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.

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

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

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.

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

getLogo(): Get Logo file name

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.

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.

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.

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

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

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(): 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

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