rpederrBird: Permutes a bird pedigree to create a plausible complete pedigree

Description

Permutes a pedigree to create a plausible complete pedigree, with errors accounted for in terms of extra-pair paternity.

Usage

rpederrBird(assumedPedigree, founders = NULL, sex = NULL, samp = NULL,  sireS = NULL, damS = NULL, cohort = NULL, first = NULL,  last = NULL, broods = NULL, monoecey = 0, broodData = NULL,  EPPsireData = NULL, propEPPbroods = 1,  propEPPchicksGivenEPPbrood = 0.5,  propEPPbroodsTwoFathers = 0,  modifyAssumedPedigree = 0,EPPlambda=0.001, malePhenotypes=NULL,EPPbeta=0,EPPgamma=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

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

broods

A numeric vector the same length as the pedigree indicating the brood to which each individual belongs. Can be any integer value for indivduals that do not belong to broods as spedified in broodData (see below).

monoecey

An indicator specifying whether or not bisexuality is allowed (0=no (default), 1=yes)

broodData

A five column data frame containing (1) brood IDs corresponding to broods, (2) years, (3) brood latitudes, (4) brood longitudes, and (5) an indicator (0=no or 1=yes) specifying whether or not the particular brood potentially contains extra-pair chicks.

EPPsireData

A four column data frame with (1) ids of all sires that may be extra-pair fathers, (2) years (cohorts) in which an indivdual might have been an extra pair father (one separate line for each year), and (3) latitude and (4) longitude in each year.

propEPPbroods

Proportion of broods with extra-pair chicks.

propEPPchicksGivenEPPbrood

Mean proportion of chicks that have extra-pair fathers in extra-pair broods.

propEPPbroodsTwoFathers

Proportion of extra-pair broods that have two extra-pair fathers

modifyAssumedPedigree

An indicator variable specifying whether or not an assumed pedigree with errors but no missing links should be supplied.

EPPlambda

The rate of decline of the probability of extra pair paternity with distance between males and nests.

malePhenotypes

(optional) if specified, zp will take these values in the calculation of male relative fertilities, see details

EPPbeta

(optional) coefficient of linear selection acting through undetected extra-pair breeding success, see details

EPPgamma

(optional) coefficient of quadratic selection acting through undetected extra-pair breeding success, see details

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, 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

Run this code

## test data for a single brood
id<-   c("a1","a2","a3","a4","a5","a6","a7","a8","a9")
dam<-  c(NA,NA,NA,NA,"a1","a1","a1","a1","a1")
sire<-  c(NA,NA,NA,NA,"a2","a2","a2","a2","a2")
broods<- c(NA,NA,NA,NA,"r1","r1","r1","r1","r1")
founders<-c(1,1,1,1,0,0,0,0,0)
samp<- c(1,1,1,1,1,1,1,1,1)
sex<-  c(1,0,0,0,0,0,1,0,0)
sireS<- rep(1,9)
damS<- rep(1,9)
cohort<-c(1,1,1,1,2,2,2,2,2)
first<-c(2,2,2,3,3,3,3,3,3)
last<-c(2,2,2,3,3,3,3,3,3)

broodIDs<-c("r1")
broodYears<-2
broodN<-c(10)
broodE<-c(10)
broodEPPpotential<-c(1)
EPPsireIDs<-c("a2","a3","a4")
EPPsireYears<-c(2,2,2)
sireN<-c(10,11,5)
sireE<-c(10,11,5)
EPPlambda<- 0.4

## put the test data in the required forms
assumedPedigree<-as.data.frame(cbind(id,sire,dam))
broodData<-as.data.frame(cbind(broodIDs,broodYears,broodN,
                                            broodE,broodEPPpotential))
EPPsireData<-as.data.frame(cbind(EPPsireIDs,EPPsireYears,sireN,sireE))

## simulate extra-pair paternity (try a few times and see how often
## the paterity goes to the nearer candidate EPP father):
rpederrBird(assumedPedigree=assumedPedigree,
        founders=founders,sex=sex,
        samp=samp,sireS=sireS,damS=damS,
        cohort=cohort,first=first,
        last=last,broods=broods,broodData=broodData,
        EPPsireData=EPPsireData,
        propEPPbroods=1,propEPPchicksGivenEPPbrood=0.5,
        propEPPbroodsTwoFathers=0,modifyAssumedPedigree=0)