fpederr: Simulates a pedigree with errors and missing data from a complete pedigree.

Description

Implements the 'forward' approach to producing pairs of pedigrees for power and sensitivity analyses.

Usage

fpederr(truePedigree, founders = NULL, sex = NULL, samp = NULL, 
          sireE = NULL, damE = NULL, sireA = NULL, damA = NULL, 
          cohort = NULL, first = NULL, last = NULL, monoecey = 0, 
          modifyAssumedPedigree = 0)

Arguments

truePedigree

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.

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

Run this code

# NOT RUN {
testData<-as.data.frame(matrix(c(
1,	NA,	NA,	1,	1,	1,	2,	2,
2,	NA,	NA,	1,	1,	1,	2,	2,
3,	NA,	NA,	1,	1,	1,	2,	2,
4,	NA,	NA,	1,	0,	1,	2,	2,
5,	NA,	NA,	1,	0,	1,	2,	2,
6,	1,	4,	0,	-1,	2,	3,	3,
7,	1,	4,	0,	-1,	2,	3,	3,
8,	1,	4,	0,	-1,	2,	3,	3,
9,	1,	4,	0,	-1,	2,	3,	3,
10,	2,	5,	0,	-1,	2,	3,	3,
11,	2,	5,	0,	-1,	2,	3,	3,
12,	2,	5,	0,	-1,	2,	3,	3,
13,	2,	5,	0,	-1,	2,	3,	3,
14,	3,	5,	0,	-1,	2,	3,	3,
15,	3,	5,	0,	-1,	2,	3,	3,
16,	3,	5,	0,	-1,	2,	3,	3,
17,	3,	5,	0,	-1,	2,	3,	3),
17,8,byrow=TRUE))

names(testData)<-c("id","dam","sire","founder","sex",
                                  "cohort","first","last")
pedigree<-as.data.frame(cbind(testData$id,testData$dam,
                                           testData$sire))
for(x in 1:3) pedigree[,x]<-as.factor(pedigree[,x])
names(pedigree)<-c("id","dam","sire")
pedigree

## some missing sire links:
fpederr(truePedigree=pedigree,founders=testData$founder,
        sex=testData$sex,sireA=0.5,cohort=testData$cohort,
        first=testData$first,last=testData$last)$assumedPedigree

## some erroneous sire links:
fpederr(truePedigree=pedigree,founders=testData$founder,
        sex=testData$sex,sireE=0.5,cohort=testData$cohort,
        first=testData$first,last=testData$last)$assumedPedigree
# }