addAnimalsWithNoRelative
                        Adds an NA value for all animals without a
                        relative
addBackSecondParents    Add back single parents trimmed pedigree
addErrTxt               Concatenates any errors from nprcgenekeeprErr
                        into narrative form
addGenotype             Add genotype data to pedigree file
addGroupOfUnusedAnimals
                        addGroupOfUnusedAnimals adds a group to the
                        saved groups if needed
addIdRecords            addIdRecords Adds Ego records added having NAs
                        for parent IDs
addParents              Add parents
addSexAndAgeToGroup     Forms a dataframe with Id, Sex, and current Age
                        given a list of Ids and a pedigree
addUIds                 Eliminates partial parentage situations by
                        adding unique placeholder IDs for the unknown
                        parent.
agePyramidPlot          Form age pyramid plot
allTrueNoNA             Returns 'TRUE' if every member of the vector is
                        'TRUE'.
alleleFreq              Calculates the count of each allele in the
                        provided vector.
assignAlleles           Assign parent alleles randomly
calcA                   Calculates 'a', the number of an individual's
                        alleles that are rare in each simulation.
calcAge                 Calculate animal ages.
calcFE                  Calculates founder Equivalents
calcFEFG                Calculates Founder Equivalents and Founder
                        Genome Equivalents
calcFG                  Calculates Founder Genome Equivalents
calcGU                  Calculates genome uniqueness for each ID that
                        is part of the population.
calcRetention           Calculates Allelic Retention
calculateSexRatio       Calculates the sex ratio (number of non-males /
                        number of males) given animal Ids and their
                        pedigree
checkChangedColAndErrorLst
                        checkChangedColAndErrorLst examines errorLst
                        for errors and errorLst$changeCols non-empty
                        fields
checkChangedColsLst     checkChangedColsLst examines list for non-empty
                        fields
checkErrorLst           checkErrorLst examines list for non-empty
                        fields
checkGenotypeFile       Check genotype file
checkParentAge          Check parent ages to be at least 'minParentAge'
checkRequiredCols       Examines column names, 'cols' for required
                        column names
chooseAlleles           Combines two vectors of alleles by randomly
                        selecting one allele or the other at each
                        position.
chooseAllelesChar       Combines two vectors of alleles when alleles
                        are character vectors.
chooseDate              Choose date based on 'earlier' flag.
colChange               colChange internal function to describe column
                        names transformation
convertAncestry         Converts the ancestry information to a
                        standardized code
convertDate             Converts date columns formatted as characters
                        to be of type datetime
convertFromCenter       Converts the fromCenter information to a
                        standardized code
convertRelationships    Converts pairwise kinship values to a
                        relationship category descriptor.
convertSexCodes         Converts sex indicator for an individual to a
                        standardized codes.
convertStatusCodes      Converts status indicators to a Standardized
                        code
correctParentSex        Sets sex for animals listed as either a sire or
                        dam.
countFirstOrder         Count first-order relatives.
countLoops              Count the number of loops in a pedigree tree.
createExampleFiles      Creates a folder with CSV files containing
                        example pedigrees and ID lists used to
                        demonstrate the package.
createPedOne            createPedOne makes the pedOne data object
createPedSix            createPedSix makes the pedSix data object
createPedTree           Create a pedigree tree (PedTree).
create_wkbk             Creates an Excel workbook with worksheets.
dataframe2string        dataframe2string converts a data.frame object
                        to a character vector
exampleNprcgenekeeprConfig
                        exampleNprcgenekeeprConfig is a loadable
                        version of the example configuration file
                        'example_nprcgenekeepr_config'
examplePedigree         examplePedigree is a pedigree object created by
                        'qcStudbook'
fillBins                fillBins Fill bins represented by list of two
                        lists 'males' and 'females'.
fillGroupMembers        Forms and fills list of animals groups based on
                        provided constraints
fillGroupMembersWithSexRatio
                        Forms breeding group(s) with an effort to match
                        a specified sex ratio
filterAge               Removes kinship values where an animal is less
                        than the minAge
filterKinMatrix         Filters a kinship matrix to include only the
                        egos listed in 'ids'
filterPairs             Filters kinship values from a long-format
                        kinship table based on the sexes of the two
                        animals involved.
filterReport            Filters a genetic value report down to only the
                        specified animals
filterThreshold         Filters kinship to remove rows with kinship
                        values less than the specified threshold
finalRpt                finalRpt is a list object created from the list
                        object _rpt_ prepared by 'reportGV'. It is
                        created inside 'orderReport'. This version is
                        at the state just prior to calling
                        'rankSubjects' inside 'orderReport'.
findGeneration          Determines the generation number for each id.
findLoops               Find loops in a pedigree tree
findOffspring           Finds the number of total offspring for each
                        animal in the provided pedigree.
findPedigreeNumber      Determines the generation number for each id.
fixColumnNames          fixColumnNames changes original column names
                        and into standardized names.
