swh:1:snp:813359ba77493c9d5dd1abad9a1f53490a8abf57
Tip revision: 90f2c7b70515c6d4548c47199d4103312a0c9a5c authored by Torsten Hothorn on 02 February 2006, 00:00:00 UTC
version 0.4-4
version 0.4-4
Tip revision: 90f2c7b
InitMethods.R
### new("CovarianceMatrix", ...)
setMethod(f = "initialize",
signature = "CovarianceMatrix",
definition = function(.Object, x) {
.Object@covariance <- x
.Object
}
)
### new("Variance", ...)
setMethod(f = "initialize",
signature = "Variance",
definition = function(.Object, x) {
.Object@variance <- x
.Object
}
)
### new("IndependenceProblem", ...)
### initialized data
setMethod(f = "initialize",
signature = "IndependenceProblem",
definition = function(.Object, x, y, block = NULL, weights = NULL) {
if (any(is.na(x)))
stop(sQuote("x"), " contains missing values")
if (any(is.na(y)))
stop(sQuote("y"), " contains missing values")
if (!is.null(block) && !is.factor(block))
stop(sQuote("block"), " is not a factor")
if (!is.null(block) && any(is.na(block)))
stop(sQuote("block"), " contains missing values")
if (!is.null(weights) && any(is.na(weights)))
stop(sQuote("weights"), " contains missing values")
.Object@x <- x
.Object@y <- y
if (is.null(block)) {
.Object@block <- factor(rep(0, nrow(x)))
} else {
if (any(table(block) < 2))
stop(sQuote("block"),
" contains levels with less than two observations")
.Object@block <- block
}
if (is.null(weights)) {
.Object@weights <- rep(1.0, nrow(x))
} else {
.Object@weights <- as.double(weights)
}
if (!validObject(.Object))
stop("not a valid object of class ",
sQuote("IndependenceProblem"))
.Object
}
)
### new("IndependenceTestProblem", ...)
### set up test problem, i.e., transformations of the data
setMethod(f = "initialize",
signature = "IndependenceTestProblem",
definition = function(.Object, ip, xtrafo = trafo, ytrafo = trafo,
xscores = NULL, yscores = NULL, ...) {
if (!extends(class(ip), "IndependenceProblem"))
stop("Argument ", sQuote("ip"), " is not of class ",
sQuote("IndependenceProblem"))
.Object <- copyslots(ip, .Object)
x <- ip@x
y <- ip@y
tr <- check_trafo(xtrafo(x), ytrafo(y))
.Object@xtrans <- tr$xtrafo
.Object@ytrans <- tr$ytrafo
.Object@xtrafo <- xtrafo
.Object@ytrafo <- ytrafo
p <- ncol(.Object@xtrans)
q <- ncol(.Object@ytrans)
.Object@scores <- diag(p * q)
xORDINAL <- sapply(x, is.ordered)
yORDINAL <- sapply(y, is.ordered)
### <FIXME> implement handling of multiple ordered factors
if ((any(xORDINAL) && length(xORDINAL) > 1) ||
(any(yORDINAL) && length(yORDINAL) > 1))
stop("handling of multiple ordered factors currently not implemented")
.Object@has_scores <- xORDINAL || yORDINAL
.Object@xordinal <- any(xORDINAL)
.Object@yordinal <- any(yORDINAL)
xscores <- c()
for (i in 1:ncol(x)) {
if (is.ordered(x[[i]])) {
sc <- attr(x[[i]], "scores")
if (is.null(sc)) sc <- 1:nlevels(x[[i]])
} else {
sc <- rep(0, sum(attr(tr$xtrafo, "assign") == i))
}
xscores <- c(xscores, sc)
}
yscores <- c()
for (i in 1:ncol(y)) {
if (is.ordered(y[[i]])) {
sc <- attr(y[[i]], "scores")
if (is.null(sc)) sc <- 1:nlevels(y[[i]])
} else {
sc <- rep(0, sum(attr(tr$ytrafo, "assign") == i))
}
yscores <- c(yscores, sc)
}
if (any(xORDINAL) && !any(yORDINAL))
.Object@scores <- .Call("R_scmatleft",
as.double(xscores), as.integer(p * q),
PACKAGE = "coin")
if (any(xORDINAL) && any(yORDINAL))
### grrr: class(kronecker(1:4, 1:3)) == "array"
.Object@scores <- matrix(kronecker(yscores, xscores), nrow = 1)
if (!any(xORDINAL) && any(yORDINAL))
.Object@scores <- .Call("R_scmatright",
as.double(yscores), as.integer(p * q),
PACKAGE = "coin")
### </FIXME>
.Object
}
)
