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# Read a pedfile (which includes the variable names in the top line)
# and build haplotypes using the markers which appear third, second, and
# first in the pedfile.
filespec <- file.path(.path.package("tdthap"),"tests","test.ped")
ped <- read.table(filespec)
# call hap.transmit, tdt.select, and tdt.rr
haps <- hap.transmit(ped, markers=c(3,2,1))
hap.use <- tdt.select(haps, markers=1:2)
table(hap.use$trans)
table(hap.use$untrans)
rr <- tdt.rr(hap.use)
rr
# To do a Geary_Moran test on a 10 marker haplotype
gaps <- c(0, 50, 60, 80, 20, 30, 50, 40, 50, 100, 0)
set.similarity(nloci=10, spacing=gaps, power=0.5)
get.similarity(nloci=10)
test <- tdt.quad(hap.use, nsim=10000, keep=T)
names(test)
summary(test$sim)
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