rpederr: Permutes a pedigree to create a plausible complete pedigree

In pedantics: Functions to Facilitate Power and Sensitivity Analyses for Genetic Studies of Natural Populations

Description

Given estimates of indivdiual life histories and rates and patterns of errors in pedigree links, rpederr probabilistically assigns "true" parents given an incomplete and potentially eroneous pedigree.

Usage

rpederr(assumedPedigree, founders = NULL, sex = NULL, samp = NULL, 
         sireE = NULL, damE = NULL, sireS = NULL, damS = NULL, 
         cohort = NULL, first = NULL, last = NULL, monoecey = 0, 
         modifyAssumedPedigree = 0)

Arguments

assumedPedigree	A pedigree
founders	A vector of indicator variables denoting founder status (1=founder, 0=non-founder)
sex	A vector of indicator variables denoting sex (0=male,1=female,anything else=unknown)
samp	A vector denoting whether or not individuals are sampled (1), or dummy indivdiuals (0) added to the pedigree for the purpose of simulating potential "true" pedigree links that go outside the sampled population
sireE	Sire assignment error rates, see details
damE	Dam assignment error rates, see details
sireS	Proportion of "true" simulated sires that are to be taken from the unsampled portion of the pedgiree.
damS	Proportion of "true" simulated dams that are to be taken from the unsampled portion of the pedgiree.
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	echos the supplied pedigree
truePedigree	A plausible pedigree with no errors and no missing links
supplementalPedigree	A plausible pedigree with errors but no missing links

Author(s)

Michael Morrissey [e-mail]

References

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.

Examples

id<-   c("a1","a2","a3","a4","a5","a6","a7","a8","a9")
dam<-  c(NA,NA,NA,"a1","a1","a1","a4","a4","a4")
sire<- c(NA,NA,NA,NA,NA,NA,"a5","a5","a5")
found<-c(1,1,1,0,0,0,0,0,0)
samp<- c(1,1,1,1,1,1,1,1,1)
sex<-  c(1,0,0,1,0,0,1,0,0)
dade<- rep(0,9)
mume<- rep(0,9)
dads<- rep(1,9)
mums<- rep(1,9)
cohort<-c(1,1,1,2,2,2,3,3,3)
first<-c(2,2,2,3,3,3,4,4,4)
last<-c(2,2,2,3,3,3,4,4,4)
pedigree<-as.data.frame(cbind(id,sire,dam))

### don't simulate any errors, just fill in the missing sires
rpederr(assumedPedigree=pedigree,founders=found,sex=sex,
                  samp=samp,cohort=cohort,first=first,last=last)

## fill in the missing sires, and additionally simulate a problem 
## with the second maternal sibship note that it is probabilistic, 
## so this example may need to be run a couple of times before the
## error comes up, given the very small example dataset
fatherErrors<-c(0,0,0,0,0,0,0.8,0.8,0.8)
rpederr(assumedPedigree=pedigree,founders=found,sex=sex,samp=samp,
           sireE=fatherErrors,cohort=cohort,first=first,last=last)

pedantics documentation built on May 1, 2019, 10:54 p.m.