addAnimalsWithNoRelative
                        Add an NA value for animals with no relative
addBackSecondParents    Add back single parents trimmed pedigree
addGenotype             Add genotype data to pedigree file
addIdRecords            Add ego records with NA parent IDs
addParents              Add parents
addSexAndAgeToGroup     Build a group data frame with ID, sex, and age
addUIds                 Add placeholder IDs for unknown parents
alleleFreq              Count each allele in a vector
appServer               Main Application Server for nprcgenekeepr
appUI                   Main Application UI for nprcgenekeepr
applyKinshipOverrides   Apply outside-information kinship overrides to
                        a kinship matrix
assignAlleles           Assign parent alleles randomly
calcA                   Count each individual's rare alleles per
                        simulation
calcAge                 Calculate animal ages
calcFE                  Calculate founder equivalents
calcFEFG                Calculate founder equivalents and founder
                        genome equivalents
calcFG                  Calculate founder genome equivalents
calcFGSE                Calculate the standard error of founder genome
                        equivalents
calcGU                  Calculate genome uniqueness for each population
                        ID
calcGUSE                Calculate the standard error of genome
                        uniqueness
calcGeneDiversity       Calculate gene diversity from founder genome
                        equivalents
calcNeSexRatio          Calculate the demographic sex-ratio effective
                        population size
calcNeVariance          Calculate the variance effective population
                        size
calcRetention           Calculate allelic retention
calculateSexRatio       Calculate the sex ratio of a set of animals
checkChangedColsLst     Check a changed-columns list for non-empty
                        fields
checkErrorLst           Check an error list for non-empty fields
checkGenotypeFile       Check genotype file
checkKinshipOverrides   Validate a kinship overrides table
checkParentAge          Check parent ages against a minimum age
checkRequiredCols       Check column names for required columns
chooseAlleles           Combine two allele vectors by Mendelian
                        sampling
chooseDate              Choose the earlier or later of two dates
convertAncestry         Convert ancestry information to a standard code
convertDate             Convert character date columns to Date type
convertFromCenter       Convert from-center information to a logical
                        value
convertRelationships    Convert pairwise kinship values to relationship
                        categories
convertSexCodes         Convert a sex indicator to a standardized code
convertStatusCodes      Convert status indicators to a standardized
                        code
correctParentSex        Correct the sex of animals listed as a sire or
                        dam
countFirstOrder         Count first-order relatives
countKinshipValues      Count kinship-value occurrences across
                        simulated pedigrees
countLoops              Count the number of loops in a pedigree tree
createExampleFiles      Create example pedigree and ID-list CSV files
createPedTree           Create a pedigree tree (PedTree)
createSimKinships       Build kinship matrices from simulated pedigrees
create_wkbk             Create an Excel workbook with worksheets
cumulateSimKinships     Compute kinship summary statistics across
                        simulations
dataframe2string        Convert a data frame to a character vector
exampleNprcgenekeeprConfig
                        Example nprcgenekeepr configuration file
                        (loadable)
examplePedigree         Example pedigree object (from
                        ExamplePedigree.csv)
fillGroupMembersWithSexRatio
                        Form breeding groups to match a target sex
                        ratio
filterKinMatrix         Filter a kinship matrix to selected IDs
filterPairs             Filter kinship pairs by the animals' sexes
filterReport            Filter a genetic value report to selected
                        animals
filterThreshold         Filter out kinship pairs below a threshold
finalRpt                Genetic-value report list prior to ranking
findGeneration          Determine the generation number for each ID
findLoops               Find loops in a pedigree tree
findOffspring           Count total offspring for each animal
findPedigreeNumber      Determine the pedigree number for each ID
fixColumnNames          Standardize pedigree column names
focalAnimals            Focal animal IDs from examplePedigree
geneDrop                Simulate gene dropping through a pedigree
getAncestors            Recursively collect an individual's ancestors
getAnimalsWithHighKinship
                        List each animal's high-kinship relatives
getAutoIdFormat         Get the auto-generated unknown-ID format
getBoxWhiskerDescription
                        Get Box and Whisker Plot Description
getChangedColsTab       Build the changed-columns tab panel
getConfigFileName       Get the configuration file name for the system
getCurrentAge           Calculate current age in years from a birth
                        date
getDateErrorsAndConvertDatesInPed
