R/cpt.class.R

In changepoint.np: Methods for Nonparametric Changepoint Detection

setClass("cpt",slots=list(data.set="ts", cpttype="character", method="character", 	test.stat="character",pen.type="character",pen.value="numeric",minseglen="numeric",cpts="numeric",ncpts.max="numeric",param.est="list",date="character",version="character"),prototype=prototype(cpttype="Not Set",date=date(),version=as(packageVersion("changepoint"),'character')))

setClass("cpt.reg",slots=list(data.set="matrix", cpttype="character", method="character", test.stat="character",pen.type="character",pen.value="numeric",minseglen="numeric",cpts="numeric",ncpts.max="numeric",param.est="list",date="character",version="character"),prototype=prototype(cpttype="regression",date=date(),version=as(packageVersion("changepoint"),"character")))

#   setClass("cpt", representation(), prototype())
# # cpts is the optimal segementation
#   
setClass("cpt.range",slots=list(cpts.full="matrix", pen.value.full="numeric"), prototype=prototype(), contains="cpt")
# cpts.full is the entire matrix
# pen.value.full (beta) values as an extra slot (vector)

# retrival functions for slots
if(!isGeneric("data.set")) {
  if (is.function("data.set")){
    fun <- data.set
  }
  else {fun <- function(object){
    standardGeneric("data.set")
  }
  }
  setGeneric("data.set", fun)
}
setMethod("data.set","cpt",function(object) coredata(object@data.set))
setMethod("data.set","cpt.reg",function(object) coredata(object@data.set))

if(!isGeneric("data.set.ts")) {
  if (is.function("data.set.ts")){
    fun <- data.set.ts
  }
  else {fun <- function(object){
    standardGeneric("data.set.ts")
  }
  }
  setGeneric("data.set.ts", fun)
}
setMethod("data.set.ts","cpt",function(object) object@data.set)

if(!isGeneric("cpttype")) {
  if (is.function("cpttype")){
    fun <- cpttype
  }
  else {fun <- function(object){
    standardGeneric("cpttype")
  }
  }
  setGeneric("cpttype", fun)
}
setMethod("cpttype","cpt",function(object) object@cpttype)
setMethod("cpttype","cpt.reg",function(object) object@cpttype)

if(!isGeneric("method")) {
  if (is.function("method")){
    fun <- method
  }
  else {fun <- function(object){
    standardGeneric("method")
  }
  }
  setGeneric("method", fun)
}
setMethod("method","cpt",function(object) object@method)
setMethod("method","cpt.reg",function(object) object@method)

# distribution remains for backwards compatability, changed to test.stat version 1.0
if(!isGeneric("distribution")) {
  if (is.function("distribution")){
    fun <- distribution
  }
  else {fun <- function(object){
    standardGeneric("distribution")
  }
  }
  setGeneric("distribution", fun)
}
setMethod("distribution","cpt",function(object) object@test.stat)
setMethod("distribution","cpt.reg",function(object) object@test.stat)

if(!isGeneric("test.stat")) {
  if (is.function("test.stat")){
    fun <- test.stat
  }
  else {fun <- function(object){
    standardGeneric("test.stat")
  }
  }
  setGeneric("test.stat", fun)
}
setMethod("test.stat","cpt",function(object) object@test.stat)
setMethod("test.stat","cpt.reg",function(object) object@test.stat)

if(!isGeneric("pen.type")) {
  if (is.function("pen.type")){
    fun <- pen.type
  }
  else {fun <- function(object){
    standardGeneric("pen.type")
  }
  }
  setGeneric("pen.type", fun)
}
setMethod("pen.type","cpt",function(object) object@pen.type)
setMethod("pen.type","cpt.reg",function(object) object@pen.type)

if(!isGeneric("pen.value")) {
  if (is.function("pen.value")){
    fun <- pen.value
  }
  else {fun <- function(object){
    standardGeneric("pen.value")
  }
  }
  setGeneric("pen.value", fun)
}
setMethod("pen.value","cpt",function(object) object@pen.value)
setMethod("pen.value","cpt.reg",function(object) object@pen.value)

