Package index • nprcgenekeepr

Data objects

exampleNprcgenekeeprConfig: Example nprcgenekeepr configuration file (loadable)
examplePedigree: Example pedigree object (from ExamplePedigree.csv)
finalRpt: Genetic-value report list prior to ranking
focalAnimals: Focal animal IDs from examplePedigree
lacy1989Ped: Small hypothetical pedigree (Lacy 1989)
lacy1989PedAlleles: Gene-drop alleles for lacy1989Ped (5000 iterations)
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
qcBreeders: Potential breeder IDs (29 baboons)
qcPed: Example quality-controlled baboon pedigree
qcPedGvReport: Genetic-value report for qcPed
rhesusGenotypes: Rhesus genotypes (two haplotypes per animal)
rhesusPedigree: Obfuscated rhesus pedigree object
smallPed: Hypothetical 17-animal pedigree
smallPedTree: Pedigree tree built from smallPed
speciesGestation: Per-species reproductive parameters

Major Features and Functions

Brief codebook and Major Functions

nprcgenekeepr nprcgenekeepr-package: nprcgenekeepr: Genetic Tools for Colony Management

Primary interactive functions

Funtions designed for interactive use

addBackSecondParents(): Add back single parents trimmed pedigree
addGenotype(): Add genotype data to pedigree file
addParents(): Add parents
addUIds(): Add placeholder IDs for unknown parents
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
calcRetention(): Calculate allelic retention
checkGenotypeFile(): Check genotype file
checkParentAge(): Check parent ages against a minimum age
correctParentSex(): Correct the sex of animals listed as a sire or dam
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)
findGeneration(): Determine the generation number for each ID
findLoops(): Find loops in a pedigree tree
findPedigreeNumber(): Determine the pedigree number for each ID
geneDrop(): Simulate gene dropping through a pedigree
getAncestors(): Recursively collect an individual's ancestors
getDatedFilename(): Prepend the date and time to a file name
getDemographics(): Get demographic data
getFocalAnimalPed(): Get pedigree based on list of focal animals
getFocalAnimalPedFromFile(): Get a focal-animal pedigree from a pedigree file
getGenotypes(): Get genotypes from file
getGVGenotype(): Extract genotype data for a genetic value report
getGVPopulation(): Get the population of interest for the Genetic Value analysis
getLkDirectAncestors(): Get the direct ancestors of selected animals
getLkDirectRelatives(): Get the direct relatives of selected animals from the LabKey EHR
getPedigree(): Get pedigree from file
getPedMaxAge(): Get the maximum age of any animal in the pedigree
getPossibleCols(): Get possible column names for a studbook
getPyramidPlot(): Create an age-sex pyramid plot of a pedigree
getRequiredCols(): Get required column names for a studbook
getSiteInfo(): Get site information
kinship(): Generate a kinship matrix
makeExamplePedigreeFile(): Write copy of nprcgenekeepr::examplePedigree into a file
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
print(<summary.nprcgenekeeprErr>) print(<summary.nprcgenekeeprGV>): Print an nprcgenekeepr summary object
qcStudbook(): Run quality control on a studbook or pedigree
rankSubjects(): Rank animals by genetic value
kinMatrix2LongForm(): Reformat a kinship matrix into long form
removeDuplicates(): Remove duplicate records from pedigree
removeUninformativeFounders(): Remove uninformative founders
removeUnknownAnimals(): Remove placeholder animals added for unknown parents
runGeneKeepR(): Run the GeneKeepR Shiny Application
trimPedigree(): Trim a pedigree to a group's ancestors
summary(<nprcgenekeeprErr>) summary(<nprcgenekeeprGV>): Summarize a studbook quality-control error list

All exposed functions

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
applyKinshipOverrides(): Apply outside-information kinship overrides to a kinship matrix
appServer(): Main Application Server for nprcgenekeepr
appUI(): Main Application UI for nprcgenekeepr
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
calcGeneDiversity(): Calculate gene diversity from founder genome equivalents
calcGU(): Calculate genome uniqueness for each population ID
calcGUSE(): Calculate the standard error of genome uniqueness
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
create_wkbk(): Create an Excel workbook with worksheets
createExampleFiles(): Create example pedigree and ID-list CSV files
createPedTree(): Create a pedigree tree (PedTree)
createSimKinships(): Build kinship matrices from simulated pedigrees
cumulateSimKinships(): Compute kinship summary statistics across simulations
dataframe2string(): Convert a data frame to a character vector
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
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
geneDrop(): Simulate gene dropping through a pedigree
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
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
getDatedFilename(): Prepend the date and time to a file name
getDateErrorsAndConvertDatesInPed(): Find date errors and convert dates in a pedigree
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
getGeneticDiversityStats(): Assemble breeding-group genetic diversity heat-map statistics
getGenotypes(): Get genotypes from file
getGVGenotype(): Extract genotype data for a genetic value report
getGVPopulation(): Get the population of interest for the Genetic Value analysis
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
getPedigree(): Get pedigree from file
getPedMaxAge(): Get the maximum age of any animal in the pedigree
getPossibleCols(): Get possible column names for a studbook
getPotentialParents() experimental: 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
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
is_valid_date_str(): Test whether a string is a valid date
isFounder(): Identify the founders in a pedigree
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
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
processQcStudbookResult(): Process qcStudbook Result into UI-Friendly Format
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
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
set_seed(): Set a reproducible RNG seed across R versions
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
shouldShowChangedColsTab(): Determine if Changed Columns tab should be displayed
shouldShowOripTab(): Determine if the ORIP Reporting tab should be displayed
summarizeKinshipValues(): Summarize imputed kinship values
toCharacter(): Force dataframe columns to character
trimPedigree(): Trim a pedigree to a group's ancestors
withinIntegerRange(): Get integer within a range