man/removePotentialSires.Rd man/removeUninformativeFounders.Rd man/removeUnknownAnimals.Rd man/reportGV.Rd man/rhesusGenotypes.Rd man/rhesusPedigree.Rd man/runGeneKeepR.Rd man/saveDataframesAsFiles.Rd man/setExit.Rd man/setPopulation.Rd man/set_seed.Rd man/smallPed.Rd man/smallPedTree.Rd man/summarizeKinshipValues.Rd man/summary.Rd man/toCharacter.Rd man/trimPedigree.Rd man/withinIntegerRange.Rd tests/spelling.R tests/testthat.R tests/testthat/test-set_seed.R tests/testthat/test_addAnimalsWithNoRelative.R tests/testthat/test_addBackSecondParents.R tests/testthat/test_addErrTxt.R tests/testthat/test_addGenotype.R tests/testthat/test_addIdRecords.R tests/testthat/test_addParents.R tests/testthat/test_addSecondParents.R tests/testthat/test_addSexAndAgeToGroup.R tests/testthat/test_addUIds.R tests/testthat/test_allTrueNoNA.R tests/testthat/test_alleleFreq.R tests/testthat/test_assignAlleles.R tests/testthat/test_basic.R tests/testthat/test_calcA.R tests/testthat/test_calcAge.R tests/testthat/test_calcFE.R tests/testthat/test_calcFEFG.R tests/testthat/test_calcFG.R tests/testthat/test_calcGU.R tests/testthat/test_calcRetention.R tests/testthat/test_calculatetSexRatio.R tests/testthat/test_checkChangedColsLst.R tests/testthat/test_checkErrorLst.R tests/testthat/test_checkGenotypeFile.R tests/testthat/test_checkParentAge.R tests/testthat/test_checkRequiredCols.R tests/testthat/test_chooseAllelesChar.R tests/testthat/test_chooseDate.R tests/testthat/test_convertAncestry.R tests/testthat/test_convertDate.R tests/testthat/test_convertFromCenter.R tests/testthat/test_convertRelationships.R tests/testthat/test_convertSexCodes.R tests/testthat/test_convertStatusCodes.R tests/testthat/test_correctParentSex.R tests/testthat/test_countFirstOrder.R tests/testthat/test_countKinshipValues.R tests/testthat/test_countLoops.R tests/testthat/test_createExampleFiles.R tests/testthat/test_createPedOne.R tests/testthat/test_createPedSix.R tests/testthat/test_createPedTree.R tests/testthat/test_createSimKinships.R tests/testthat/test_create_wkbk.R tests/testthat/test_cumulateSimKinships.R tests/testthat/test_dataframe2string.R tests/testthat/test_fillBins.R tests/testthat/test_fillGroupMembers.R tests/testthat/test_fillGroupMembersWithSexRatio.R tests/testthat/test_filterAge.R tests/testthat/test_filterKinMatrix.R tests/testthat/test_filterPairs.R tests/testthat/test_filterReport.R tests/testthat/test_filterThreshold.R tests/testthat/test_findGeneration.R tests/testthat/test_findLoops.R tests/testthat/test_findPedigreeNumber.R tests/testthat/test_fixGenotypeCols.R tests/testthat/test_geneDrop.R tests/testthat/test_getChangedColsTab.R tests/testthat/test_getConfigFileName.R tests/testthat/test_getDatedFilename.R tests/testthat/test_getDemographics.R tests/testthat/test_getErrorTab.R tests/testthat/test_getFocalAnimalPed.R tests/testthat/test_getGVPopulation.R tests/testthat/test_getGenotypes.R tests/testthat/test_getIncludeColumns.R tests/testthat/test_getIndianOriginStatus.R tests/testthat/test_getLkDirectAncestors.R tests/testthat/test_getLkDirectRelatives.R tests/testthat/test_getLogo.R tests/testthat/test_getMaxAx.R tests/testthat/test_getMinParentAge.R tests/testthat/test_getOffspring.R