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# Untitled

a guest May 24th, 2012 157 Never
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1. ## caracal for
3. ## paired data (two dependent groups)
4. x1 <- c(99, 99.5, 65, 100, 99, 99.5, 99, 99.5, 99.5, 57, 100, 99.5,
5.         99.5, 99, 99, 99.5, 89.5, 99.5, 100, 99.5)
6. y1 <- c(99, 99.5, 99.5, 0, 50, 100, 99.5, 99.5, 0, 99.5, 99.5, 90,
7.         80, 0, 99, 0, 74.5, 0, 100, 49.5)
8.
9. ## shorten data to something where we can do a complete permutation test
10. Nexact <- 12
11. x1 <- x1[1:Nexact]
12. y1 <- y1[1:Nexact]
13. DV <- c(x1, y1)
14. IV <- factor(rep(c("A", "B"), c(length(x1), length(y1))))
15. id <- factor(rep(1:length(x1), 2))
16.
17. library(lmPerm)                        # for aovp()
18. summary(aovp(DV ~ IV + Error(id/IV)))  # p-value is far off from correct, see below
19.
20. library(coin)                          # for oneway_test()
21. oneway_test(DV ~ IV | id, alternative="two.sided", distribution=approximate(B=9999))  # close to correct
22.
23. ## exact test (two-sided) for correct permutation p-value
24. DVd    <- y1-x1
25. sgnLst <- lapply(numeric(Nexact), function(x) { c(-1, 1) } )
26. sgnMat <- as.matrix(expand.grid(sgnLst))
27. getMD  <- function(x) { mean(abs(DVd) * x) }
28. resMD  <- apply(sgnMat, 1, getMD)
29. (pVal  <- sum(abs(resMD) >= abs(mean(DVd))) / length(resMD))
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