if(!isGeneric("pen.value.full")) {
  if (is.function("pen.value.full")){
    fun <- pen.value.full
  }
  else {fun <- function(object){
    standardGeneric("pen.value.full")
  }
  }
  setGeneric("pen.value.full", fun)
}
setMethod("pen.value.full","cpt.range",function(object) object@pen.value.full)

if(!isGeneric("minseglen")) {
  if (is.function("minseglen")){
    fun <- minseglen
  }
  else {fun <- function(object){
    standardGeneric("minseglen")
  }
  }
  setGeneric("minseglen", fun)
}
setMethod("minseglen","cpt",function(object) object@minseglen)

if(!isGeneric("cpts")) {
  if (is.function("cpts")){
    fun <- cpts
  }
  else {fun <- function(object){
    standardGeneric("cpts")
  }
  }
  setGeneric("cpts", fun)
}
setMethod("cpts","cpt",function(object) object@cpts[-length(object@cpts)])
setMethod("cpts","cpt.reg",function(object) object@cpts[-length(object@cpts)])

if(!isGeneric("cpts.full")) {
  if (is.function("cpts.full")){
    fun <- cpts.full
  }
  else {fun <- function(object){
    standardGeneric("cpts.full")
  }
  }
  setGeneric("cpts.full", fun)
}
setMethod("cpts.full","cpt.range",function(object) object@cpts.full)

if(!isGeneric("cpts.ts")) {
  if (is.function("cpts.ts")){
    fun <- cpts.ts
  }
  else {fun <- function(object){
    standardGeneric("cpts.ts")
  }
  }
  setGeneric("cpts.ts", fun)
}
setMethod("cpts.ts","cpt",function(object) index(data.set.ts(object))[cpts(object)] )

if(!isGeneric("ncpts.max")) {
  if (is.function("ncpts.max")){
    fun <- ncpts.max
  }
  else {fun <- function(object){
    standardGeneric("ncpts.max")
  }
  }
  setGeneric("ncpts.max", fun)
}
setMethod("ncpts.max","cpt",function(object) object@ncpts.max)
setMethod("ncpts.max","cpt.reg",function(object) object@ncpts.max)

if(!isGeneric("param.est")) {
  if (is.function("param.est")){
    fun <- param.est
  }
  else {fun <- function(object){
    standardGeneric("param.est")
  }
  }
  setGeneric("param.est", fun)
}
setMethod("param.est","cpt",function(object) object@param.est)
setMethod("param.est","cpt.reg",function(object) object@param.est)


setMethod("coef","cpt",function(object) object@param.est)
setMethod("coef","cpt.reg",function(object) object@param.est)

# ncpts function
if(!isGeneric("ncpts")) {
  if (is.function("ncpts")){
    fun <- ncpts
  }
  else {fun <- function(object){
    standardGeneric("ncpts")
  }
  }
  setGeneric("ncpts", fun)
}
setMethod("ncpts","cpt",function(object) length(cpts(object)))
setMethod("ncpts","cpt.reg",function(object) length(cpts(object)))

# seg.len function
if(!isGeneric("seg.len")) {
  if (is.function("seg.len")){
    fun <- seg.len
  }
  else {fun <- function(object){
    standardGeneric("seg.len")
  }
  }
  setGeneric("seg.len", fun)
}
setMethod("seg.len","cpt",function(object){object@cpts-c(0,object@cpts[-length(object@cpts)])})
setMethod("seg.len","cpt.reg",function(object){object@cpts-c(0,object@cpts[-length(object@cpts)])})
#i.e. if there is a changepoint in the data, return segment length. If not, return length of the data

# nseg function
if(!isGeneric("nseg")) {
  if (is.function("nseg")){
    fun <- nseg
  }
  else {fun <- function(object){
    standardGeneric("nseg")
  }
  }
  setGeneric("nseg", fun)
}
setMethod("nseg","cpt",function(object){ncpts(object)+1})
setMethod("nseg","cpt.reg",function(object){ncpts(object)+1})