fixGenotypeCols         Reformat names of observed genotype columns
focalAnimals            focalAnimals is a dataframe with one column
                        (_id_) containing the of animal Ids from the
                        __examplePedigree__ pedigree.
geneDrop                Gene drop simulation based on the provided
                        pedigree information
getAncestors            Recursively create a character vector of
                        ancestors for an individual ID.
getAnimalsWithHighKinship
                        Forms a list of animal Ids and animals related
                        to them
getChangedColsTab       getChangedColsTab skeleton of list of errors
getConfigFileName       getConfigFileName returns the configuration
                        file name appropriate for the system.
getCurrentAge           Age in years using the provided birthdate.
getDateColNames         Vector of date column names
getDateErrorsAndConvertDatesInPed
                        Converts columns of dates in text form to
                        'Date' object columns
getDatedFilename        Returns a character vector with an file name
                        having the date prepended.
getDemographics         Get demographic data
getEmptyErrorLst        Creates a empty errorLst object
getErrorTab             getErrorTab skeleton of list of errors
getFocalAnimalPed       Get pedigree based on list of focal animals
getGVGenotype           Get Genetic Value Genotype data structure for
                        reportGV function.
getGVPopulation         Get the population of interest for the Genetic
                        Value analysis.
getGenoDefinedParentGenotypes
                        Assigns parental genotype contributions to an
                        IDs genotype by attributing alleles to sire or
                        dam
getGenotypes            Get genotypes from file
getIdsWithOneParent     getIdsWithOneParent extracts IDs of animals
                        pedigree without either a sire or a dam
getIncludeColumns       Get the superset of columns that can be in a
                        pedigree file.
getIndianOriginStatus   Get Indian-origin status of group
getLkDirectAncestors    Get the direct ancestors of selected animals
getLkDirectRelatives    Get the direct ancestors of selected animals
getLogo                 Get Logo file name
getMaxAx                Get the maximum of the absolute values of the
                        negative (males) and positive (female) animal
                        counts.
getMinParentAge         Get minimum parent age.
getOffspring            Get offspring to corresponding animal IDs
                        provided
getParamDef             Get parameter definitions from tokens found in
                        configuration file.
getParents              Get parents to corresponding animal IDs
                        provided
getPedMaxAge            Get the maximum age of live animals in the
                        pedigree.
getPedigree             Get pedigree from file
getPossibleCols         Get possible column names for a studbook.
getPotentialSires       Provides list of potential sires
getProbandPedigree      Gets pedigree to ancestors of provided group
                        leaving uninformative ancestors.
getProductionStatus     Get production status of group
getProportionLow        Get proportion of Low genetic value animals
getPyramidAgeDist       Get the age distribution for the pedigree
getPyramidPlot          Creates a pyramid plot of the pedigree
                        provided.
getRecordStatusIndex    Returns record numbers with selected
                        'recordStatus'.
getRequiredCols         Get required column names for a studbook.
getSexRatioWithAdditions
                        getSexRatioWithAdditions returns the sex ratio
                        of a group.
getSiteInfo             Get site information
getTokenList            Gets tokens from character vector of lines
getVersion              getVersion Get the version number of
                        nprcgenekeepr
get_and_or_list         Returns a one element character string with
                        correct punctuation for a list made up of the
                        elements of the character vector argument.
get_elapsed_time_str    Returns the elapsed time since start_time.
groupAddAssign          Add animals to an existing breeding group or
                        forms groups:
groupMembersReturn      Forms return list of groupAddAssign function
hasBothParents          hasBothParents checks to see if both parents
                        are identified.
hasGenotype             Check for genotype data in dataframe
headerDisplayNames      Convert internal column names to display or
                        header names.
initializeHaremGroups   Make the initial groupMembers animal list
insertChangedColsTab    insertChangedColsTab insert a list of changed
                        columns found by 'qcStudbook' in the pedigree
                        file
insertErrorTab          insertErrorTab insert a list of errors found by
                        'qcStudbook' in the pedigree file
insertSeparators        insertSeparators inserts the character "-"
                        between year and month and between month and
                        day portions of a date string in %Y%m%d format.
isEmpty                 Is vector empty or all NA values.
is_valid_date_str       Returns TRUE if the string is a valid date.
kinMatrix2LongForm      Reformats a kinship matrix into a long-format
                        table.
kinship                 Generates a kinship matrix.
lacy1989Ped             lacy1989Ped small hypothetical pedigree
lacy1989PedAlleles      lacy1989PedAlleles is a dataframe produced by
                        'geneDrop' on 'lacy1989Ped' with 5000
                        iterations.
makeAvailable           Convenience function to make the initial
                        available animal list
makeCEPH                Make a CEPH-style pedigree for each id
makeExamplePedigreeFile
                        Write copy of nprcgenekeepr::examplePedigree
                        into a file
makeGroupMembers        Convenience function to make the initial
                        groupMembers animal list
makeGrpNum              Convenience function to make the initial grpNum
                        list
makeRelationClassesTable
                        Make relation classes table from 'kin'
                        dataframe.
makeRoundUp             Round up the provided integer vector 'int'
                        according to the 'modulus'.
makesLoop               'makesLoop' tests for a common ancestor.
