swh:1:snp:813359ba77493c9d5dd1abad9a1f53490a8abf57
Tip revision: b7346fb4a36014a61289b3e1ec88cc08bb794cae authored by Torsten Hothorn on 28 August 2019, 10:50:06 UTC
version 1.3-1
version 1.3-1
Tip revision: b7346fb
InitMethods.R
### new("CovarianceMatrix", ...)
setMethod("initialize",
signature = "CovarianceMatrix",
definition = function(.Object, covariance, ...) {
callNextMethod(.Object, covariance = covariance, ...)
}
)
### new("Variance", ...)
setMethod("initialize",
signature = "Variance",
definition = function(.Object, variance, ...) {
callNextMethod(.Object, variance = variance, ...)
}
)
### new("IndependenceProblem", ...)
### initialized data
setMethod("initialize",
signature = "IndependenceProblem",
definition = function(.Object, x, y, block = NULL, weights = NULL, ...) {
if (NROW(x) == 0L && NROW(y) == 0L)
stop(sQuote("x"), " and ", sQuote("y"),
" do not contain data")
if (length(x) == 0L) {
dn <- dimnames(x)
x <- data.frame(x = rep.int(1L, nrow(x)))
dimnames(x) <- dn
}
if (anyNA(x))
stop(sQuote("x"), " contains missing values")
if (anyNA(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) && anyNA(block))
stop(sQuote("block"), " contains missing values")
if (!is.null(weights) && anyNA(weights))
stop(sQuote("weights"), " contains missing values")
.Object@x <- droplevels(x)
.Object@y <- droplevels(y)
.Object@block <- if (is.null(block))
factor(rep.int(0L, nrow(x)))
else {
blockname <- attr(block, "blockname", exact = TRUE)
block <- droplevels(block)
if (!is.null(blockname))
attr(block, "blockname") <- blockname
if (any(table(block) < 2L))
stop(sQuote("block"), " contains levels with",
" less than two observations")
block
}
.Object@weights <- if (is.null(weights))
rep.int(1.0, nrow(x))
else
as.double(weights)
if (!validObject(.Object))
stop("not a valid object of class ", dQuote("IndependenceProblem"))
.Object
}
)
### new("IndependenceTestProblem", ...)
### set up test problem, i.e., transformations of the data
setMethod("initialize",
signature = "IndependenceTestProblem",
definition = function(.Object, object, xtrafo = trafo, ytrafo = trafo, ...) {
if (!inherits(object, "IndependenceProblem"))
stop(sQuote("object"), " is not of class ",
dQuote("IndependenceProblem"))
tr <- check_trafo(xtrafo(object@x), ytrafo(object@y))
.Object <- copyslots(object, .Object)
.Object@xtrans <- tr$xtrafo
.Object@ytrans <- tr$ytrafo
.Object@xtrafo <- xtrafo
.Object@ytrafo <- ytrafo
.Object
}
)
### new("IndependenceLinearStatistic", ...)
### compute test statistics and their expectation / covariance matrix
setMethod("initialize",
signature = "IndependenceLinearStatistic",
definition = function(.Object, object, varonly = FALSE, ...) {
if (!inherits(object, "IndependenceTestProblem"))
stop(sQuote("object"), " is not of class ",
dQuote("IndependenceTestProblem"))
nm <- statnames(object)$names # pretty names
ecs <- .Call(R_ExpectationCovarianceStatistic,
object@xtrans, object@ytrans, object@weights, integer(0),
object@block, varonly, sqrt_eps)
.Object <- copyslots(object, .Object)
.Object@linearstatistic <- drop(ecs$LinearStatistic)
.Object@expectation <- setNames(ecs$Expectation, nm)
.Object@covariance <-
if (varonly) {
new("Variance", setNames(drop(ecs$Variance), nm))
} else {
pq <- length(nm)
cov <- matrix(0, nrow = pq, ncol = pq, dimnames = list(nm, nm))
cov[lower.tri(cov, diag = TRUE)] <- ecs$Covariance
cov <- cov + t(cov)
diag(cov) <- diag(cov) / 2
new("CovarianceMatrix", cov)
}
if (any(variance(.Object) < sqrt_eps))
warning("The conditional covariance matrix has ",
"zero diagonal elements")
.Object
}
)
### new("ScalarIndependenceTestStatistic", ...)
### the basis of well known univariate tests
setMethod("initialize",
signature = "ScalarIndependenceTestStatistic",
definition = function(.Object, object,
alternative = c("two.sided", "less", "greater"), paired = FALSE, ...) {
if (!inherits(object, "IndependenceLinearStatistic"))
stop(sQuote("object"), " is not of class ",
dQuote("IndependenceLinearStatistic"))
ss <- (object@linearstatistic - expectation(object)) /
sqrt(variance(object))
.Object <- copyslots(object, .Object)
.Object@teststatistic <- unname(ss)
.Object@standardizedlinearstatistic <- ss
.Object@alternative <- match.arg(alternative)
.Object@paired <- paired
.Object
}
)
### new("MaxTypeIndependenceTestStatistic", ...)
setMethod("initialize",
signature = "MaxTypeIndependenceTestStatistic",
definition = function(.Object, object,
alternative = c("two.sided", "less", "greater"), ...) {
if (!inherits(object, "IndependenceLinearStatistic"))
stop(sQuote("object"), " is not of class ",
dQuote("IndependenceLinearStatistic"))
ss <- (object@linearstatistic - expectation(object)) /
sqrt(variance(object))
.Object <- copyslots(object, .Object)
.Object@teststatistic <-
switch(alternative,
"less" = min(ss),
"greater" = max(ss),
"two.sided" = max(abs(ss))
)
.Object@standardizedlinearstatistic <- ss
.Object@alternative <- match.arg(alternative)
.Object
}
)
### new("QuadTypeIndependenceTestStatistic", ...)
setMethod("initialize",
signature = "QuadTypeIndependenceTestStatistic",
definition = function(.Object, object, paired = FALSE, ...) {
if (!inherits(object, "IndependenceLinearStatistic"))
stop(sQuote("object"), " is not of class ",
dQuote("IndependenceLinearStatistic"))
cs <- object@linearstatistic - expectation(object)
mp <- MPinv(covariance(object), ...)
.Object <- copyslots(object, .Object)
.Object@teststatistic <- drop(cs %*% mp$MPinv %*% cs)
.Object@standardizedlinearstatistic <- cs / sqrt(variance(object))
.Object@covarianceplus <- mp$MPinv
.Object@df <- mp$rank
.Object@paired <- paired
.Object
}
)
### new("SymmetryProblem", ...)
### initialized data
setMethod("initialize",
signature = "SymmetryProblem",
definition = function(.Object, x, y, block = NULL, weights = NULL, ...) {
if (anyNA(x))
stop(sQuote("x"), " contains missing values")
if (!is.factor(x[[1L]]) || length(unique(table(x[[1L]]))) != 1L)
stop(sQuote("x"), " is not a balanced factor")
if (anyNA(y))
stop(sQuote("y"), " contains missing values")
if (!is.null(block) && anyNA(y))
stop(sQuote("block"), " contains missing values")
.Object@x <- x
.Object@y <- y
.Object@block <- if (is.null(block))
factor(rep.int(seq_len(nrow(x) / nlevels(x[[1L]])),
nlevels(x[[1L]])))
else
block
.Object@weights <- if (is.null(weights))
rep.int(1.0, nrow(x))
else
as.double(weights)
if (!validObject(.Object))
stop("not a valid object of class ", sQuote("SymmetryProblem"))
.Object
}
)