sequoia (version 2.11.1)

getGenerations: Count Generations

Description

For each individual in a pedigree, count the number of generations since its most distant pedigree founder.

Usage

getGenerations(Ped, StopIfInvalid = TRUE)

Value

A vector with the generation number for each individual, starting at 0 for founders. Offspring of G0 X G0 are G1, offspring of G0 X G1 or G1 x G1 are G2, etc. NA indicates a pedigree loop where an individual is its own ancestor (or that the pedigree has >1000 generations).

If no output name is specified, no results are returned, only an error message when the pedigree contains a loop.

To get more details about a pedigree loop, you can use https://github.com/JiscaH/sequoiaExtra/blob/main/find_pedigree_loop.R

Arguments

Ped

dataframe, pedigree with the first three columns being id - dam - sire. Column names are ignored, as are additional columns.

StopIfInvalid

if a pedigree loop is detected, stop with an error (TRUE, default) or return the Pedigree, to see where the problem(s) occur.

See Also

GetAncestors, GetDescendants to get all ancestors resp. descendants of a specific individual (with a warning if it is its own ancestor); FindFamilies to find connected sub-pedigrees.

Examples

# returns nothing if OK, else error:
getGenerations(SeqOUT_griffin$Pedigree)

# returns vector with generation numbers:
G <- getGenerations(SeqOUT_griffin$Pedigree, StopIfInvalid=FALSE)
table(G, useNA='ifany')
Ped_plus_G <- cbind(SeqOUT_griffin$Pedigree, G)