computeAELRTESS: Compute an approximation (AELRTESS) to the expected...
In jraffa/pedRSP: Calculates the Relatedness Summary Parameters (RSPs) in Pedigrees

Description Usage Arguments Details Value Author(s) See Also Examples

This function computes an approximation (AELRTESS) to the expecation of the likelihood ratio test statistic from a pedRSP object and uses this to calculate power. This function uses the effective number of sibpairs approximation.

1	computeAELRTESS(pedRSP, truehsq, null, sig.level = 0.05)

`pedRSP`	a pedRSP object computed using the computeRSPs function
`truehsq`	a vector of at least length 1 of the true heritability. Exactly one of truehsq and null must have length 1.
`null`	a vector of at least length 1 of the null hypothesis heritability.
`sig.level`	a scalar of the significance level of the hypothesis test

This function calculates the approximate ELRT/power from a pedRSP object using only the actual study size and the variance of the log-eigenvalues. This approximation is usually a good approximation for intermediate levels of heritability. When heritability is small or large, it can be overly conservative (under estimate power/ELRT). See paper for more details

a pedELRT object with the approximated ELRT and power.

Jesse D. Raffa

computeRSPs

require(kinship2)
test1 <- data.frame(id  =c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14),
mom =c(0, 0, 0, 0, 2, 2, 4, 4, 6,  2,  0,  0, 12, 13),
dad =c(0, 0, 0, 0, 1, 1, 3, 3, 3,  7,  0,  0, 11, 10),
sex =c(1, 2, 1, 2, 1, 2, 1, 2, 1, 1, 1, 2, 2, 2))
tped <- with(test1, pedigree(id, dad, mom, sex))
x <- computeRSPs(ped=tped)
elrtess <- computeAELRTESS(pedRSP=x,truehsq=0.3,null=seq(0.1,0.8,0.1))
plot(elrtess)