Man pages for rmsharp/nprcmanager
Genetic Tools for Colony Management
| 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... |
| addGenotype | Add genotype data to pedigree file |
| addGroupOfUnusedAnimals | addGroupOfUnusedAnimals adds a group to the saved groups if... |
| 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... |
| addUIds | Eliminates partial parentage situations by adding unique... |
| 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... |
| 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... |
| calcRetention | Calculates Allelic Retention |
| calculateSexRatio | Calculates the sex ratio (number of non-males / number of... |
| checkChangedColAndErrorLst | checkChangedColAndErrorLst examines errorLst for errors and... |
| 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... |
| chooseAllelesChar | Combines two vectors of alleles when alleles are character... |
| chooseDate | Choose date based on 'earlier' flag. |
| colChange | colChange internal function to describe column names... |
| convertAncestry | Converts the ancestry information to a standardized code |
| convertDate | Converts date columns formatted as characters to be of type... |
| convertFromCenter | Converts the fromCenter information to a standardized code |
| convertRelationships | Converts pairwise kinship values to a relationship category... |
| convertSexCodes | Converts sex indicator for an individual to a standardized... |
| 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... |
| 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... |
| exampleNprcgenekeeprConfig | exampleNprcgenekeeprConfig is a loadable version of the... |
| examplePedigree | examplePedigree is a pedigree object created by 'qcStudbook' |
| fillBins | fillBins Fill bins represented by list of two lists 'males'... |
| fillGroupMembers | Forms and fills list of animals groups based on provided... |
| fillGroupMembersWithSexRatio | Forms breeding group(s) with an effort to match a specified... |
| filterAge | Removes kinship values where an animal is less than the... |
| filterKinMatrix | Filters a kinship matrix to include only the egos listed in... |
| filterPairs | Filters kinship values from a long-format kinship table based... |
| filterReport | Filters a genetic value report down to only the specified... |
| filterThreshold | Filters kinship to remove rows with kinship values less than... |
| finalRpt | finalRpt is a list object created from the list object _rpt_... |
| 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... |
| findPedigreeNumber | Determines the generation number for each id. |
| fixColumnNames | fixColumnNames changes original column names and into... |
| fixGenotypeCols | Reformat names of observed genotype columns |
| focalAnimals | focalAnimals is a dataframe with one column (_id_) containing... |
| geneDrop | Gene drop simulation based on the provided pedigree... |
| getAncestors | Recursively create a character vector of ancestors for an... |
| get_and_or_list | Returns a one element character string with correct... |
| 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... |
| 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... |
| getDateErrorsAndConvertDatesInPed | Converts columns of dates in text form to 'Date' object... |
| getDemographics | Get demographic data |
| get_elapsed_time_str | Returns the elapsed time since start_time. |
| 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... |
| getGenotypes | Get genotypes from file |
| getGVGenotype | Get Genetic Value Genotype data structure for reportGV... |
| getGVPopulation | Get the population of interest for the Genetic Value... |
| getIdsWithOneParent | getIdsWithOneParent extracts IDs of animals pedigree without... |
| 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... |
| getMinParentAge | Get minimum parent age. |
| getOffspring | Get offspring to corresponding animal IDs provided |
| getParamDef | Get parameter definitions from tokens found in configuration... |
| 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... |
| 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 |
| 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... |
| insertErrorTab | insertErrorTab insert a list of errors found by 'qcStudbook'... |
| insertSeparators | insertSeparators inserts the character "-" between year and... |
| 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... |
| makeAvailable | Convenience function to make the initial available animal... |
| 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... |
| 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... |
| makesLoop | 'makesLoop' tests for a common ancestor. |
| mapIdsToObfuscated | Map IDs to Obfuscated IDs |
| meanKinship | Calculates the mean kinship for each animal in a kinship... |
| nprcgenekeepr | Genetic Management Functions |
| obfuscateDate | obfucateDate adds a random number of days bounded by plus and... |
| obfuscateId | obfucateId creates a vector of ID aliases of specified length |
| obfuscatePed | obfuscatePed takes a pedigree object and creates aliases for... |
| offspringCounts | Finds the total number of offspring for each animal in the... |
| orderReport | Order the results of the genetic value analysis for use in a... |
| ped1Alleles | ped1Alleles is a dataframe created by the geneDrop function |
| pedDuplicateIds | pedDuplicateIds is a dataframe with 9 rows and 5 columns... |
| pedFemaleSireMaleDam | pedFemaleSireMaleDam is a dataframe with 8 rows and 5 columns... |
| pedGood | pedGood is a dataframe with 8 rows and 5 columns (ego_id,... |
| pedInvalidDates | pedInvalidDates is a dataframe with 8 rows and 5 columns... |
| pedMissingBirth | pedMissingBirth is a dataframe with 8 rows and 5 columns... |
| pedOne | pedOne is a loadable version of a pedigree file fragment used... |
| pedSameMaleIsSireAndDam | pedSameMaleIsSireAndDam is a dataframe with 8 rows and 5... |
| pedSix | pedSix is a loadable version of a pedigree file fragment used... |
| pedWithGenotype | pedWithGenotype is a dataframe produced from qcPed by adding... |
| pedWithGenotypeReport | pedWithGenotypeReport is a list containing the output of... |
| print.summary.nprcgenekeepr print.summary.nprcgenekeeprGV | |
| qcBreeders | qcBreeders is a list of 29 baboon IDs that are potential... |
| 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... |
| removePotentialSires | Removes potential sires from list of Ids |
| removeSelectedAnimalFromAvailableAnimals | Updates list of available animals by removing the selected... |
| removeUninformativeFounders | Remove uninformative founders. |
| removeUnknownAnimals | removeUnknownAnimals Removes unknown animals added to... |
| 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... |
| 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... |
| 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... |
| summary | summary.nprcgenekeeprErr Summary function for class... |
| toCharacter | Force dataframe columns to character |
| trimPedigree | Trim pedigree to ancestors of provided group by removing... |
| unknown2NA | Removing IDs having "UNKNOWN" regardless of case |
| withinIntegerRange | Get integer within a range |
