swh:1:snp:813359ba77493c9d5dd1abad9a1f53490a8abf57
Tip revision: 1d1da53d71a24a7cd371709574597ca3332c7d69 authored by Torsten Hothorn on 14 March 2005, 00:00:00 UTC
version 0.2-9
version 0.2-9
Tip revision: 1d1da53
zAccess.R
### generic method for extracting pvalues from objects
setGeneric("pvalue", function(object, ...)
standardGeneric("pvalue"))
setMethod(f = "pvalue",
signature = "NullDistribution",
definition = function(object, q, ...) {
object@pvalue(q)
}
)
setMethod(f = "pvalue",
signature = "IndependenceTest",
definition = function(object, q, ...) {
pvalue(object@distribution, q = q)
}
)
setMethod(f = "pvalue",
signature = "ScalarIndependenceTest",
definition = function(object, ...) {
object@distribution@pvalue(object@statistic@teststatistic)
}
)
setMethod(f = "pvalue",
signature = "MaxTypeIndependenceTest",
definition = function(object, adjusted = FALSE, ...) {
x <- object@statistic
if (adjusted) {
padj <- 1 - sapply(abs(x@standardizedlinearstatistic), pperm,
object = object, ...)
RET <- matrix(padj, nrow = ncol(x@xtrans),
ncol = ncol(x@ytrans),
dimnames = list(colnames(x@xtrans),
colnames(x@ytrans)))
} else {
RET <- pvalue(object@distribution,
object@statistic@teststatistic)
}
return(RET)
}
)
setMethod(f = "pvalue",
signature = "QuadTypeIndependenceTest",
definition = function(object, ...) {
pvalue(object@distribution, object@statistic@teststatistic)
}
)
### generic method for the permutation distribution from objects
setGeneric("pperm", function(object, q, ...)
standardGeneric("pperm"))
setMethod(f = "pperm",
signature = "NullDistribution",
definition = function(object, q, ...) {
object@p(q)
}
)
setMethod(f = "pperm",
signature = "IndependenceTest",
definition = function(object, q, ...) {
pperm(object@distribution, q = q)
}
)
setMethod(f = "pperm",
signature = "ScalarIndependenceTest",
definition = function(object, q, ...) {
pperm(object@distribution, q)
}
)
setMethod(f = "pperm",
signature = "MaxTypeIndependenceTest",
definition = function(object, q, ...) {
pperm(object@distribution, q)
}
)
setMethod(f = "pperm",
signature = "QuadTypeIndependenceTest",
definition = function(object, q, ...) {
pperm(object@distribution, q)
}
)
### generic method for the permutation distribution from objects
setGeneric("qperm", function(object, p, ...)
standardGeneric("qperm"))
setMethod(f = "qperm",
signature = "NullDistribution",
definition = function(object, p, ...) {
object@q(p)
}
)
setMethod(f = "qperm",
signature = "IndependenceTest",
definition = function(object, p, ...) {
qperm(object@distribution, p)
}
)
setMethod(f = "qperm",
signature = "ScalarIndependenceTest",
definition = function(object, p, ...) {
qperm(object@distribution, p)
}
)
setMethod(f = "qperm",
signature = "MaxTypeIndependenceTest",
definition = function(object, p, ...) {
qperm(object@distribution, p)
}
)
setMethod(f = "qperm",
signature = "QuadTypeIndependenceTest",
definition = function(object, p, ...) {
qperm(object@distribution, p)
}
)
### generic method for the permutation distribution from objects
setGeneric("dperm", function(object, x, ...)
standardGeneric("dperm"))
setMethod(f = "dperm",
signature = "NullDistribution",
definition = function(object, x, ...) {
object@d(x)
}
)
setMethod(f = "dperm",
signature = "IndependenceTest",
definition = function(object, x, ...) {
dperm(object@distribution, x)
}
)
setMethod(f = "dperm",
signature = "ScalarIndependenceTest",
definition = function(object, x, ...) {
dperm(object@distribution, x)
}
)
setMethod(f = "dperm",
signature = "MaxTypeIndependenceTest",
definition = function(object, x, ...) {
dperm(object@distribution, x)
}
)
setMethod(f = "dperm",
signature = "QuadTypeIndependenceTest",
definition = function(object, x, ...) {
dperm(object@distribution, x)
}
)
### generic method for the permutation distribution from objects
setGeneric("support", function(object, p, ...)
