rpederr

0th

Percentile

Permutes a pedigree to create a plausible complete pedigree

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.

Keywords
datagen
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

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.

Aliases
  • rpederr
Examples
# NOT RUN {
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)
# }
Documentation reproduced from package pedantics, version 1.7, License: GPL-2 | GPL-3

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