Returns the pedigree with all animals, adding a status column
describing each animal as ALIVE or DECEASED and a
computed age column (age at exit for deceased animals). All
animals are returned, not only living ones. An animal is DECEASED
when it has an exit date or when its birth date is NA; otherwise it
is ALIVE. When ped is NULL (the default), the
packaged qcPed example data are used.
Value
A pedigree with the six columns of ped (id,
sire, dam, sex, birth, exit) and a
status column added, which describes the
animal as ALIVE or DECEASED and a age column added,
which has the animal's age in years or NA if it cannot be calculated.
The exit column values have been remapped to valid dates or NA.
Details
The columns of ped are read by position, not by name: the first six
columns must be the id, sire, dam, sex, birth and exit values in that order,
and are renamed accordingly. Any further columns are dropped. If birth is
not in the fifth column and of class Date, POSIXct or
character, the error message reports that the birth column is of
the wrong class.
The lubridate package is used here because of the way the modern Gregorian calendar is constructed, there is no straightforward arithmetic method that produces a person’s age, stated according to common usage — common usage meaning that a person’s age should always be an integer that increases exactly on a birthday.
Examples
library(nprcgenekeepr)
ped <- getPyramidAgeDist()