set.seed(290875)

library("party")

### get rid of the NAMESPACE

attach(asNamespace("party"))

### 

###

###    Regression tests for independence tests

###    

###    functions defined in file `./src/IndependenceTest.c'    

### tests for function C_IndependenceTest

xval <- rnorm(60)

x <- matrix(rank(xval), ncol = 1)

yf <- gl(2, 30)

y <- sapply(levels(yf), function(l) as.numeric(yf == l))[,1,drop = FALSE]

weights <- rep(1, nrow(x))

varctrl <- new("VariableControl")

lec <- new("LinStatExpectCovar", ncol(x), ncol(y))

res <- .Call("R_IndependenceTest", x, y, weights,  

              lec, varctrl, PACKAGE = "party")

print(res)

wmw <- wilcox.test(xval ~ yf, exact = FALSE, correct = FALSE)

print(wmw)

stopifnot(isequal(res[2], wmw$p.value))

xval <- rnorm(60)

x <- matrix(rank(xval), ncol = 1)

yf <- gl(3, 20)

y <- sapply(levels(yf), function(l) as.numeric(yf == l))

weights <- rep(1, nrow(x))

varctrl <- new("VariableControl")

varctrl@teststat <- factor("quad", levels = c("max", "quad"))

print(varctrl)

lec <- new("LinStatExpectCovarMPinv", ncol(x), ncol(y))

lec@rank <- 0

lec@MPinv <- matrix(0, nrow = ncol(x) * ncol(y), ncol = ncol(x) * ncol(y))

lec@svdmem <- new("svd_mem", ncol(x) * ncol(y))

res <- .Call("R_IndependenceTest", x, y, weights,  

              lec, varctrl, PACKAGE = "party")

print(res)

kw <- kruskal.test(xval ~ yf)

print(kw)

stopifnot(isequal(res[2], kw$p.value))

stopifnot(isequal(lec@rank, kw$parameter))

tmp <- x

x <- y

y <- tmp

varctrl <- new("VariableControl")

varctrl@teststat <- factor("quad", levels = c("max", "quad"))

print(varctrl)

lec <- new("LinStatExpectCovarMPinv", ncol(x), ncol(y))

lec@rank <- 0

lec@MPinv <- matrix(0, nrow = ncol(x) * ncol(y), ncol = ncol(x) * ncol(y))

lec@svdmem <- new("svd_mem", ncol(x) * ncol(y))

res <- .Call("R_IndependenceTest", x, y, weights,  

              lec, varctrl, PACKAGE = "party")

print(res)

kw <- kruskal.test(xval ~ yf)

print(kw)

stopifnot(isequal(res[2], kw$p.value))

xf <- gl(3, 2000)

x <- sapply(levels(xf), function(l) as.numeric(xf == l))

yf <- gl(3, 2000)[sample(1:6000)]

y <- sapply(levels(yf), function(l) as.numeric(yf == l))

weights <- rep(1, nrow(x))

varctrl <- new("VariableControl")

varctrl@teststat <- factor("quad", levels = c("max", "quad"))

print(varctrl)

lec <- new("LinStatExpectCovarMPinv", ncol(x), ncol(y))

lec@rank <- 0

lec@MPinv <- matrix(0, nrow = ncol(x) * ncol(y), ncol = ncol(x) * ncol(y))

lec@svdmem <- new("svd_mem", ncol(x) * ncol(y))

res <- .Call("R_IndependenceTest", x, y, weights,  

              lec, varctrl, PACKAGE = "party")

print(res)

chis <- chisq.test(table(xf, yf), correct = FALSE)

print(chis)

stopifnot(isequal(round(res[2],3), round(chis$p.value,3)))

