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##################################################################################
##' Class "NpdeObject"
##'
##' An object of class NpdeObject
##'
##' @name NpdeObject-class
##' @aliases NpdeObject print,NpdeObject-method
##' showall,NpdeObject-method summary,NpdeObject-method test,NpdeObject-method
##' npde.main,NpdeObject npde.save,NpdeObject npde.graphs,NpdeObject plot,NpdeObject
##' @docType class
##' @section Objects from the Class: NpdeObject objects are typically created by calls to \code{\link{npde}} or \code{\link{autonpde}}. They contain the following slots:
##'
##' \describe{
##' \item{data}{an object of class NpdeData, containing the observed data}
##' \item{sim.data}{an object of class NpdeSimData, containing the simulated data}
##' \item{results}{an object of class NpdeRes, containing the results}
##' \item{options}{a list of options}
##' \item{prefs}{a list of graphical preferences for the plots}
##' }
##' @section Methods:
##' \describe{
##' \item{print(x):}{Prints a summary of object}
##' \item{show(x):}{Prints a short summary of object}
##' \item{showall(x):}{Prints a detailed summary of object}
##' \item{plot(x):}{Diagnostic and other plots. More details can be found in \code{\link{plot.NpdeObject}}}
##' \item{summary(x):}{Returns a summary of object x in list format}
##' \item{gof.test(x, parametric=TRUE, ...):}{Returns goodness-of-fit tests}
##' \item{set.plotoptions(x):}{Sets options for graphs (internal method used in plots)}
##' }
##' @seealso \code{\link{npde}}, \code{\link{autonpde}}, \code{\link{NpdeData}}, \code{\link{NpdeSimData}}, \code{\link{NpdeRes}}, \code{\link{gof.test}}
##' @keywords classes
##' @examples
##' methods(class="NpdeObject")
##'
##' showClass("NpdeObject")
##'
##' @exportClass NpdeObject
##' @include NpdeRes.R
setClass(Class="NpdeObject",
representation=representation(
data="NpdeData", # Data
results="NpdeRes", # Fit results
sim.data="NpdeSimData", # Simulated data
options="list", # Options and parameters for algorithm
prefs="list" # Options for graphs
),
validity=function(object){
# cat ("--- Checking NpdeObject object ---\n")
validObject(object@data)
validObject(object@sim.data)
return(TRUE)
}
)
setMethod(
f="initialize",
signature="NpdeObject",
definition= function (.Object,data,sim.data,options=list(),prefs=list()){
.Object@data<-data
.Object@sim.data<-sim.data
.Object@results<-new(Class="NpdeRes")
.Object@results["ntot.obs"]<-data["ntot.obs"]
.Object@results["not.miss"]<-data["not.miss"]
.Object@results["icens"]<-data["icens"]
opt<-npdeControl()
if(length(options)>0) {
for(i in names(options)) {
if(length(grep(i,names(opt)))==0) message(paste("Option",i, "not found, check spelling")) else
opt[i]<-options[i]
}
i1<-grep("namsav",names(options))
if(length(i1)!=0 && !is.na(i1)) {
opt$namres<-paste(options[i1],".npde",sep="")
opt$namgr<-paste(options[i1],".",opt$type.graph,sep="")
}
}
# Checking options
opt<-check.control.options(opt)
.Object@options<-opt
graph.opt<-set.plotoptions(.Object)
if(length(prefs)>0) {
for(i in names(prefs)) {
if(length(grep(i,names(graph.opt)))==0) message(paste("Graphical option",i, "not found, check spelling")) else graph.opt[i]<-prefs[i]
}
}
.Object@prefs<-graph.opt
# Object validation
validObject(.Object)
return (.Object )
}
)
##################################################################################
#' @rdname extract-methods
#' @aliases [,NpdeObject-method [<-,NpdeObject-method
#' @exportMethod [
#' @exportMethod [<-
# Getteur
setMethod(
f ="[",
signature = "NpdeObject" ,
definition = function (x,i,j,drop ){
switch (EXPR=i,
"data"={return(x@data)},
"sim.data"={return(x@sim.data)},
"results"={return(x@results)},
"options"={return(x@options)},
"prefs"={return(x@prefs)},
stop("No such attribute\n")
)
}
)
# Setteur
setReplaceMethod(
f ="[",
signature = "NpdeObject" ,
definition = function (x,i,j,value){
switch (EXPR=i,
"data"={x@data<-value},
"sim.data"={x@sim.data<-value},
"results"={x@results<-value},
"options"={x@options<-value},
"prefs"={x@prefs<-value},
stop("No such attribute\n")
)
validObject(x)
return(x)
}
)
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