%\VignetteIndexEntry{BuyseTest: wilcoxon test}
%\VignetteEngine{R.rsp::asis}
%\VignetteKeyword{PDF}
%\VignetteKeyword{vignette}
%\VignetteKeyword{package}

## * Single Wilcoxon test
## ** Exact test

## chunk 2
x <- c(0.80, 0.83, 1.89, 1.04, 1.45, 1.38, 1.91, 1.64, 0.73, 1.46)
y <- c(1.15, 0.88, 0.90, 0.74, 1.21)
df <- rbind(data.frame(value = x, group="x"),
            data.frame(value = y, group="y"))

## chunk 3
wilcox.test(value ~ group, data = df)

## chunk 4
asht::wmwTest(value ~ group, data = df, method = "exact.ce")

## chunk 5
eperm.BT <- BuyseTest(group ~ cont(value), data = df, add.halfNeutral = TRUE,
                      method.inference = "permutation", n.resampling = 1e4,
                      trace = FALSE, cpus = 5, seed = 10)
confint(eperm.BT, statistic = "favorable")

## chunk 6
eU.BT <- suppressWarnings(BuyseTest(group ~ cont(value), data = df,
                                    add.halfNeutral = TRUE))
confint(eU.BT, statistic = "favorable")

## chunk 7
etperm.BT <- BuyseTest(group ~ cont(value), data = df, add.halfNeutral = TRUE,
                      method.inference = "studentized permutation", n.resampling = 1e4,
                      trace = FALSE, seed = 10)
confint(etperm.BT, statistic = "favorable")

## ** Approximate test

## chunk 8
set.seed(10)
df2 <- rbind(data.frame(value = round(rnorm(50),2), group="x"),
             data.frame(value = round(rnorm(50),2), group="y"))
any(duplicated(df2$value)) ## test whether there are any ties

## chunk 9
wilcox.test(value ~ group, data = df2)

## chunk 10
wmwTest(value ~ group, data = df2)

## chunk 11
wmwTest(value ~ group, data = df2, correct = FALSE)

## chunk 12
eperm.BT2 <- BuyseTest(group ~ cont(value), data = df2, add.halfNeutral = TRUE,
                       method.inference = "varexact-permutation")
confint(eperm.BT2, statistic = "favorable")

## chunk 13
eperm.BT2 <- BuyseTest(group ~ cont(value), data = df2, add.halfNeutral = TRUE,
                       method.inference = "permutation", n.resampling = 1e4,
                       trace = FALSE, cpus = 5, seed = 10)
confint(eperm.BT2, statistic = "favorable", method.ci.resampling = "gaussian")

## * Multiple Wilcoxon tests

## chunk 14
set.seed(35)
dt <- simBuyseTest(n.T=25, n.strata = 5)
dt$id <- paste0("id",1:NROW(dt))
dt$strata <- as.character(dt$strata) 
print(head(dt), class = FALSE)

## chunk 15
BuyseTest.options(order.Hprojection=1);BuyseTest.options(trace=0)

ls.BT <- list("b-a=0" = BuyseTest(strata ~ cont(score), add.halfNeutral = TRUE,
                                  data = dt[dt$strata %in% c("a","b"),],
                                  method.inference = "u-statistic"),
              "c-a=0" = BuyseTest(strata ~ cont(score), add.halfNeutral = TRUE,
                                  data = dt[dt$strata %in% c("a","c"),],
                                  method.inference = "u-statistic"),
              "d-a=0" = BuyseTest(strata ~ cont(score), add.halfNeutral = TRUE,
                                  data = dt[dt$strata %in% c("a","d"),],
                                  method.inference = "u-statistic"),
              "e-a=0" = BuyseTest(strata ~ cont(score), add.halfNeutral = TRUE,
                                  data = dt[dt$strata %in% c("a","e"),],
                                  method.inference = "u-statistic")
              )

M.confint <- do.call(rbind,lapply(ls.BT,confint, statistic = "favorable"))
cbind(M.confint,adj.p.value = p.adjust(M.confint[,"p.value"], method = "bonferroni"))

## chunk 16
set.seed(1)
e.mc <- BuyseMultComp(ls.BT, statistic = "favorable", cluster = "id", global = TRUE)
print(e.mc, cols = c("estimate","se","p.value","adj.p.value"))

## chunk 17
M.cor <- cor(lava::iid(e.mc))
dimnames(M.cor) <- list(names(ls.BT),names(ls.BT))
M.cor

## * References
