Package index • nprcgenekeepr

All 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
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.
alleleFreq(): Calculates the count of each allele in the provided vector.
appServer(): Main Application Server for nprcgenekeepr
appUI(): Main Application UI for nprcgenekeepr
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
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.
chooseDate(): Choose date based on earlier flag.
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.
countKinshipValues(): Counts the number of occurrences of each kinship value seen for a pair of individuals in a series of simulated pedigrees.
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).
createSimKinships(): Makes a list object of kinship matrices from simulated pedigrees of possible parents for animals with unknown parents
create_wkbk(): Creates an Excel workbook with worksheets.
cumulateSimKinships(): Makes a list object containing kinship summary statistics using the list object from createSimKinships.
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
fillGroupMembersWithSexRatio(): Forms breeding group(s) with an effort to match a specified sex ratio
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.
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
getAutoIdFormat(): Get the auto-generated unknown-ID format
getBoxWhiskerDescription(): Get Box and Whisker Plot Description
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.
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
getDescendantPedigree(): Gets pedigree with descendants of provided group.
getEmptyErrorLst(): Creates a empty errorLst object
getErrorTab(): getErrorTab skeleton of list of errors
getFocalAnimalPed(): Get pedigree based on list of focal animals
getFounders(): Gets the founder ids from a pedigree
getGVGenotype(): Get Genetic Value Genotype data structure for reportGV function.
getGVPopulation(): Get the population of interest for the Genetic Value analysis.
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.
getLkDirectAncestors(): Get the direct ancestors of selected animals
getLkDirectRelatives(): Get the direct ancestors of selected animals
getOffspring(): Get offspring to corresponding animal IDs provided
getParents(): Get parents to corresponding animal IDs provided
getPedDirectRelatives(): Get the direct ancestors of selected animals from supplied pedigree.
getPedMaxAge(): Get the maximum age of live animals in the pedigree.
getPedigree(): Get pedigree from file
getPossibleCols(): Get possible column names for a studbook.
getPotentialParents() experimental: Get the lists of portential parents for all individuals born in the colony with one or two unknown parents.
getPotentialSires(): Provides list of potential sires
getProbandPedigree(): Gets pedigree to ancestors of provided group leaving uninformative ancestors.
getPyramidAgeDist(): Get the age distribution for the pedigree
getPyramidPlot(): Creates a pyramid plot of the pedigree provided.
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
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:
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.
isFounder(): Identifies the founders in a pedigree
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.
kinshipMatricesToKValues(): Forms kValue matrix from list of kinship matrices
kinshipMatrixToKValues(): Extracts a dataframe with a row for each kinship coeficient in the kinship matrix
lacy1989Ped: lacy1989Ped small hypothetical pedigree
lacy1989PedAlleles: lacy1989PedAlleles is a dataframe produced by geneDrop on lacy1989Ped with 5000 iterations.
loadSiteConfig(): Load the site configuration for the modular Shiny application
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
makeGeneticSummaryTable(): Create Genetic Summary Statistics HTML Table
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.
makeSimPed(): Makes a simulated pedigree using representative sires and dams
mapIdsToObfuscated(): Map IDs to Obfuscated IDs
meanKinship(): Calculates the mean kinship for each animal in a kinship matrix
modBreedingGroupsServer(): Breeding Groups Module - Server Function
modBreedingGroupsUI(): Breeding Groups 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
nprcgenekeepr: Genetic Tools for Colony Management
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
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.nprcgenekeeprGV>): print.summary.nprcgenekeepr print.summary.nprcgenekeeprGV
processQcStudbookResult(): Process qcStudbook Result into UI-Friendly Format
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.
removeAutoGenIds(): Remove automatically generated IDs from pedigree
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.
rhesusGenotypes: rhesusGenotypes is a dataframe with two haplotypes per animal
rhesusPedigree: rhesusPedigree is a pedigree object
runGeneKeepR(): Run the GeneKeepR Shiny Application (Deprecated)
runModularApp(): Run the Modular Version of GeneKeepR
runQcStudbook(): Run Quality Control on Studbook with UI-Friendly Results
safeExecute(): Safe Execution Wrapper 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(): 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
shouldShowChangedColsTab(): Determine if Changed Columns tab should be displayed
shouldShowOripTab(): Determine if the ORIP Reporting tab should be displayed
smallPed: smallPed is a hypothetical pedigree
smallPedTree: smallPedTree is a pedigree tree made from smallPed
summarizeKinshipValues(): Summary statistics for imputed kinship values
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
withinIntegerRange(): Get integer within a range