Man pages for nprcgenekeepr
Genetic Tools for Colony Management
| 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... |
| 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 |
| 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 |
| dataframe2string | Convert a data frame to a character vector |
| exampleNprcgenekeeprConfig | Example nprcgenekeepr configuration file (loadable) |
| examplePedigree | Example pedigree object (from ExamplePedigree.csv) |
| 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 |
| geneDrop | Simulate gene dropping through a pedigree |
| getAncestors | Recursively collect an individual's ancestors |
| get_and_or_list | Join a character vector into an and/or list |
| 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 |
| get_elapsed_time_str | Format the elapsed time since a start time |
| getEmptyErrorLst | Create an empty errorLst object |
| getErrorTab | Build the error-list tab panel |
| getFileDirectRelatives | Get the direct relatives of selected animals from a pedigree... |
| 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... |
| 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... |
| getSpeciesMinBreedingAge | Look up the minimum breeding age (years) for one or more... |
| 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 |
| isFounder | Identify the founders in a pedigree |
| is_valid_date_str | Test whether a string is a valid date |
| 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 |
| 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... |
| 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... |
| modGvAndBgDescUI | Genetic Value and Breeding Group Description Module - UI... |
| 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 |
| nprcgenekeepr-package | nprcgenekeepr: Genetic Tools for Colony Management |
| 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 |
| 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 an nprcgenekeepr summary object | |
| processQcStudbookResult | Process qcStudbook Result into UI-Friendly Format |
| 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 |
| 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 |
| 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 | Summarize a studbook quality-control error list |
| toCharacter | Force dataframe columns to character |
| trimPedigree | Trim a pedigree to a group's ancestors |
| withinIntegerRange | Get integer within a range |