### new("IndependenceTestStatistic", ...)
### compute test statistics and their expectation / covariance matrix
setMethod(f = "initialize",
signature = "IndependenceTestStatistic",
definition = function(.Object, itp, varonly = FALSE) {
if (!extends(class(itp), "IndependenceTestProblem"))
stop("Argument ", sQuote("itp"), " is not of class ",
sQuote("IndependenceTestProblem"))
.Object <- copyslots(itp, .Object)
xtrans <- itp@xtrans
ytrans <- itp@ytrans
weights <- itp@weights
SCORES <- itp@has_scores
S <- itp@scores
varonly <- varonly && (!SCORES)
if (SCORES) {
.Object@linearstatistic <- drop(S %*% LinearStatistic(xtrans,
ytrans, weights))
} else {
.Object@linearstatistic <- drop(LinearStatistic(xtrans,
ytrans, weights))
}
### <REMINDER>
### for teststat = "maxtype" and distribution = "approx"
### we don't need to covariance matrix but the variances only
### </REMINDER>
### possibly stratified by block
if (nlevels(itp@block) == 1) {
expcov <- ExpectCovarLinearStatistic(xtrans, ytrans, weights,
varonly = varonly)
exp <- expcov@expectation
cov <- expcov@covariance
} else {
exp <- 0
cov <- 0
for (lev in levels(itp@block)) {
indx <- (itp@block == lev)
ec <- ExpectCovarLinearStatistic(xtrans[indx,,drop = FALSE],
ytrans[indx,,drop = FALSE],
weights[indx],
varonly = varonly)
exp <- exp + ec@expectation
cov <- cov + ec@covariance
}
}
### multiply with score matrix if necessary
if (SCORES) {
.Object@expectation <- drop(S %*% exp)
.Object@covariance <- new("CovarianceMatrix", S %*% cov %*% t(S))
} else {
.Object@expectation <- drop(exp)
if (varonly) {
.Object@covariance <- new("Variance", drop(cov))
} else {
.Object@covariance <- new("CovarianceMatrix", cov)
}
}
### pretty names
nm <- statnames(itp)$names
names(.Object@expectation) <- nm
if (extends(class(.Object@covariance), "CovarianceMatrix")) {
colnames(.Object@covariance@covariance) <- nm
rownames(.Object@covariance@covariance) <- nm
}
if (extends(class(.Object@covariance), "Variance"))
names(.Object@covariance@variance) <- nm
if (any(variance(.Object) < eps()))
warning("The conditional covariance matrix has ",
"zero diagonal elements")
.Object
}
)
### new("ScalarIndependenceTestStatistic", ...)
### the basis of well known univariate tests
setMethod(f = "initialize",
signature = "ScalarIndependenceTestStatistic",
definition = function(.Object, its,
alternative = c("two.sided", "less", "greater")) {
if (!extends(class(its), "IndependenceTestStatistic"))
stop("Argument ", sQuote("its"), " is not of class ",
sQuote("IndependenceTestStatistic"))
.Object <- copyslots(its, .Object)
.Object@alternative <- match.arg(alternative)
standstat <- (its@linearstatistic - expectation(its)) /
sqrt(variance(its))
.Object@teststatistic <- drop(standstat)
.Object@standardizedlinearstatistic <- drop(standstat)
.Object
}
)
### new("MaxTypeIndependenceTestStatistic", ...)
setMethod(f = "initialize",
signature = "MaxTypeIndependenceTestStatistic",
definition = function(.Object, its,
alternative = c("two.sided", "less", "greater")) {
if (!extends(class(its), "IndependenceTestStatistic"))
stop("Argument ", sQuote("its"), " is not of class ",
sQuote("IndependenceTestStatistic"))
.Object <- copyslots(its, .Object)
.Object@alternative <- match.arg(alternative)
standstat <- (its@linearstatistic - expectation(its)) /
sqrt(variance(its))
.Object@teststatistic <- switch(alternative,
"less" = drop(min(standstat)),
"greater" = drop(max(standstat)),
"two.sided" = drop(max(abs(standstat)))
)
.Object@standardizedlinearstatistic <- standstat
.Object
}
)
### new("QuadTypeIndependenceTestStatistic", ...)
setMethod(f = "initialize",
signature = "QuadTypeIndependenceTestStatistic",
definition = function(.Object, its, ...) {
if (!extends(class(its), "IndependenceTestStatistic"))
stop("Argument ", sQuote("its"), " is not of class ",
sQuote("IndependenceTestStatistic"))
.Object <- copyslots(its, .Object)
covm <- covariance(its)
mp <- MPinv(covm, ...)
.Object@covarianceplus <- mp$MPinv
.Object@df <- mp$rank
stand <- (its@linearstatistic - expectation(its))
.Object@teststatistic <-
drop(stand %*% .Object@covarianceplus %*% stand)
standstat <- (its@linearstatistic - expectation(its)) /
sqrt(variance(its))
.Object@standardizedlinearstatistic <- standstat
.Object
}
)
### new("SymmetryProblem", ...)
### initialized data
setMethod(f = "initialize",
signature = "SymmetryProblem",
definition = function(.Object, x, y, block = NULL, weights = NULL) {
if (any(is.na(x)))
stop(sQuote("x"), " contains missing values")
if (!is.factor(x[[1]]) || length(unique(table(x[[1]]))) != 1)
stop(sQuote("x"), " is not a balanced factor")
if (any(is.na(y)))
stop(sQuote("y"), " contains missing values")
if (!is.null(block) && any(is.na(y)))
stop(sQuote("block"), " contains missing values")
.Object@x <- x
.Object@y <- y
if (is.null(block)) {
nbl <- nrow(x)/nlevels(x[[1]])
lindx <- tapply(1:nrow(x), x[[1]], function(x) x)
bl <- rep(0, nrow(x))
for (l in lindx)
bl[l] <- 1:nbl
.Object@block <- factor(unlist(bl))
} else {
.Object@block <- block
}
if (is.null(weights)) {
.Object@weights <- rep(1.0, nrow(x))
} else {
.Object@weights <- as.double(weights)
}
.Object
}
)