Example pedigree object (from ExamplePedigree.csv)

A pedigree object created by qcStudbook. Represents pedigree from ExamplePedigree.csv.

id

– character column of animal IDs

sire

– the male parent of the animal indicated by the id column. Unknown sires are indicated with NA

dam

– the female parent of the animal indicated by the id column. Unknown dams are indicated with NA

sex

– factor with levels: "F", "M", "H", "U". Sex specifier for an individual.

gen

– generation number (integers beginning with 0 for the founder generation) of the animal indicated by the id column.

birth

– Date vector of birth dates

exit

– Date vector of exit dates

age

– numerical vector of age in years

ancestry

– factor with levels: INDIAN, CHINESE, HYBRID, JAPANESE, OTHER, UNKNOWN indicating the geographic population of origin.

origin

– character vector or NA (optional) that indicates the name of the facility that the individual was imported from if other than local.

status

– character vector or NA. Flag indicating an individual's status as alive, dead, sold, etc. Transformed to factor {levels: ALIVE, DECEASED, SHIPPED, UNKNOWN}. Vector of standardized status codes with the possible values ALIVE, DECEASED, SHIPPED, or UNKNOWN

recordStatus

– character vector with value of "added" or "original".

fromCenter

– logical vector indicating whether the animal was born at the local center (colony-origin), derived from origin and recordStatus: TRUE when origin is blank and recordStatus is "original"; FALSE for animals imported from elsewhere (non-blank origin) or for synthetic placeholder second-parent rows (recordStatus == "added") whose true origin is not confirmed. Required by getPotentialParents to identify in-colony candidate parents.

Usage

data(examplePedigree)

Format

An object of class data.frame with 3694 rows and 13 columns.

Examples

library(nprcgenekeepr)
data("examplePedigree")
exampleTree <- createPedTree(examplePedigree)
exampleLoops <- findLoops(exampleTree)