### unbalanced data

xval <- rnorm(60)

x <- matrix(rank(xval), ncol = 1)

yf <- factor(rnorm(60) > 1)

y <- sapply(levels(yf), function(l) as.numeric(yf == l)) #[,1,drop = FALSE]

weights <- rep(1, nrow(x))

varctrl <- new("VariableControl")

lec <- new("LinStatExpectCovar", ncol(x), ncol(y))

res <- .Call("R_IndependenceTest", x, y, weights,

              lec, varctrl, PACKAGE = "party")

print(res)

wmw <- wilcox.test(xval ~ yf, exact = FALSE, correct = FALSE)

print(wmw)

stopifnot(isequal(res[2], wmw$p.value))

varctrl <- new("VariableControl")

lec <- new("LinStatExpectCovar", ncol(y), ncol(x))

res <- .Call("R_IndependenceTest", y, x, weights,

              lec, varctrl, PACKAGE = "party")

print(res)

wmw <- wilcox.test(xval ~ yf, exact = FALSE, correct = FALSE)

print(wmw)

stopifnot(isequal(res[2], wmw$p.value))

xf <- factor(cut(rnorm(6000), breaks = c(-Inf, -2, 0.5, Inf)))

x <- sapply(levels(xf), function(l) as.numeric(xf == l))

yf <- factor(cut(rnorm(6000), breaks = c(-Inf, -0.5, 1.5, Inf)))

y <- sapply(levels(yf), function(l) as.numeric(yf == l))

weights <- rep(1, nrow(x))

varctrl <- new("VariableControl")

varctrl@teststat <- factor("quad", levels = c("max", "quad"))

print(varctrl)

lec <- new("LinStatExpectCovarMPinv", ncol(x), ncol(y))

lec@rank <- 0

lec@MPinv <- matrix(0, nrow = ncol(x) * ncol(y), ncol = ncol(x) * ncol(y))

lec@svdmem <- new("svd_mem", ncol(x) * ncol(y))

res <- .Call("R_IndependenceTest", x, y, weights,  

              lec, varctrl, PACKAGE = "party")

print(res)

chis <- chisq.test(table(xf, yf), correct = FALSE)

print(chis)

stopifnot(isequal(round(res[2],3), round(chis$p.value,3)))

### Multiple Variables

gtctrl <- new("GlobalTestControl")

tlev <- levels(gtctrl@testtype)   

gtctrl@testtype <- factor("Univariate", levels = tlev)

mydata = data.frame(y = gl(2, 50), x1 = rnorm(100),

                    x2 = rnorm(100), x3 = rnorm(100))

inp <- initVariableFrame(mydata[,c("x1", "x2", "x3"),drop = FALSE], 

    trafo = function(data) ptrafo(data, numeric_trafo = rank))

resp <- initVariableFrame(mydata[,"y",drop = FALSE], trafo = NULL, response = TRUE)

ls <- new("LearningSample", inputs = inp, responses = resp,

          weights = rep(1, inp@nobs), nobs = nrow(mydata), 

          ninputs = inp@ninputs)

tm <- ctree_memory(ls)

varctrl <- new("VariableControl")

pvals <- .Call("R_GlobalTest", ls, ls@weights, tm, varctrl, gtctrl, PACKAGE = "party")[[2]]

wpvals <- rep(0, 3)

wpvals[1] <- wilcox.test(x1 ~ y, data = mydata,

                         correct = FALSE, exact = FALSE)$p.value

wpvals[2] <- wilcox.test(x2 ~ y, data = mydata, 

                         correct = FALSE, exact = FALSE)$p.value

wpvals[3] <- wilcox.test(x3 ~ y, data = mydata, 

                         correct = FALSE, exact = FALSE)$p.value

stopifnot(isequal(wpvals, 1 - pvals))

varctrl <- new("VariableControl")

gtctrl@testtype <- factor("MonteCarlo", levels = tlev)

gtctrl@nresample <- as.integer(19999)

inp <- initVariableFrame(mydata[,"x1",drop = FALSE], trafo = function(data)

    ptrafo(data, numeric_trafo = rank))

resp <- initVariableFrame(mydata[,"y",drop = FALSE], trafo = NULL, response = TRUE)

ls <- new("LearningSample", inputs = inp, responses = resp,

          weights = rep(1, inp@nobs), nobs = nrow(mydata), 

          ninputs = as.integer(1))

pvals <- .Call("R_GlobalTest", ls, ls@weights, tm, varctrl, gtctrl, PACKAGE = "party")[[2]]

stopifnot(abs((1 - pvals) - wilcox.test(x1 ~ y, data = mydata, 

    exact = TRUE)$p.value) < 1e-2)