Function reference • nprcgenekeepr

Data objects
`exampleNprcgenekeeprConfig`	exampleNprcgenekeeprConfig is a loadable version of the example configuration file `example_nprcgenekeepr_config`
`examplePedigree`	examplePedigree is a pedigree object created by `qcStudbook`
`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`.
`focalAnimals`	focalAnimals is a dataframe with one column (_id_) containing the of animal Ids from the __examplePedigree__ pedigree.
`lacy1989Ped`	lacy1989Ped small hypothetical pedigree
`lacy1989PedAlleles`	lacy1989PedAlleles is a dataframe produced by `geneDrop` on `lacy1989Ped` with 5000 iterations.
`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`.
`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
`rhesusGenotypes`	rhesusGenotypes is a dataframe with two haplotypes per animal
`rhesusPedigree`	rhesusPedigree is a pedigree object
`smallPed`	smallPed is a hypothetical pedigree
`smallPedTree`	smallPedTree is a pedigree tree made from `smallPed`
Major Features and Functions Brief codebook and Major Functions
`nprcgenekeepr`	Genetic Management Functions
Primary interactive functions Funtions designed for interactive use
`addBackSecondParents()`	Add back single parents trimmed pedigree
`addErrTxt()`	Concatenates any errors from nprcgenekeeprErr into narrative form
`addGenotype()`	Add genotype data to pedigree file
`addParents()`	Add parents
`addUIds()`	Eliminates partial parentage situations by adding unique placeholder IDs for the unknown parent.
`agePyramidPlot()`	Form age pyramid plot
`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
`checkGenotypeFile()`	Check genotype file
`checkParentAge()`	Check parent ages to be at least `minParentAge`
`correctParentSex()`	Sets sex for animals listed as either a sire or dam.
`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.
`createPedTree()`	Create a pedigree tree (PedTree).
`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
`findPedigreeNumber()`	Determines the generation number for each id.
`fixGenotypeCols()`	Reformat names of observed genotype columns
`geneDrop()`	Gene drop simulation based on the provided pedigree information
`getAncestors()`	Recursively create a character vector of ancestors for an individual ID.
`getDatedFilename()`	Returns a character vector with an file name having the date prepended.
`getDemographics()`	Get demographic data
`getFocalAnimalPed()`	Get pedigree based on list of focal animals
`getGenotypes()`	Get genotypes from file
`getGVGenotype()`	Get Genetic Value Genotype data structure for reportGV function.
`getGVPopulation()`	Get the population of interest for the Genetic Value analysis.
`getLkDirectAncestors()`	Get the direct ancestors of selected animals
`getLkDirectRelatives()`	Get the direct ancestors of selected animals
`getPedigree()`	Get pedigree from file
`getPedMaxAge()`	Get the maximum age of live animals in the pedigree.
`getPossibleCols()`	Get possible column names for a studbook.
`getPyramidPlot()`	Creates a pyramid plot of the pedigree provided.
`getRequiredCols()`	Get required column names for a studbook.
`getSiteInfo()`	Get site information
`kinship()`	Generates a kinship matrix.
`makeExamplePedigreeFile()`	Write copy of nprcgenekeepr::examplePedigree into a file
`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.
`print(<summary.nprcgenekeeprErr>)` `print(<summary.nprcgenekeeprGV>)`	print.summary.nprcgenekeepr print.summary.nprcgenekeeprGV
`qcStudbook()`	Quality Control for the Studbook or pedigree
`rankSubjects()`	Ranks animals based on genetic value.
`kinMatrix2LongForm()`	Reformats a kinship matrix into a long-format table.
`removeDuplicates()`	Remove duplicate records from pedigree
`removeUninformativeFounders()`	Remove uninformative founders.
`removeUnknownAnimals()`	removeUnknownAnimals Removes unknown animals added to pedigree that serve as placeholders for unknown parents.
`runGeneKeepR()`	Allows running `shiny` application with `nprcgenekeepr::runGeneKeepR()`
`trimPedigree()`	Trim pedigree to ancestors of provided group by removing uninformative individuals
`summary(<nprcgenekeeprErr>)` `summary(<nprcgenekeeprGV>)`	summary.nprcgenekeeprErr Summary function for class nprcgenekeeprErr
All exposed functions
`addAnimalsWithNoRelative()`	Adds an NA value for all animals without a relative
`addBackSecondParents()`	Add back single parents trimmed pedigree
`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
`alleleFreq()`	Calculates the count of each allele in the provided vector.
`allTrueNoNA()`	Returns `TRUE` if every member of the vector is `TRUE`.
`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
`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
`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
`geneDrop()`	Gene drop simulation based on the provided pedigree information
`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.
`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
`getDatedFilename()`	Returns a character vector with an file name having the date prepended.
`getDateErrorsAndConvertDatesInPed()`	Converts columns of dates in text form to `Date` object columns
`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
`getGenoDefinedParentGenotypes()`	Assigns parental genotype contributions to an IDs genotype by attributing alleles to sire or dam
`getGenotypes()`	Get genotypes from file
`getGVGenotype()`	Get Genetic Value Genotype data structure for reportGV function.
`getGVPopulation()`	Get the population of interest for the Genetic Value analysis.
`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
`getPedigree()`	Get pedigree from file
`getPedMaxAge()`	Get the maximum age of live animals in the pedigree.
`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.
`getSiteInfo()`	Get site information
`getTokenList()`	Gets tokens from character vector of lines
`getVersion()`	getVersion Get the version number of nprcgenekeepr
`groupAddAssign()`	Add animals to an existing breeding group or forms groups:
`groupMembersReturn()`	Forms return list of groupAddAssign function
`hasGenotype()`	Check for genotype data in dataframe
`hasBothParents()`	hasBothParents checks to see if both parents are identified.
`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.
`kinship()`	Generates a kinship matrix.
`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
`offspringCounts()`	Finds the total number of offspring for each animal in the pedigree
`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.
`orderReport()`	Order the results of the genetic value analysis for use in a report.
`print(<summary.nprcgenekeeprErr>)` `print(<summary.nprcgenekeeprGV>)`	print.summary.nprcgenekeepr print.summary.nprcgenekeeprGV
`qcStudbook()`	Quality Control for the Studbook or pedigree
`rankSubjects()`	Ranks animals based on genetic value.
`rbindFill()`	Append the rows of one dataframe to another.
`removeGroupIfNoAvailableAnimals()`	Remove group numbers when all available animals have been used
`removeSelectedAnimalFromAvailableAnimals()`	Updates list of available animals by removing the selected animal
`kinMatrix2LongForm()`	Reformats a kinship matrix into a long-format table.
`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
`removePotentialSires()`	Removes potential sires from list of Ids
`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.
`runGeneKeepR()`	Allows running `shiny` application with `nprcgenekeepr::runGeneKeepR()`
`saveDataframesAsFiles()`	Write copy of dataframes to either CSV, TXT, or Excel file.
`setPopulation()`	Population designation function
`getSexRatioWithAdditions()`	getSexRatioWithAdditions returns the sex ratio of a group.
`setExit()`	Sets the exit date, if there is no exit column in the table
`set_seed()`	Work around for unit tests using sample() among various versions of R
`str_detect_fixed_all()`	Returns a logical vector with results of stri_detect() for each pattern in second parameters character vector.
`summary(<nprcgenekeeprErr>)` `summary(<nprcgenekeeprGV>)`	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

Reference

Data objects

Major Features and Functions

Primary interactive functions

All exposed functions