# replacement functions for slots
setGeneric("data.set<-", function(object, value) standardGeneric("data.set<-"))
setReplaceMethod("data.set", "cpt", function(object, value) {
  if(is.ts(value)){object@data.set <- value}else{object@data.set <- ts(value)}
  return(object)
})
setReplaceMethod("data.set", "cpt.reg", function(object, value) {
  object@data.set <- value
  return(object)
})

setGeneric("cpttype<-", function(object, value) standardGeneric("cpttype<-"))
setReplaceMethod("cpttype", "cpt", function(object, value) {
  object@cpttype <- value
  return(object)
})
setReplaceMethod("cpttype", "cpt.reg", function(object, value) {
  object@cpttype <- value
  return(object)
})

setGeneric("method<-", function(object, value) standardGeneric("method<-"))
setReplaceMethod("method", "cpt", function(object, value) {
  object@method <- value
  return(object)
})
setReplaceMethod("method", "cpt.reg", function(object, value) {
  object@method <- value
  return(object)
})

# distribution remains for backwards compatability, changed to test.stat version 1.0
setGeneric("distribution<-", function(object, value) standardGeneric("distribution<-"))
setReplaceMethod("distribution", "cpt", function(object, value) {
  object@test.stat <- value
  return(object)
})
setReplaceMethod("distribution", "cpt.reg", function(object, value) {
  object@test.stat <- value
  return(object)
})

setGeneric("test.stat<-", function(object, value) standardGeneric("test.stat<-"))
setReplaceMethod("test.stat", "cpt", function(object, value) {
  object@test.stat <- value
  return(object)
})
setReplaceMethod("test.stat", "cpt.reg", function(object, value) {
  object@test.stat <- value
  return(object)
})

setGeneric("pen.type<-", function(object, value) standardGeneric("pen.type<-"))
setReplaceMethod("pen.type", "cpt", function(object, value) {
  object@pen.type <- value
  return(object)
})
setReplaceMethod("pen.type", "cpt.reg", function(object, value) {
  object@pen.type <- value
  return(object)
})

setGeneric("pen.value<-", function(object, value) standardGeneric("pen.value<-"))
setReplaceMethod("pen.value", "cpt", function(object, value) {
  object@pen.value <- value
  return(object)
})
setReplaceMethod("pen.value", "cpt.reg", function(object, value) {
  object@pen.value <- value
  return(object)
})

setGeneric("minseglen<-", function(object, value) standardGeneric("minseglen<-"))
setReplaceMethod("minseglen", "cpt", function(object, value) {
  object@minseglen <- value
  return(object)
})
setReplaceMethod("minseglen", "cpt.range", function(object, value) {
  object@minseglen <- value
  return(object)
})
setReplaceMethod("minseglen", "cpt.reg", function(object, value) {
  object@minseglen <- value
  return(object)
})

setGeneric("cpts<-", function(object, value) standardGeneric("cpts<-"))
setReplaceMethod("cpts", "cpt", function(object, value) {
  if((cpttype(object)=="meanar")|(cpttype(object)=="trendar")){
    n=length(object@data.set)-1
  }
  else{n=length(object@data.set)}
  
  if(value[length(value)]==n){object@cpts <- value}
  else{		object@cpts <- c(value,n)  }
  return(object)
})
setReplaceMethod("cpts", "cpt.reg", function(object, value) {
  if(value[length(value)]==nrow(object@data.set)){object@cpts <- value}
  else{  	object@cpts <- c(value,nrow(object@data.set))  }
  return(object)
})

setGeneric("ncpts.max<-", function(object, value) standardGeneric("ncpts.max<-"))
setReplaceMethod("ncpts.max", "cpt", function(object, value) {
  object@ncpts.max <- value
  return(object)
})
setReplaceMethod("ncpts.max", "cpt.reg", function(object, value) {
  object@ncpts.max <- value
  return(object)
})