                        Find date errors and convert dates in a
                        pedigree
getDatedFilename        Prepend the date and time to a file name
getDemographics         Get demographic data
getDescendantPedigree   Reduce a pedigree to a group and its
                        descendants
getEmptyErrorLst        Create an empty errorLst object
getErrorTab             Build the error-list tab panel
getFileDirectRelatives
                        Get the direct relatives of selected animals
                        from a pedigree file
getFocalAnimalPed       Get pedigree based on list of focal animals
getFocalAnimalPedFromFile
                        Get a focal-animal pedigree from a pedigree
                        file
getFounders             Get the founder ids from a pedigree
getGVGenotype           Extract genotype data for a genetic value
                        report
getGVPopulation         Get the population of interest for the Genetic
                        Value analysis
getGeneticDiversityStats
                        Assemble breeding-group genetic diversity
                        heat-map statistics
getGenotypes            Get genotypes from file
getIdsWithOneParent     Get ids of animals with only one parent
getIncludeColumns       Get the superset of columns that can be in a
                        pedigree file
getLkDirectAncestors    Get the direct ancestors of selected animals
getLkDirectRelatives    Get the direct relatives of selected animals
                        from the LabKey EHR
getOffspring            Get offspring to corresponding animal IDs
                        provided
getParents              Get parents to corresponding animal IDs
                        provided
getPedDirectRelatives   Get the direct relatives of selected animals
                        from a pedigree
getPedMaxAge            Get the maximum age of any animal in the
                        pedigree
getPedigree             Get pedigree from file
getPossibleCols         Get possible column names for a studbook
getPotentialParents     Get potential parents for animals with unknown
                        parents
getPotentialSires       List potential sires
getProbandPedigree      Reduce a pedigree to probands and their
                        ancestors
getPyramidAgeDist       Get the age distribution for the pedigree
getPyramidPlot          Create an age-sex pyramid plot of a pedigree
getRequiredCols         Get required column names for a studbook
getSiteInfo             Get site information
getSpeciesGestation     Look up the maximum gestation period (days) for
                        one or more species
getSpeciesMinBreedingAge
                        Look up the minimum breeding age (years) for
                        one or more species and sexes
getTokenList            Get tokens from a character vector of lines
getVersion              Get the version number of nprcgenekeepr
get_and_or_list         Join a character vector into an and/or list
get_elapsed_time_str    Format the elapsed time since a start time
groupAddAssign          Add animals to a breeding group or form new
                        groups
gvaConvergence          Recommend gene-drop iterations for a pedigree
hasBothParents          Check whether an animal has both parents
hasGenotype             Check for genotype data in dataframe
headerDisplayNames      Convert internal column names to display or
                        header names
isFounder               Identify the founders in a pedigree
is_valid_date_str       Test whether a string is a valid date
kinMatrix2LongForm      Reformat a kinship matrix into long form
kinship                 Generate a kinship matrix
kinshipMatricesToKValues
                        Build a kValue table from a list of kinship
                        matrices
kinshipMatrixToKValues
                        Extract a kValue table from a kinship matrix
lacy1989Ped             Small hypothetical pedigree (Lacy 1989)
lacy1989PedAlleles      Gene-drop alleles for lacy1989Ped (5000
                        iterations)
loadSiteConfig          Load the site configuration for the modular
                        Shiny application
loadSpeciesOverrides    Load user-configurable species
                        reproductive-parameter overrides
logModuleEvent          Log module events
makeCEPH                Make a CEPH-style pedigree for each id
makeExamplePedigreeFile
                        Write copy of nprcgenekeepr::examplePedigree
                        into a file
makeFounderStatsTable   Create Founder Statistics HTML Table
makeGeneticDiversityHeatmap
                        Make a genetic diversity heat map
makeGeneticSummaryTable
                        Create Genetic Summary Statistics HTML Table
makeGroupMembers        Make the initial groupMembers animal list
makeGroupNum            Make the initial grpNum list
makeGrpNum              Deprecated alias for makeGroupNum
makeRelationClassesTable
                        Make a relation classes table from kinship
                        pairs
makeSimPed              Make a simulated pedigree from representative
                        sires and dams
mapIdsToObfuscated      Map IDs to Obfuscated IDs
meanKinship             Calculate mean kinship for each animal in a
                        kinship matrix
modBreedingGroupsServer
                        Breeding Groups Module - Server Function
modBreedingGroupsUI     Breeding Groups Module - UI Function
