# Generated by roxygen2: do not edit by hand

S3method(print,summary.nprcgenekeeprErr)
S3method(print,summary.nprcgenekeeprGV)
S3method(summary,nprcgenekeeprErr)
S3method(summary,nprcgenekeeprGV)
export(addAnimalsWithNoRelative)
export(addBackSecondParents)
export(addGenotype)
export(addIdRecords)
export(addParents)
export(addSexAndAgeToGroup)
export(addUIds)
export(alleleFreq)
export(appServer)
export(appUI)
export(applyKinshipOverrides)
export(assignAlleles)
export(calcA)
export(calcAge)
export(calcFE)
export(calcFEFG)
export(calcFG)
export(calcFGSE)
export(calcGU)
export(calcGUSE)
export(calcGeneDiversity)
export(calcNeSexRatio)
export(calcNeVariance)
export(calcRetention)
export(calculateSexRatio)
export(checkChangedColsLst)
export(checkErrorLst)
export(checkGenotypeFile)
export(checkKinshipOverrides)
export(checkParentAge)
export(checkRequiredCols)
export(chooseAlleles)
export(chooseDate)
export(convertAncestry)
export(convertDate)
export(convertFromCenter)
export(convertRelationships)
export(convertSexCodes)
export(convertStatusCodes)
export(correctParentSex)
export(countFirstOrder)
export(countKinshipValues)
export(countLoops)
export(createExampleFiles)
export(createPedTree)
export(createSimKinships)
export(create_wkbk)
export(cumulateSimKinships)
export(dataframe2string)
export(fillGroupMembersWithSexRatio)
export(filterKinMatrix)
export(filterPairs)
export(filterReport)
export(filterThreshold)
export(findGeneration)
export(findLoops)
export(findOffspring)
export(findPedigreeNumber)
export(fixColumnNames)
export(geneDrop)
export(getAncestors)
export(getAnimalsWithHighKinship)
export(getAutoIdFormat)
export(getBoxWhiskerDescription)
export(getChangedColsTab)
export(getConfigFileName)
export(getCurrentAge)
export(getDateErrorsAndConvertDatesInPed)
export(getDatedFilename)
export(getDemographics)
export(getDescendantPedigree)
export(getEmptyErrorLst)
export(getErrorTab)
export(getFileDirectRelatives)
export(getFocalAnimalPed)
export(getFocalAnimalPedFromFile)
export(getFounders)
export(getGVGenotype)
export(getGVPopulation)
export(getGeneticDiversityStats)
export(getGenotypes)
export(getIdsWithOneParent)
export(getIncludeColumns)
export(getLkDirectAncestors)
export(getLkDirectRelatives)
export(getOffspring)
export(getParents)
export(getPedDirectRelatives)
export(getPedMaxAge)
export(getPedigree)
export(getPossibleCols)
export(getPotentialParents)
export(getPotentialSires)
export(getProbandPedigree)
export(getPyramidAgeDist)
export(getPyramidPlot)
export(getRequiredCols)
export(getSiteInfo)
export(getSpeciesGestation)
export(getSpeciesMinBreedingAge)
export(getTokenList)
export(getVersion)
export(get_and_or_list)
export(get_elapsed_time_str)
export(groupAddAssign)
export(gvaConvergence)
export(hasBothParents)
export(hasGenotype)
export(headerDisplayNames)
export(isFounder)
export(is_valid_date_str)
export(kinMatrix2LongForm)
export(kinship)
export(kinshipMatricesToKValues)
export(kinshipMatrixToKValues)
export(loadSiteConfig)
export(loadSpeciesOverrides)
export(logModuleEvent)
export(makeCEPH)
export(makeExamplePedigreeFile)
export(makeFounderStatsTable)
export(makeGeneticDiversityHeatmap)
export(makeGeneticSummaryTable)
export(makeGroupMembers)
export(makeGroupNum)
export(makeGrpNum)
export(makeRelationClassesTable)
export(makeSimPed)
export(mapIdsToObfuscated)
export(meanKinship)
export(modBreedingGroupsServer)
export(modBreedingGroupsUI)
export(modGeneticDiversityServer)
export(modGeneticDiversityUI)
export(modGeneticValueServer)
export(modGeneticValueUI)
export(modGvAndBgDescServer)
export(modGvAndBgDescUI)
export(modInputServer)
export(modInputUI)
export(modORIPReportingServer)
export(modORIPReportingUI)
export(modPedigreeServer)
export(modPedigreeUI)
export(modPotentialParentsServer)
export(modPotentialParentsUI)
export(modPyramidServer)
export(modPyramidUI)
export(modSummaryStatsServer)
export(modSummaryStatsUI)
export(obfuscateDate)
export(obfuscateId)
export(obfuscatePed)
export(offspringCounts)
export(processQcStudbookResult)
export(qcStudbook)
export(rankSubjects)
export(readKinshipOverrides)
export(removeAutoGenIds)
export(removeDuplicates)
export(removeEarlyDates)
export(removePotentialSires)
export(removeUninformativeFounders)
export(removeUnknownAnimals)
export(reportGV)
export(runGeneKeepR)
export(runModularApp)
export(runQcStudbook)
export(safeExecute)