setGeneric("param.est<-", function(object, value) standardGeneric("param.est<-"))
setReplaceMethod("param.est", "cpt", function(object, value) {
  object@param.est <- value
  return(object)
})
setReplaceMethod("param.est", "cpt.reg", function(object, value) {
  object@param.est <- value
  return(object)
})

setGeneric("cpts.full<-", function(object, value) standardGeneric("cpts.full<-"))
setReplaceMethod("cpts.full", "cpt.range", function(object, value) {
  object@cpts.full <- value
  return(object)
})
setGeneric("pen.value.full<-", function(object, value) standardGeneric("pen.value.full<-"))
setReplaceMethod("pen.value.full", "cpt.range", function(object, value) {
  object@pen.value.full <- value
  return(object)
})
# 	setGeneric("pen.value.input<-", function(object, value) standardGeneric("pen.value.input<-"))
# 	setReplaceMethod("pen.value.input", "cpt", function(object, value) {
# 	  object@pen.value.input <- value
# 	  return(object)
# 	})


# parameter functions
setGeneric("param", function(object,...) standardGeneric("param"))
setMethod("param", "cpt", function(object,shape,...) {			
  param.mean=function(object){
    cpts=c(0,object@cpts)
    #nseg=length(cpts)-1
    data=data.set(object)
    tmpmean=NULL
    for(j in 1:nseg(object)){
      tmpmean[j]=mean(data[(cpts[j]+1):(cpts[j+1])])
    }
    return(tmpmean)
  }
  param.var=function(object){
    cpts=c(0,object@cpts)
    #nseg=length(cpts)-1
    data=data.set(object)
    seglen=seg.len(object)
    tmpvar=NULL
    for(j in 1:nseg(object)){
      tmpvar[j]=var(data[(cpts[j]+1):(cpts[j+1])])
    }
    tmpvar=tmpvar*(seglen-1)/seglen # correctly for the fact that the MLE estimate is /n but the var function is /n-1
    return(tmpvar)
  }
  param.scale=function(object,shape){
    cpts=c(0,object@cpts)
    #nseg=length(cpts)-1
    data=data.set(object)
    y=c(0,cumsum(data))
    tmpscale=NULL
    for(j in 1:nseg(object)){
      tmpscale[j]=(y[(cpts[j+1]+1)]-y[(cpts[j]+1)])/((cpts[j+1]-cpts[j])*shape)
    }
    return(tmpscale)			
  }
  param.trend=function(object){
    cpts=c(0,object@cpts)
    seglen=seg.len(object)
    data=data.set(object)
    n=length(data)
    sumstat=cbind(cumsum(c(0,data)),cumsum(c(0,data*c(1:n))))
    cptsumstat=matrix(sumstat[object@cpts+1,]-sumstat[c(0,cpts(object))+1,],ncol=2)
    cptsumstat[,2]=cptsumstat[,2]-cptsumstat[,1]*c(0,cpts(object)) # i.e. creating newx3
    
    thetaS=(2*cptsumstat[,1]*(2*seglen + 1) - 6*cptsumstat[,2]) / (2*seglen*(2*seglen + 1) - 3*seglen*(seglen+1))
    thetaT=(6*cptsumstat[,2])/((seglen+1)*(2*seglen+1)) + (thetaS * (1-((3*seglen)/((2*seglen)+1))))
    return(cbind(thetaS,thetaT))
  }
  param.meanar=function(object){
    seglen=seg.len(object)
    data=data.set(object)
    n=length(data)-1
    sumstat=cbind(cumsum(c(0,data[-1])),cumsum(c(0,data[-(n+1)])),cumsum(c(0,data[-1]*data[-(n+1)])),cumsum(c(0,data[-1]^2)),cumsum(c(0,data[-(n+1)]^2)))
    cptsumstat=matrix(sumstat[object@cpts+1,]-sumstat[c(0,cpts(object))+1,],ncol=5)
    beta2=(2*seglen*cptsumstat[,3]-cptsumstat[,1]*cptsumstat[,2])/(2*seglen*cptsumstat[,5]*(1-cptsumstat[,2]^2));
    beta1=(2*cptsumstat[,1]-beta2*cptsumstat[,2])/(2*seglen);
    