tests/testthat/test_getParamDef.R tests/testthat/test_getParents.R tests/testthat/test_getPedDirectRelatives.R tests/testthat/test_getPedMaxAge.R tests/testthat/test_getPedigree.R tests/testthat/test_getPossibleCols.R tests/testthat/test_getPotentialParents.R tests/testthat/test_getProbandPedigree.R tests/testthat/test_getProductionStatus.R tests/testthat/test_getProportionLow.R tests/testthat/test_getPyramidAgeDist.R tests/testthat/test_getPyramidPlot.R tests/testthat/test_getRecordStatusIndex.R tests/testthat/test_getSiteInfo.R tests/testthat/test_getTokenList.R tests/testthat/test_getVersion.R tests/testthat/test_get_elapsed_time_str.R tests/testthat/test_groupAddAssign.R tests/testthat/test_hasGenotype.R tests/testthat/test_headerDisplayNames.R tests/testthat/test_insertErrorTab.R tests/testthat/test_insertSeparators.R tests/testthat/test_is_valid_date_str.R tests/testthat/test_kinMatrix2LongForm.R tests/testthat/test_kinship.R tests/testthat/test_kinshipMatricesToKValues.R tests/testthat/test_makeExamplePedigreeFile.R tests/testthat/test_makeGeneticDiversityDashboard.R tests/testthat/test_makeGroupMembers.R tests/testthat/test_makeRelationsClasses.R tests/testthat/test_makeRoundup.R tests/testthat/test_makeSimPed.R tests/testthat/test_mapIdsToObfuscated.R tests/testthat/test_meanKinship.R tests/testthat/test_obfuscateDate.R tests/testthat/test_obfuscateId.R tests/testthat/test_obfuscatePed.R tests/testthat/test_orderReport.R tests/testthat/test_print.summary.nprcgenekeeprErr.R tests/testthat/test_print.summary.nprcgenekeeprGV.R tests/testthat/test_qcStudbook.R tests/testthat/test_rankSubjects.R tests/testthat/test_removeDuplicates.R tests/testthat/test_removeEarlyDates.R tests/testthat/test_removeUninformativeFounders.R tests/testthat/test_removeUnknownAnimals.R tests/testthat/test_reportGV.R tests/testthat/test_resetGroup.R tests/testthat/test_resetPopulation.R tests/testthat/test_saveDataframesAsFiles.R tests/testthat/test_setExit.R tests/testthat/test_summarizeKinshipValues.R tests/testthat/test_summary.nprcgenekeeprErr.R tests/testthat/test_summary.nprcgenekeeprGV.R tests/testthat/test_trimPedigree.R tests/testthat/test_withinIntegerRange.R vignettes/ColonyManagerTutorial.Rmd vignettes/a2interactive.Rmd vignettes/a3manual.Rmd vignettes/manual_components/_bg_algorithm.Rmd vignettes/manual_components/_bg_formation.Rmd vignettes/manual_components/_breeding_group_algorithm.Rmd vignettes/manual_components/_breeding_group_formation.Rmd vignettes/manual_components/_database_access.Rmd vignettes/manual_components/_genetic_value_analysis.Rmd vignettes/manual_components/_genome_uniqueness_algorithm.Rmd vignettes/manual_components/_gv_and_bg_desc.Rmd vignettes/manual_components/_input.Rmd vignettes/manual_components/_installation.Rmd vignettes/manual_components/_introduction.Rmd vignettes/manual_components/_online_documentation.Rmd vignettes/manual_components/_orip_reporting.Rmd vignettes/manual_components/_pedigree_browser.Rmd vignettes/manual_components/_running_shiny_application.Rmd vignettes/manual_components/_software_development.Rmd vignettes/manual_components/_summary_of_major_functions.Rmd vignettes/manual_components/_summary_statistics.Rmd vignettes/simulatedKValues.Rmd