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# fdnonpar package
# require(plyr)
#'@import stats
#'@import plyr
#'@import plutils
#'
#'@name fdnonpar-package
#'
#'@aliases fdnonpar-package fdnonpar
#'@docType package
#'@title The fdnonpar package
#'@description
#' The package \pkg{fdnonpar} is a collection of tools for visualisation
#' and nonparametric analysis of grouped data that consist of an independent (\eqn{x}-)
#' variable and a dependent (\eqn{y}-) variable. Such data could be time
#' series or values of a function, or generally any multivariate data.
#' In the latter case, \eqn{x} is just an index variable.
#'
#' The proposed tests do not take the \eqn{x}-variable into account. Since the
#' \eqn{x}-values are usually equidistant, this does not really matter.
#' In the current version, it is assumed that the data samples to be compared
#' share the same (equidistant) \eqn{x}-variables.
# (changes are on the way).
#'
#'@section Data classes, visualisation of data:
#' \tabular{ll}{
#' \code{\link{fdsample}} \tab basic data type, a sample of curves
#' \cr\code{fdenvelope} \tab two boundary curves of an envelope, a specialized
#' \code{fdsample} object
#' \cr\code{\link{print.fdsample}} \tab print brief details of an fdsample
#' \cr\code{\link{plot.fdsample}} \tab plot the individual members of an fdsample
#' \cr\code{\link{plot.fdenvelope}} \tab plot an \code{envelope} object
#' \cr\code{\link{summaryplot}}\tab plot individual curves, envelopes or summary functions
#' \cr\tab such as the mean of an \code{\link{fdsample}} objectr
#' \cr\code{\link{funsample}} \tab another basic data type, a sample of functions.
#' A funsample is actually a multivariate R-function. It can be converted into
#' an fdsample.
#' }
#'@section {Manipulation and summary functions}:
#' \tabular{ll}{
#' \code{\link{[.fdsample}} \tab extract or replace curves form a sample
#' \cr\code{\link{apply.fdsample}} \tab apply a summary function to the function values
#' \cr\code{\link{mean.fdsample}} \tab mean of the function values
#' \cr\code{\link{median.fdsample}} \tab median of the function values
#' \cr\code{\link{quantile.fdsample}} \tab quantiles of the function values
#' \cr\code{\link{pwEnvelope}} \tab pointwise envelope
#' }
#'@section {Tests}:
#' \tabular{ll}{
#' \code{\link{tL2.permtest}} \tab Comparison of two groups,
#' \cr\tab using square integrated Welch-t-statistic
#' \cr\code{\link{rankEnv.test}} \tab Rank envelope test: compare a single
#' observation to a group (e.g. simulated data)
#' \cr\code{\link{rankCount.test}} \tab Rank count test: refined p-value for rank envelope test
# \cr\code{\link{tbar.L2ptest}} \tab Comparison of two groups,
# \cr\tab a variant of \code{\link{t.L2ptest}}\cr
#' }
#'@author Ute Hahn, \email{ute@@imf.au.dk}
#'@references
#'Hahn, U. (2012) A studentized permutation test for
#'the comparison of spatial point patterns.
#'\emph{Journal of the American Statistical Association} \strong{107} (498), 754--764.
#'
#'M. Myllymaki, T. Mrkvicka, P. Grabarnik, H. Seijo and Ute Hahn (2015)
#'\emph{Global envelope tests for spatial processes},
#'\url{http://arxiv.org/abs/1307.0239v3}.
#'
#'@keywords package
#'@examples
#' # simulated data sets, consisting of 8 and 9
#' x <- seq(0, 1, .1)
#' y1 <- replicate(8, rnorm(length(x), mean = x, sd = .2))
#' y2 <- replicate(7, rnorm(length(x), mean = x*1.3, sd = .2))
#' y1b <- replicate(7, rnorm(length(x), mean = x, sd = .2))
#'
#' xy1 <- fdsample(x, y1)
#' xy2 <- fdsample(x, y2)
#' xy1b <- fdsample(x, y1b)
#'
#'# visualize the data sets
#'# require plutils which contains the generic to "summaryplot"
#'require(plutils)
#'
#'summaryplot(xy1, envprob=1)
#'summaryplot(xy1b, add = TRUE, col = "blue")
#'summaryplot(xy2, add = TRUE, col = "red")
#'
#'# there should be significant difference between xyl1
#'# and xyl2, but not between xyl1 and xyl1b.
#'# However, with simulated data, everything is possible...
#'
#'tL2.permtest(xy1, xy2)
#'tL2.permtest(xy1, xy1b)
NA
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