mapIdsToObfuscated      Map IDs to Obfuscated IDs
meanKinship             Calculates the mean kinship for each animal in
                        a kinship matrix
nprcgenekeepr           Genetic Management Functions
obfuscateDate           obfucateDate adds a random number of days
                        bounded by plus and minus max delta
obfuscateId             obfucateId creates a vector of ID aliases of
                        specified length
obfuscatePed            obfuscatePed takes a pedigree object and
                        creates aliases for all IDs and adjusts all
                        date within a specified amount.
offspringCounts         Finds the total number of offspring for each
                        animal in the pedigree
orderReport             Order the results of the genetic value analysis
                        for use in a report.
ped1Alleles             ped1Alleles is a dataframe created by the
                        geneDrop function
pedDuplicateIds         pedDuplicateIds is a dataframe with 9 rows and
                        5 columns (ego_id, sire, dam_id, sex,
                        birth_date) representing a full pedigree with a
                        duplicated record.
pedFemaleSireMaleDam    pedFemaleSireMaleDam is a dataframe with 8 rows
                        and 5 columns (ego_id, sire, dam_id, sex,
                        birth_date) representing a full pedigree with
                        the errors of having a sire labeled as female
                        and a dam labeled as male.
pedGood                 pedGood is a dataframe with 8 rows and 5
                        columns (ego_id, sire, dam_id, sex, birth_date)
                        representing a full pedigree with no errors.
pedInvalidDates         pedInvalidDates is a dataframe with 8 rows and
                        5 columns (ego_id, sire, dam_id, sex,
                        birth_date) representing a full pedigree with
                        values in the 'birth_date' column that are not
                        valid dates.
pedMissingBirth         pedMissingBirth is a dataframe with 8 rows and
                        5 columns (ego_id, sire, dam_id, sex,
                        birth_date) representing a full pedigree with
                        no errors.
pedOne                  pedOne is a loadable version of a pedigree file
                        fragment used for testing and demonstration
pedSameMaleIsSireAndDam
                        pedSameMaleIsSireAndDam is a dataframe with 8
                        rows and 5 columns (ego_id, sire, dam_id, sex,
                        birth_date) representing a full pedigree with
                        no errors.
pedSix                  pedSix is a loadable version of a pedigree file
                        fragment used for testing and demonstration
pedWithGenotype         pedWithGenotype is a dataframe produced from
                        qcPed by adding made up genotypes.
pedWithGenotypeReport   pedWithGenotypeReport is a list containing the
                        output of 'reportGV'.
print.summary.nprcgenekeeprErr
                        print.summary.nprcgenekeepr
                        print.summary.nprcgenekeeprGV
qcBreeders              qcBreeders is a list of 29 baboon IDs that are
                        potential breeders
qcPed                   qcPed is a dataframe with 277 rows and 6
                        columns
qcPedGvReport           qcPedGvReport is a genetic value report
qcStudbook              Quality Control for the Studbook or pedigree
rankSubjects            Ranks animals based on genetic value.
rbindFill               Append the rows of one dataframe to another.
readExcelPOSIXToCharacter
                        Read in Excel file and convert POSIX dates to
                        character
removeDuplicates        Remove duplicate records from pedigree
removeEarlyDates        removeEarlyDates removes dates before a
                        specified year
removeGroupIfNoAvailableAnimals
                        Remove group numbers when all available animals
                        have been used
removePotentialSires    Removes potential sires from list of Ids
removeSelectedAnimalFromAvailableAnimals
                        Updates list of available animals by removing
                        the selected animal
removeUninformativeFounders
                        Remove uninformative founders.
removeUnknownAnimals    removeUnknownAnimals Removes unknown animals
                        added to pedigree that serve as placeholders
                        for unknown parents.
reportGV                Generates a genetic value report for a provided
                        pedigree.
resetGroup              Update or add the "group" field of a Pedigree.
rhesusGenotypes         rhesusGenotypes is a dataframe with two
                        haplotypes per animal
rhesusPedigree          rhesusPedigree is a pedigree object
runGeneKeepR            Allows running 'shiny' application with
                        'nprcgenekeepr::runGeneKeepR()'
saveDataframesAsFiles   Write copy of dataframes to either CSV, TXT, or
                        Excel file.
setExit                 Sets the exit date, if there is no exit column
                        in the table
setPopulation           Population designation function
set_seed                Work around for unit tests using sample() among
                        various versions of R
smallPed                smallPed is a hypothetical pedigree
smallPedTree            smallPedTree is a pedigree tree made from
                        'smallPed'
str_detect_fixed_all    Returns a logical vector with results of
                        stri_detect() for each pattern in second
                        parameters character vector.
summary.nprcgenekeeprErr
                        summary.nprcgenekeeprErr Summary function for
                        class nprcgenekeeprErr
toCharacter             Force dataframe columns to character
trimPedigree            Trim pedigree to ancestors of provided group by
                        removing uninformative individuals
unknown2NA              Removing IDs having "UNKNOWN" regardless of
                        case
withinIntegerRange      Get integer within a range
