grandmother: Dataset for missing grandchildren paper

In fam2r: From 'Familias' to R

Description

The datasets are used for examples in Kling et al. (2017) or to validate conditional simulation of marker data followed by likelihood calculation for alternative pedigrees. Further brief description is given for the examples below, see FamiliasConditional or paramlinkConditional for examples involving computations.

Usage

data(grandmother)
data(Demo3Markers)
data(symmetric)
data(F21)
data(dc)
data(adoption)

Format

A list with components pedigrees, datamatrix, loci, see FamiliasLocus

Examples

data(grandmother) #One marker
data(Demo3Markers) #Three markers, one with mutation
#Three pedigrees, Half-sibs, avuncular and grandparent:
data(symmetric) 
data(E004) # E zero zero four
pedigrees = E004$pedigrees
datamatrix = E004$datamatrix
loci = E004$loci
avail = 7
persons = rownames(datamatrix)
x = Familias2linkdat(pedigrees, datamatrix, loci) 
missing.person.plot(x[[2]][[1]], missing=avail, marker=1:2, newdev=TRUE,
                    frametitle=c("H1", "H2"), dev.height=3.3, dev.width=9)
x=Familias2linkdat(pedigrees, datamatrix, loci)
missing.person.plot(x[[2]][[1]], missing=avail, marker=1:2, newdev=TRUE,
                    frametitle=c("H1", "H2"))
## Not run:  #Takes a few minutes
Nsim=1000
res.new = conditionalLR(Nsim=Nsim, datamatrix, loci, pedigrees, available=avail,
                     seed=1483118516, program = "Familias", ref=1 )
LRnew.mean =cbind(res.new[,,1][,2],res.new[,,2][,2])
apply(LRnew.mean,2,quantile)

## End(Not run)

fam2r documentation built on May 2, 2019, 1:09 p.m.