    return(cbind(beta1,beta2))
  }
  param.trendar=function(object){
    seglen=seg.len(object)
    data=data.set(object)
    n=length(data)-1
    sumstat=cbind(cumsum(c(0,data[-1])),cumsum(c(0,data[-(n+1)])),cumsum(c(0,data[-1]*data[-(n+1)])),cumsum(c(0,data[-1]*c(1:n))),cumsum(c(0,data[-(n+1)]*c(0:(n-1)))),cumsum(c(0,data[-1]^2)),cumsum(c(0,data[-(n+1)]^2)))
    cptsumstat=matrix(sumstat[object@cpts+1,]-sumstat[c(0,cpts(object))+1,],ncol=7)
    cptsumstat[,4]=cptsumstat[,4]-cptsumstat[,1]*c(0,cpts(object)) # i.e. creating newx4
    cptsumstat[,5]=cptsumstat[,5]-cptsumstat[,2]*c(0,cpts(object)) # i.e. creating newx5
    betatop=seglen*(seglen-1)*(seglen*(seglen-1)*cptsumstat[,3] + 2*(2*seglen+1)*cptsumstat[,1]*(cptsumstat[,5]-seglen*cptsumstat[,2]) + 6*cptsumstat[,4]*(cptsumstat[,2]-cptsumstat[,5]))
    betabottom=seglen*(seglen-1)*cptsumstat[,7] + 2*(2*seglen+1)*cptsumstat[,2]*(seglen*cptsumstat[,2]-cptsumstat[,5]) + 6*cptsumstat[,5]*(cptsumstat[,5]-cptsumstat[,2]);
    beta=betatop/betabottom;  
    thetajpo=(6*(seglen+2)*(cptsumstat[,4]-beta*cptsumstat[,5]))/((seglen+1)*(2*seglen+1)) - 2*(cptsumstat[,1]-beta*cptsumstat[,2])
    thetaj=(2*(2*seglen+1)*(cptsumstat[,1]-beta*cptsumstat[,2])-6*(cptsumstat[,4]-beta*cptsumstat[,5]))/(seglen-1)
    
    return(cbind(beta,thetajpo,thetaj))
  }
  if(cpttype(object)=="mean"){
    param.est(object)<-list(mean=param.mean(object))
  }
  else if(cpttype(object)=="variance"){
    param.est(object)<-list(variance=param.var(object))
  }
  else if(cpttype(object)=="mean and variance"){
    if(test.stat(object)=="Normal"){
      param.est(object)<-list(mean=param.mean(object),variance=param.var(object))
    }
    else if(test.stat(object)=="Gamma"){
      param.est(object)<-list(scale=param.scale(object,shape=shape),shape=shape)
    }
    else if(test.stat(object)=="Exponential"){
      param.est(object)<-list(rate=1/param.mean(object))
    }
    else if(test.stat(object)=="Poisson"){
      param.est(object)<-list(lambda=param.mean(object))
    }
    else{
      stop("Unknown test statistic for a change in mean and variance")
    }
  }
  else if(cpttype(object)=="trend"){
    if(test.stat(object)=="Normal"){
      tmp=param.trend(object)
      param.est(object)<-list(thetaS=tmp[,1],thetaT=tmp[,2])
    }
    else{
      stop("Unknown test statistic for a change in trend")
    }
  }
  else if(cpttype(object)=="trendar"){
    if(test.stat(object)=="Normal"){
      tmp=param.trendar(object)
      param.est(object)<-list(beta=tmp[,1],thetajpo=tmp[,2],thetaj=tmp[,3])
    }
    else{
      stop("Unknown test statistic for a change in trend+ar")
    }
  }
  else if(cpttype(object)=="meanar"){
    if(test.stat(object)=="Normal"){
      tmp=param.meanar(object)
      param.est(object)<-list(beta1=tmp[,1],beta2=tmp[,2])
    }
    else{
      stop("Unknown test statistic for a change in mean+ar")
    }
  }
  else{
    stop("Unknown changepoint type, must be 'mean', 'variance', 'mean and variance', 'trend', 'meanar' or 'trendar'.")
  }
  return(object)
})

