A C D E F G H I K L M N O P Q R S T U W
addAnimalsWithNoRelative | Adds an NA value for all animals without a relative |
addBackSecondParents | Add back single parents trimmed pedigree |
addErrTxt | Concatenates any errors from nprcgenekeeprErr into narrative form |
addGenotype | Add genotype data to pedigree file |
addGroupOfUnusedAnimals | addGroupOfUnusedAnimals adds a group to the saved groups if needed |
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. |
agePyramidPlot | Form age pyramid plot |
alleleFreq | Calculates the count of each allele in the provided vector. |
allTrueNoNA | Returns 'TRUE' if every member of the vector is 'TRUE'. |
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 |
checkChangedColAndErrorLst | checkChangedColAndErrorLst examines errorLst for errors and errorLst$changeCols non-empty fields |
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. |
chooseAllelesChar | Combines two vectors of alleles when alleles are character vectors. |
chooseDate | Choose date based on 'earlier' flag. |
colChange | colChange internal function to describe column names transformation |
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. |
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. |
createPedOne | createPedOne makes the pedOne data object |
createPedSix | createPedSix makes the pedSix data object |
createPedTree | Create a pedigree tree (PedTree). |
create_wkbk | Creates an Excel workbook with worksheets. |
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' |
fillBins | fillBins Fill bins represented by list of two lists 'males' and 'females'. |
fillGroupMembers | Forms and fills list of animals groups based on provided constraints |
fillGroupMembersWithSexRatio | Forms breeding group(s) with an effort to match a specified sex ratio |
filterAge | Removes kinship values where an animal is less than the minAge |
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. |
fixGenotypeCols | Reformat names of observed genotype columns |
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. |
getDateColNames | Vector of date column names |
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 |
getGenoDefinedParentGenotypes | Assigns parental genotype contributions to an IDs genotype by attributing alleles to sire or dam |
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. |
getIndianOriginStatus | Get Indian-origin status of group |
getLkDirectAncestors | Get the direct ancestors of selected animals |
getLkDirectRelatives | Get the direct ancestors of selected animals |
getLogo | Get Logo file name |
getMaxAx | Get the maximum of the absolute values of the negative (males) and positive (female) animal counts. |
getMinParentAge | Get minimum parent age. |
getOffspring | Get offspring to corresponding animal IDs provided |
getParamDef | Get parameter definitions from tokens found in configuration file. |
getParents | Get parents to corresponding animal IDs provided |
getPedigree | Get pedigree from file |
getPedMaxAge | Get the maximum age of live animals in the pedigree. |
getPossibleCols | Get possible column names for a studbook. |
getPotentialSires | Provides list of potential sires |
getProbandPedigree | Gets pedigree to ancestors of provided group leaving uninformative ancestors. |
getProductionStatus | Get production status of group |
getProportionLow | Get proportion of Low genetic value animals |
getPyramidAgeDist | Get the age distribution for the pedigree |
getPyramidPlot | Creates a pyramid plot of the pedigree provided. |
getRecordStatusIndex | Returns record numbers with selected 'recordStatus'. |
getRequiredCols | Get required column names for a studbook. |
getSexRatioWithAdditions | getSexRatioWithAdditions returns the sex ratio of a group. |
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: |
groupMembersReturn | Forms return list of groupAddAssign function |
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. |
initializeHaremGroups | Make the initial groupMembers animal list |
insertChangedColsTab | insertChangedColsTab insert a list of changed columns found by 'qcStudbook' in the pedigree file |
insertErrorTab | insertErrorTab insert a list of errors found by 'qcStudbook' in the pedigree file |
insertSeparators | insertSeparators inserts the character "-" between year and month and between month and day portions of a date string in %Y%m%d format. |
isEmpty | Is vector empty or all NA values. |
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. |
lacy1989Ped | lacy1989Ped small hypothetical pedigree |
lacy1989PedAlleles | lacy1989PedAlleles is a dataframe produced by 'geneDrop' on 'lacy1989Ped' with 5000 iterations. |
makeAvailable | Convenience function to make the initial available animal list |
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. |
makeRoundUp | Round up the provided integer vector 'int' according to the 'modulus'. |
makesLoop | 'makesLoop' tests for a common ancestor. |
mapIdsToObfuscated | Map IDs to Obfuscated IDs |
meanKinship | Calculates the mean kinship for each animal in a kinship matrix |
nprcgenekeepr | Genetic Management Functions |
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 |
orderReport | Order the results of the genetic value analysis for use in a report. |
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 |
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. |
rbindFill | Append the rows of one dataframe to another. |
readExcelPOSIXToCharacter | Read in Excel file and convert POSIX dates to character |
removeDuplicates | Remove duplicate records from pedigree |
removeEarlyDates | removeEarlyDates removes dates before a specified year |
removeGroupIfNoAvailableAnimals | Remove group numbers when all available animals have been used |
removePotentialSires | Removes potential sires from list of Ids |
removeSelectedAnimalFromAvailableAnimals | Updates list of available animals by removing the selected animal |
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. |
resetGroup | Update or add the "group" field of a 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' |
str_detect_fixed_all | Returns a logical vector with results of stri_detect() for each pattern in second parameters character vector. |
summary.nprcgenekeeprErr | summary.nprcgenekeeprErr Summary function for class 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 |
unknown2NA | Removing IDs having "UNKNOWN" regardless of case |
withinIntegerRange | Get integer within a range |