qcStudbook: Quality Control for the Studbook or pedigree
In rmsharp/nprcmanager: Genetic Tools for Colony Management

Description Usage Arguments Value Examples

Main pedigree curation function that performs basic quality control on pedigree information

1	qcStudbook(sb, minParentAge = 2, reportChanges = FALSE, reportErrors = FALSE)

`sb`	A dataframe containing a table of pedigree and demographic information. The function recognizes the following columns (optional columns will be used if present, but are not required): id — Character vector with Unique identifier for all individuals sire — Character vector with unique identifier for the father of the current id dam — Character vector with unique identifier for the mother of the current id sex — Factor levels: "M", "F", "U" Sex specifier for an individual birth — Date or `NA` (optional) with the individual's birth date departure — Date or `NA` (optional) an individual was sold or shipped from the colony death — date or `NA` (optional) Date of death, if applicable status — Factor levels: ALIVE, DEAD, SHIPPED (optional) Status of an individual origin — Character or `NA` (optional) Facility an individual originated from, if other than ONPRC ancestry — Character or `NA` (optional) Geographic population to which the individual belongs spf — Character or `NA` (optional) Specific pathogen-free status of an individual vasxOvx — Character or `NA` (optional) Indicator of the vasectomy/ovariectomy status of an animal; `NA` if animal is intact, assume all other values indicate surgical alteration condition — Character or `NA` (optional) Indicator of the restricted status of an animal. "Nonrestricted" animals are generally assumed to be naive.
`minParentAge`	numeric values to set the minimum age in years for an animal to have an offspring. Defaults to 2 years. The check is not performed for animals with missing birth dates.
`reportChanges`	logical value that if `TRUE`, the `errorLst` contains the list of changes made to the column names. Default is `FALSE`.
`reportErrors`	logical value if `TRUE` will scan the entire file and report back changes made to input and errors in a list of list where each sublist is a type of change or error found. Changes will include column names, case of categorical values (male, female, unknown), etc. Errors will include missing columns, invalid date rows, male dams, female sires, and records with one or more parents below minimum age of parents. The following changes are made to the cols. Column cols are converted to all lower case Periods (".") within column cols are collapsed to no space "" `egoid` is converted to `id` `sireid` is convert to `sire` `damid` is converted to `dam` If the dataframe (`sb` does not contain the five required columns (`id`, `sire`, `dam`, `sex`), and `birth` the function throws an error by calling `stop()`. If the `id` field has the string UNKNOWN (any case) or both the fields `sire` or `dam` have `NA` or UNKNOWN (any case), the record is removed. If either of the fields `sire` or `dam` have the string UNKNOWN (any case), they are replaced with a unique identifier with the form `Unnnn`, where `nnnn` represents one of a series of sequential integers representing the number of missing sires and dams right justified in a pattern of `0000`. See `addUIds` function. The function `addParents` is used to add records for parents missing their own record in the pedigree. The function `convertSexCodes` is used with `ignoreHerm == TRUE` to convert sex codes according to the following factors of standardized codes: F – replacing "FEMALE" or "2" M – replacing "MALE" or "1" H – replacing "HERMAPHRODITE" or "4", if ignore.herm == FALSE U – replacing "HERMAPHRODITE" or "4", if ignore.herm == TRUE U – replacing "UNKNOWN" or "3" The function `correctParentSex` is used to ensure no parent is both a sire and a dam. If this error is detected, the function throws an error and halts the program. The function `convertStatusCodes` converts status indicators to the following factors of standardized codes. Case of the original status value is ignored. "ALIVE" — replacing "alive", "A" and "1" "DECEASED" — replacing "deceased", "DEAD", "D", "2" "SHIPPED" — replacing "shipped", "sold", "sale", "s", "3" "UNKNOWN" — replacing is.na(status) "UNKNOWN" — replacing "unknown", "U", "4" The function `convertAncestry` coverts ancestry indicators using regular expressions such that the following conversions are made from character strings that match selected substrings to the following factors. "INDIAN" — replacing "ind" and not "chin" "CHINESE" — replacing "chin" and not "ind" "HYBRID" — replacing "hyb" or "chin" and "ind" "JAPANESE" — replacing "jap" "UNKNOWN" — replacing `NA` "OTHER" — replacing not matching any of the above The function `convertDate` converts character representations of dates in the columns `birth`, `death`, `departure`, and `exit` to dates using the `as.Date` function. The function `setExit` uses heuristics and the columns `death` and `departure` to set `exit` if it is not already defined. The function `calcAge` uses the `birth` and the `exit` columns to define the `age` column. The numerical values is rounded to the nearest 0.1 of a year. If `exit` is not defined, the current system date (`Sys.Date()`) is used. The function `findGeneration` is used to define the generation number for each animal in the pedigree. The function `removeDuplicates` checks for any duplicated records and removes the duplicates. I also throws an error and stops the program if an ID appears in more than one record where one or more of the other columns have a difference. Columns that cannot be used subsequently are removed and the rows are ordered by generation number and then ID. Finally the columns `id` `sire`, and `dam` are coerce to character.

A data.frame with standardized and quality controlled pedigree information.

examplePedigree <- nprcgenekeepr::examplePedigree
ped <- qcStudbook(examplePedigree, minParentAge = 2, reportChanges = FALSE,
                  reportErrors = FALSE)
names(ped)