A complete pedigree with records for all individuals and parental ID's for all non-founders
founders
A vector the same length as the pedigree containing indicator variables 1 = founder, 0 = non-founder
sex
A vector the same length as the pedigree indicating sex, 0=male, 1=female, any other value = unknown sex
samp
A vector the same length as the pedigree indicating whether or not each individual is sampled (1), or an unsampled dummy individual (0).
sireE
Value(s) indicating the paternal error rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals.
damE
Value(s) indicating the maternal error rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals.
sireA
Value(s) indicating the paternal pedigree link assignment rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals.
damA
Value(s) indicating the maternal pedigree link assignment rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals.
cohort
A numeric vector the same length as the pedigree containing cohorts
first
A numeric vector the same length as the pedigree indicating the first cohort for which an individual is to be considered a potential parent
last
A numeric vector the same length as the pedigree indicating the last cohort for which an individual is to be considered a potential parent
monoecey
An indicator specifying whether or not bisexuality is allowed (0=no (default), 1=yes)
modifyAssumedPedigree
An indicator variable specifying whether or not an assumed pedigree with errors but no missing links should be supplied.
Value
assumedPedigree
A pedigree differing from the supplied pedigree
so as to mimic patterns of pedigree errors and missing data that
might occur in a real study.
truePedigree
Echos the pedigree supplied.
supplementalPedigree
(optional) a 'assumed' pedigree containing
errorsbut no missing links.
Morrissey et al. 2007. Journal of Evolutionary Biology 20:2309-2321., Morrissey, M.B, and A.J. Wilson, 2009. pedantics, an R package for pedigree-based genetic simulation, and pedigree manipulation, characterisation, and viewing. Molecular Ecology Resources.