Genetic Tools for Colony Management

Documentation for package ‘nprcgenekeepr’ version 2.0.0

Help Pages

-- A --

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

-- C --

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
createExampleFiles	Create example pedigree and ID-list CSV files
createPedTree	Create a pedigree tree (PedTree)
createSimKinships	Build kinship matrices from simulated pedigrees
create_wkbk	Create an Excel workbook with worksheets
cumulateSimKinships	Compute kinship summary statistics across simulations

-- D --

dataframe2string

Convert a data frame to a character vector

-- E --

exampleNprcgenekeeprConfig	Example nprcgenekeepr configuration file (loadable)
examplePedigree	Example pedigree object (from ExamplePedigree.csv)

-- F --

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
finalRpt	Genetic-value report list prior to ranking
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
focalAnimals	Focal animal IDs from examplePedigree

-- G --

geneDrop	Simulate gene dropping through a pedigree
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	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
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
groupAddAssign	Add animals to a breeding group or form new groups
gvaConvergence	Recommend gene-drop iterations for a pedigree

-- H --

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

-- I --

isFounder	Identify the founders in a pedigree
is_valid_date_str	Test whether a string is a valid date

-- K --

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

-- L --

lacy1989Ped	Small hypothetical pedigree (Lacy 1989)
lacy1989PedAlleles	Gene-drop alleles for lacy1989Ped (5000 iterations)
loadSiteConfig	Load the site configuration for the modular Shiny application
loadSpeciesOverrides	Load user-configurable species reproductive-parameter overrides
logModuleEvent	Log module events

-- M --

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

-- O --

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

-- P --

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
print.summary.nprcgenekeeprErr	Print an nprcgenekeepr summary object
print.summary.nprcgenekeeprGV	Print an nprcgenekeepr summary object
processQcStudbookResult	Process qcStudbook Result into UI-Friendly Format

-- Q --

qcBreeders	Potential breeder IDs (29 baboons)
qcPed	Example quality-controlled baboon pedigree
qcPedGvReport	Genetic-value report for qcPed
qcStudbook	Run quality control on a studbook or pedigree

-- R --

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
rhesusGenotypes	Rhesus genotypes (two haplotypes per animal)
rhesusPedigree	Obfuscated rhesus pedigree object
runGeneKeepR	Run the GeneKeepR Shiny Application
runModularApp	Run the Modular Version of GeneKeepR (Deprecated)
runQcStudbook	Run Quality Control on Studbook with UI-Friendly Results

-- S --

safeExecute	Execute an expression 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	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
set_seed	Set a reproducible RNG seed across R versions
shouldShowChangedColsTab	Determine if Changed Columns tab should be displayed
shouldShowOripTab	Determine if the ORIP Reporting tab should be displayed
smallPed	Hypothetical 17-animal pedigree
smallPedTree	Pedigree tree built from smallPed
speciesGestation	Per-species reproductive parameters
summarizeKinshipValues	Summarize imputed kinship values
summary.nprcgenekeeprErr	Summarize a studbook quality-control error list
summary.nprcgenekeeprGV	Summarize a studbook quality-control error list

-- T --

toCharacter	Force dataframe columns to character
trimPedigree	Trim a pedigree to a group's ancestors

-- W --

withinIntegerRange

Get integer within a range