export(saveDataframesAsFiles)
export(savePlotToFile)
export(setAutoIdFormat)
export(setExit)
export(setLabKeyDefaults)
export(setPopulation)
export(set_seed)
export(shouldShowChangedColsTab)
export(shouldShowOripTab)
export(summarizeKinshipValues)
export(toCharacter)
export(trimPedigree)
export(withinIntegerRange)
import(Matrix)
import(shiny)
importFrom(DT,DTOutput)
importFrom(DT,renderDT)
importFrom(Rlabkey,labkey.selectRows)
importFrom(Rlabkey,labkey.setDefaults)
importFrom(anytime,anytime)
importFrom(bslib,bs_theme)
importFrom(data.table,as.data.table)
importFrom(data.table,rbindlist)
importFrom(futile.logger,DEBUG)
importFrom(futile.logger,INFO)
importFrom(futile.logger,appender.file)
importFrom(futile.logger,flog.debug)
importFrom(futile.logger,flog.info)
importFrom(futile.logger,flog.logger)
importFrom(futile.logger,flog.threshold)
importFrom(futile.logger,flog.warn)
importFrom(ggplot2,.data)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(grDevices,dev.off)
importFrom(grDevices,png)
importFrom(graphics,boxplot)
importFrom(graphics,hist)
importFrom(graphics,par)
importFrom(graphics,plot.new)
importFrom(graphics,text)
importFrom(htmlTable,htmlTable)
importFrom(lifecycle,deprecate_warn)
importFrom(lifecycle,deprecated)
importFrom(lifecycle,is_present)
importFrom(lubridate,as.duration)
importFrom(lubridate,ddays)
importFrom(lubridate,duration)
importFrom(lubridate,dyears)
importFrom(lubridate,interval)
importFrom(lubridate,is.Date)
importFrom(lubridate,mdy)
importFrom(lubridate,now)
importFrom(lubridate,today)
importFrom(lubridate,year)
importFrom(lubridate,ymd)
importFrom(openxlsx,write.xlsx)
importFrom(plotrix,color.gradient)
importFrom(plotrix,pyramid.plot)
importFrom(readxl,excel_format)
importFrom(readxl,read_excel)
importFrom(sessioninfo,package_info)
importFrom(shiny,NS)
importFrom(shiny,actionButton)
importFrom(shiny,br)
importFrom(shiny,checkboxInput)
importFrom(shiny,column)
importFrom(shiny,conditionalPanel)
importFrom(shiny,div)
importFrom(shiny,downloadButton)
importFrom(shiny,downloadHandler)
importFrom(shiny,eventReactive)
importFrom(shiny,fileInput)
importFrom(shiny,fluidRow)
importFrom(shiny,getDefaultReactiveDomain)
importFrom(shiny,h1)
importFrom(shiny,h3)
importFrom(shiny,h4)
importFrom(shiny,helpText)
importFrom(shiny,hr)
importFrom(shiny,htmlOutput)
importFrom(shiny,icon)
importFrom(shiny,incProgress)
importFrom(shiny,includeHTML)
importFrom(shiny,includeScript)
importFrom(shiny,insertTab)
importFrom(shiny,isolate)
importFrom(shiny,mainPanel)
importFrom(shiny,moduleServer)
importFrom(shiny,navbarMenu)
importFrom(shiny,navbarPage)
importFrom(shiny,numericInput)
importFrom(shiny,observe)
importFrom(shiny,observeEvent)
importFrom(shiny,p)
importFrom(shiny,plotOutput)
importFrom(shiny,radioButtons)
importFrom(shiny,reactive)
importFrom(shiny,reactiveVal)
importFrom(shiny,reactiveValues)
importFrom(shiny,removeTab)
importFrom(shiny,renderPlot)
importFrom(shiny,renderTable)
importFrom(shiny,renderUI)
importFrom(shiny,req)
importFrom(shiny,runApp)
importFrom(shiny,selectInput)
importFrom(shiny,shinyApp)
importFrom(shiny,showNotification)
importFrom(shiny,sidebarLayout)
importFrom(shiny,sidebarPanel)
importFrom(shiny,sliderInput)
importFrom(shiny,tabPanel)
importFrom(shiny,tableOutput)
importFrom(shiny,tabsetPanel)
importFrom(shiny,tagList)
importFrom(shiny,tags)
importFrom(shiny,textInput)
importFrom(shiny,uiOutput)
importFrom(shiny,updateCheckboxInput)
importFrom(shiny,updateNavbarPage)
importFrom(shiny,updateNumericInput)
importFrom(shiny,updateTabsetPanel)
importFrom(shiny,updateTextAreaInput)
importFrom(shiny,verbatimTextOutput)
importFrom(shiny,wellPanel)
importFrom(shiny,withMathJax)
importFrom(shiny,withProgress)
importFrom(stats,fivenum)
importFrom(stats,median)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stringi,stri_c)
importFrom(stringi,stri_detect_fixed)
importFrom(stringi,stri_detect_regex)
importFrom(stringi,stri_length)
importFrom(stringi,stri_pad_both)
importFrom(stringi,stri_replace_all_fixed)
importFrom(stringi,stri_replace_all_regex)
importFrom(stringi,stri_split_regex)
importFrom(stringi,stri_startswith_fixed)
importFrom(stringi,stri_sub)
importFrom(stringi,stri_trim_both)
importFrom(utils,packageVersion)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,stack)
importFrom(utils,write.csv)
importFrom(utils,write.table)
