Nothing
library(sped)
data(thompson)
# Attempt to reproduce results from Table 1 in Thompson (1986)
# cited in help pages and design doc
goo <- gammas(c("U", "V", "Q", "R", "W"), thompson)
# Table 1 only has numbers for founders B, C, F
goo <- goo[c("B", "C", "F"), ]
# transpose to match table 1
goo <- t(goo)
mygoo <- rbind(c(6, 6, 4) / 16,
c(20, 20, 8) / 64,
c(8, 0, 8) / 32,
c(8, 4, 16) / 32,
c(72, 56, 80) / 256)
all(dim(goo) == dim(mygoo))
dimnames(mygoo) <- dimnames(goo)
all.equal(goo, mygoo)
# now betas
boo <- betas(c("U", "V", "Q", "R", "W"), thompson)
# Table 1 only has numbers for founders B, C, F
boo <- boo[c("B", "C", "F"), ]
# transpose to match table 1
boo <- t(boo)
myboo <- rbind(c(2, 2, 0) / 16,
c(6, 6, 0) / 64,
c(2, 0, 0) / 32,
c(2, 0, 8) / 32,
c(20, 10, 16) / 256)
all(dim(boo) == dim(myboo))
dimnames(myboo) <- dimnames(boo)
all.equal(boo, myboo)
# now alphas
aoo <- alphas(c("U", "V", "Q", "R", "W"), thompson)
# Table 1 only has numbers for founders B, C, F
aoo <- aoo[c("B", "C", "F"), ]
# transpose to match table 1
aoo <- t(aoo)
myaoo <- rbind(c(1, 1, 0) / 16,
c(3, 3, 0) / 64,
c(1, 0, 0) / 32,
c(1, 0, 4) / 32,
c(11, 6, 8) / 256)
all(dim(aoo) == dim(myaoo))
dimnames(myaoo) <- dimnames(aoo)
all.equal(aoo, myaoo)
# now inbreeding
ioo <- inbreeding(c("U", "V", "Q", "R", "W"), thompson)
myioo <- c(1/8, 3/32, 1/16, 5/32, 25/256)
length(ioo) == length(myioo)
names(myioo) <- names(ioo)
all.equal(ioo, myioo)
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