nadiv (version 2.11)

numPed: Creates a numeric form of a pedigree

Description

This function takes a pedigree and converts it into a standard integer form used by many functions in the 'nadiv' package.

Usage

numPed(pedigree, check = TRUE)

Arguments

pedigree

A three column pedigree object, where the columns correspond to: ID, Dam, & Sire

check

A logical argument indicating if checks on the validity of the pedigree structure should be made

Value

• The pedigree, where individuals are now numbered from 1 to n and unknown parents are assigned a value of '-998'.

Details

Missing parents (e.g., base population) should be denoted by either 'NA', '0', or '*'.

Individuals must appear in the ID column in rows preceeding where they appear in either the Dam or Sire column. If check = FALSE any pedigree will be transformed into a pedigree consisting of integers and missing values denoted by '-998'. CAUTION: this should not be set to TRUE without careful thought.

Based on code from the MCMCglmm package

See Also

MCMCglmm