modGeneticDiversityServer
                        Genetic Diversity Module - Server Function
modGeneticDiversityUI   Genetic Diversity Module - UI Function
modGeneticValueServer   Genetic Value Analysis Module - Server Function
modGeneticValueUI       Genetic Value Analysis Module - UI Function
modGvAndBgDescServer    Genetic Value and Breeding Group Description
                        Module - Server Function
modGvAndBgDescUI        Genetic Value and Breeding Group Description
                        Module - UI Function
modInputServer          Data Input and Quality Control Module - Server
                        Function
modInputUI              Data Input and Quality Control Module - UI
                        Function
modORIPReportingServer
                        ORIP Reporting Module - Server Function
modORIPReportingUI      ORIP Reporting Module - UI Function
modPedigreeServer       Pedigree Browser Module - Server Function
modPedigreeUI           Pedigree Browser Module - UI Function
modPotentialParentsServer
                        Potential Parents Module - Server Function
modPotentialParentsUI   Potential Parents Module - UI Function
modPyramidServer        Age-Sex Pyramid Module - Server Function
modPyramidUI            Age-Sex Pyramid Module - UI Function
modSummaryStatsServer   Summary Statistics Module - Server Function
modSummaryStatsUI       Summary Statistics Module - UI Function
obfuscateDate           Obfuscate dates with a random day offset
obfuscateId             Create ID aliases of a specified length
obfuscatePed            Obfuscate a pedigree by aliasing IDs and
                        shifting dates
offspringCounts         Tabulate offspring counts, optionally by
                        population
ped1Alleles             Gene-drop alleles example (baboon pedigree)
pedDuplicateIds         Example studbook with a duplicated record
pedFemaleSireMaleDam    Example studbook with sex-mismatched parents
pedGood                 Valid example studbook (no QC errors)
pedInvalidDates         Example studbook with invalid birth dates
pedMissingBirth         Example studbook missing the birth date column
pedOne                  Raw pedigree-file fragment for testing (5
                        columns)
pedSameMaleIsSireAndDam
                        Example studbook with a male as both sire and
                        dam
pedSix                  Raw pedigree-file fragment for testing (7
                        columns)
pedWithGenotype         Pedigree with simulated genotypes (from qcPed)
pedWithGenotypeReport   Genetic-value report for pedWithGenotype
print.summary.nprcgenekeeprErr
                        Print an nprcgenekeepr summary object
processQcStudbookResult
                        Process qcStudbook Result into UI-Friendly
                        Format
qcBreeders              Potential breeder IDs (29 baboons)
qcPed                   Example quality-controlled baboon pedigree
qcPedGvReport           Genetic-value report for qcPed
qcStudbook              Run quality control on a studbook or pedigree
rankSubjects            Rank animals by genetic value
readKinshipOverrides    Read a kinship overrides table from a file
removeAutoGenIds        Remove automatically generated IDs from
                        pedigree
removeDuplicates        Remove duplicate records from pedigree
removeEarlyDates        Remove dates before a specified year
removePotentialSires    Remove potential sires from a list of IDs
removeUninformativeFounders
                        Remove uninformative founders
removeUnknownAnimals    Remove placeholder animals added for unknown
                        parents
reportGV                Generate a genetic value report for a pedigree
rhesusGenotypes         Rhesus genotypes (two haplotypes per animal)
rhesusPedigree          Obfuscated rhesus pedigree object
runGeneKeepR            Run the GeneKeepR Shiny Application
runModularApp           Run the Modular Version of GeneKeepR
                        (Deprecated)
runQcStudbook           Run Quality Control on Studbook with
                        UI-Friendly Results
safeExecute             Execute an expression with error handling
saveDataframesAsFiles   Write copy of dataframes to either CSV, TXT, or
                        Excel file
savePlotToFile          Save Plot to File
setAutoIdFormat         Set the auto-generated unknown-ID format
setExit                 Set the exit date when no exit column exists
setLabKeyDefaults       Configure Rlabkey authentication for the
                        current session
setPopulation           Flag animals as the population of interest
set_seed                Set a reproducible RNG seed across R versions
shouldShowChangedColsTab
                        Determine if Changed Columns tab should be
                        displayed
shouldShowOripTab       Determine if the ORIP Reporting tab should be
                        displayed
smallPed                Hypothetical 17-animal pedigree
smallPedTree            Pedigree tree built from smallPed
speciesGestation        Per-species reproductive parameters
summarizeKinshipValues
                        Summarize imputed kinship values
summary.nprcgenekeeprErr
                        Summarize a studbook quality-control error list
toCharacter             Force dataframe columns to character
trimPedigree            Trim a pedigree to a group's ancestors
withinIntegerRange      Get integer within a range