setMethod("param", "cpt.range", function(object,ncpts=NA,shape,...) {
  if(is.na(ncpts)){
    cpts=c(0,object@cpts)
  }
  else{
    ncpts.full=apply(cpts.full(object),1,function(x){sum(x>0,na.rm=TRUE)})
    tryCatch(
    {
	row<-which(ncpts.full==ncpts)
    },
    error = function(e) stop("Your input object doesn't have a segmentation with the requested number of changepoints.")
    )
    cpts=c(0,cpts.full(object)[row,1:ncpts],length(data.set(object)))
  }
  
  param.mean=function(object,cpts){
    nseg=length(cpts)-1
    data=data.set(object)
    tmpmean=NULL
    for(j in 1:nseg){
      tmpmean[j]=mean(data[(cpts[j]+1):(cpts[j+1])])
    }
    return(tmpmean)
  }
  param.var=function(object,cpts){
    nseg=length(cpts)-1
    data=data.set(object)
    seglen=seg.len(object)
    tmpvar=NULL
    for(j in 1:nseg){
      tmpvar[j]=var(data[(cpts[j]+1):(cpts[j+1])])
    }
    tmpvar=tmpvar*(seglen-1)/seglen
    return(tmpvar)
  }
  param.scale=function(object,cpts,shape){
    nseg=length(cpts)-1
    data=data.set(object)
    y=c(0,cumsum(data))
    tmpscale=NULL
    for(j in 1:nseg){
      tmpscale[j]=(y[(cpts[j+1]+1)]-y[(cpts[j]+1)])/((cpts[j+1]-cpts[j])*shape)
    }
    return(tmpscale)			
  }
  param.trend=function(object){
    cpts=c(0,object@cpts)
    seglen=seg.len(object)
    data=data.set(object)
    n=length(data)
    sumstat=cbind(cumsum(c(0,data)),cumsum(c(0,data*c(1:n))))
    cptsumstat=matrix(sumstat[object@cpts+1,]-sumstat[c(0,cpts(object))+1,],ncol=2)
    cptsumstat[,2]=cptsumstat[,2]-cptsumstat[,1]*c(0,cpts(object)) # i.e. creating newx3
    
    thetaS=(2*cptsumstat[,1]*(2*seglen + 1) - 6*cptsumstat[,2]) / (2*seglen*(2*seglen + 1) - 3*seglen*(seglen+1))
    thetaT=(6*cptsumstat[,2])/((seglen+1)*(2*seglen+1)) + (thetaS * (1-((3*seglen)/((2*seglen)+1))))
    return(cbind(thetaS,thetaT))
  }
  param.meanar=function(object){
    seglen=seg.len(object)
    data=data.set(object)
    n=length(data)-1
    sumstat=cbind(cumsum(c(0,data[-1])),cumsum(c(0,data[-(n+1)])),cumsum(c(0,data[-1]*data[-(n+1)])),cumsum(c(0,data[-1]^2)),cumsum(c(0,data[-(n+1)]^2)))
    cptsumstat=matrix(sumstat[object@cpts+1,]-sumstat[c(0,cpts(object))+1,],ncol=5)
    beta2=(2*seglen*cptsumstat[,3]-cptsumstat[,1]*cptsumstat[,2])/(2*seglen*cptsumstat[,5]*(1-cptsumstat[,2]^2));
    beta1=(2*cptsumstat[,1]-beta2*cptsumstat[,2])/(2*seglen);
    
