Genetic Tools for Colony Management


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Documentation for package ‘nprcgenekeepr’ version 1.0.8

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A C D E F G H I K L M N O P Q R S T W

-- A --

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

-- C --

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*.

-- D --

dataframe2string dataframe2string converts a data.frame object to a character vector

-- E --

exampleNprcgenekeeprConfig exampleNprcgenekeeprConfig is a loadable version of the example configuration file 'example_nprcgenekeepr_config'
examplePedigree examplePedigree is a pedigree object created by 'qcStudbook'

-- F --

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.

-- G --

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.
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
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.
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.
getPedigree Get pedigree from file
getPedMaxAge Get the maximum age of live animals in the pedigree.
getPossibleCols Get possible column names for a studbook.
getPotentialParents 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:

-- H --

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.

-- I --

is_valid_date_str Returns TRUE if the string is a valid date.

-- K --

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

-- L --

lacy1989Ped lacy1989Ped small hypothetical pedigree
lacy1989PedAlleles lacy1989PedAlleles is a dataframe produced by 'geneDrop' on 'lacy1989Ped' with 5000 iterations.

-- M --

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

-- N --

nprcgenekeepr Genetic Tools for Colony Management

-- O --

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

-- P --

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.nprcgenekeepr print.summary.nprcgenekeeprGV
print.summary.nprcgenekeeprGV print.summary.nprcgenekeepr print.summary.nprcgenekeeprGV

-- Q --

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

-- R --

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()'

-- S --

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.nprcgenekeeprErr Summary function for class nprcgenekeeprErr
summary.nprcgenekeeprGV summary.nprcgenekeeprErr Summary function for class nprcgenekeeprErr

-- T --

toCharacter Force dataframe columns to character
trimPedigree Trim pedigree to ancestors of provided group by removing uninformative individuals

-- W --

withinIntegerRange Get integer within a range