standardGeneric("support"))
setMethod(f = "support",
signature = "NullDistribution",
definition = function(object, p, ...) {
object@support(p)
}
)
setMethod(f = "support",
signature = "IndependenceTest",
definition = function(object, p, ...) {
support(object@distribution, p)
}
)
setMethod(f = "support",
signature = "ScalarIndependenceTest",
definition = function(object, p, ...) {
support(object@distribution, p)
}
)
setMethod(f = "support",
signature = "MaxTypeIndependenceTest",
definition = function(object, p, ...) {
support(object@distribution, p)
}
)
setMethod(f = "support",
signature = "QuadTypeIndependenceTest",
definition = function(object, p, ...) {
support(object@distribution, p)
}
)
### generic method for extracting statistics from objects
setGeneric("statistic", function(object,
type = c("test", "linear", "standardized"), ...)
standardGeneric("statistic")
)
setMethod(f = "statistic",
signature = "IndependenceTest",
definition = function(object,
type = c("test", "linear", "standardized"), ...) {
type <- match.arg(type)
### <FIXME> it is not sure that object@statistic exists! </FIXME>
statistic(object@statistic, type = type, ...)
}
)
setMethod(f = "statistic",
signature = "ScalarIndependenceTestStatistic",
definition = function(object,
type = c("test", "linear", "standardized"), ...) {
type <- match.arg(type)
if (type == "standardized") type <- "test"
switch(type, "test" = object@teststatistic,
"linear" = {
x <- object@linearstatistic
matrix(x, nrow = ncol(object@xtrans),
ncol = ncol(object@ytrans),
dimnames = list(colnames(object@xtrans),
colnames(object@ytrans)))
})
}
)
setMethod(f = "statistic",
signature = "MaxTypeIndependenceTestStatistic",
definition = function(object,
type = c("test", "linear", "standardized"), ...) {
type <- match.arg(type)
switch(type, "test" = object@teststatistic,
"linear" = {
x <- object@linearstatistic
matrix(x, nrow = ncol(object@xtrans),
ncol = ncol(object@ytrans),
dimnames = list(colnames(object@xtrans),
colnames(object@ytrans)))
},
"standardized" = {
x <- object@standardizedlinearstatistic
matrix(x, nrow = ncol(object@xtrans),
ncol = ncol(object@ytrans),
dimnames = list(colnames(object@xtrans),
colnames(object@ytrans)))
})
}
)
setMethod(f = "statistic",
signature = "QuadTypeIndependenceTestStatistic",
definition = function(object, type = c("test", "linear", "standardized"),
...) {
type <- match.arg(type)
switch(type, "test" = object@teststatistic,
"linear" = {
x <- object@linearstatistic
matrix(x, nrow = ncol(object@xtrans),
ncol = ncol(object@ytrans),
dimnames = list(colnames(object@xtrans),
colnames(object@ytrans)))
},
"standardized" = {
matrix((object@linearstatistic - object@expectation) /
sqrt(diag(object@covariance)),
nrow = ncol(object@xtrans),
ncol = ncol(object@ytrans),
dimnames = list(colnames(object@xtrans),
colnames(object@ytrans)))
}
)
}
)
### generic method for extracting expectations from objects
setGeneric("expectation", function(object, ...)
standardGeneric("expectation")
)
setMethod(f = "expectation",
signature = "IndependenceTest",
definition = function(object, ...)
expectation(object@statistic, ...)
)
setMethod(f = "expectation",
signature = "ScalarIndependenceTestStatistic",
definition = function(object, ...)
object@expectation
)
setMethod(f = "expectation",
signature = "MaxTypeIndependenceTestStatistic",
definition = function(object, ...) {
x <- object@expectation
matrix(x, nrow = ncol(object@xtrans),
ncol = ncol(object@ytrans),
dimnames = list(colnames(object@xtrans),
colnames(object@ytrans)))
}
)
setMethod(f = "expectation",
signature = "QuadTypeIndependenceTestStatistic",
definition = function(object, ...) {
x <- object@expectation
matrix(x, nrow = ncol(object@xtrans),
ncol = ncol(object@ytrans),
dimnames = list(colnames(object@xtrans),
colnames(object@ytrans)))
}
)
### generic method for extracting the covariance matrix from objects
setGeneric("covariance", function(object, ...)
standardGeneric("covariance")
)
setMethod(f = "covariance",
signature = "IndependenceTest",
definition = function(object, ...)
covariance(object@statistic, ...)
)
setMethod(f = "covariance",
signature = "ScalarIndependenceTestStatistic",
definition = function(object, ...)
object@covariance
)
setMethod(f = "covariance",
signature = "MaxTypeIndependenceTestStatistic",
definition = function(object, ...)
object@covariance
)
setMethod(f = "covariance",
signature = "QuadTypeIndependenceTestStatistic",
definition = function(object, ...)
object@covariance
)