    return(cbind(beta1,beta2))
  }
  param.trendar=function(object){
    seglen=seg.len(object)
    data=data.set(object)
    n=length(data)-1
    sumstat=cbind(cumsum(c(0,data[-1])),cumsum(c(0,data[-(n+1)])),cumsum(c(0,data[-1]*data[-(n+1)])),cumsum(c(0,data[-1]*c(1:n))),cumsum(c(0,data[-(n+1)]*c(0:(n-1)))))
    cptsumstat=matrix(sumstat[object@cpts+1,]-sumstat[c(0,cpts(object))+1,],ncol=7)
    cptsumstat[,4]=cptsumstat[,4]-cptsumstat[,1]*c(0,cpts(object)) # i.e. creating newx4
    cptsumstat[,5]=cptsumstat[,5]-cptsumstat[,2]*c(0,cpts(object)) # i.e. creating newx5
    betatop=seglen*(seglen-1)*(seglen*(seglen-1)*cptsumstat[,3] + 2*(2*seglen+1)*cptsumstat[,1]*(cptsumstat[,5]-seglen*cptsumstat[,2]) + 6*cptsumstat[,4]*(cptsumstat[,2]-cptsumstat[,5]))
    betabottom=seglen*(seglen-1)*cptsumstat[,7] + 2*(2*seglen+1)*cptsumstat[,2]*(seglen*cptsumstat[,2]-cptsumstat[,5]) + 6*cptsumstat[,5]*(cptsumstat[,5]-cptsumstat[,2]);
    beta=betatop/betabottom;  
    thetajpo=(6*(seglen+2)*(cptsumstat[,4]-beta*cptsumstat[,5]))/((seglen+1)*(2*seglen+1)) - 2*(cptsumstat[,1]-beta*cptsumstat[,2])
    thetaj=(2*(2*seglen+1)*(cptsumstat[,1]-beta*cptsumstat[,2])-6*(cptsumstat[,4]-beta*cptsumstat[,5]))/(seglen-1)
    
    return(cbind(beta,thetajpo,thetaj))
  }
  
  if(cpttype(object)=="mean"){
    param.est<-list(mean=param.mean(object,cpts))
  }
  else if(cpttype(object)=="variance"){
    param.est<-list(variance=param.var(object,cpts))
  }
  else if(cpttype(object)=="mean and variance"){
    if(test.stat(object)=="Normal"){
      param.est<-list(mean=param.mean(object,cpts),variance=param.var(object,cpts))
    }
    else if(test.stat(object)=="Gamma"){
      param.est<-list(scale=param.scale(object,cpts,shape=shape),shape=shape)
    }
    else if(test.stat(object)=="Exponential"){
      param.est<-list(rate=1/param.mean(object,cpts))
    }
    else if(test.stat(object)=="Poisson"){
      param.est<-list(lambda=param.mean(object,cpts))
    }
    else{
      stop("Unknown test statistic for a change in mean and variance")
    }
  }
  else if(cpttype(object)=="trend"){
    if(test.stat(object)=="Normal"){
      tmp=param.trend(object)
      param.est(object)<-list(thetaS=tmp[,1],thetaT=tmp[,2])
    }
    else{
      stop("Unknown test statistic for a change in trend")
    }
  }
  else if(cpttype(object)=="trendar"){
    if(test.stat(object)=="Normal"){
      tmp=param.trendar(object)
      param.est(object)<-list(beta=tmp[,1],thetajpo=tmp[,2],thetaj=tmp[,3])
    }
    else{
      stop("Unknown test statistic for a change in trend+ar")
    }
  }
  else if(cpttype(object)=="meanar"){
    if(test.stat(object)=="Normal"){
      tmp=param.meanar(object)
      param.est(object)<-list(beta1=tmp[,1],beta2=tmp[,2])
    }
    else{
      stop("Unknown test statistic for a change in mean+ar")
    }
  }
  else{
    stop("Unknown changepoint type, must be 'mean', 'variance', 'mean and variance', 'trend', 'meanar' or 'trendar'")
  }
  if(is.na(ncpts)){
    param.est(object)=param.est
    return(object)
  }
  out=new('cpt.range')
  param.est(out)=param.est
  return(out)
})

setMethod("param", "cpt.reg", function(object,shape,...) {			
  param.norm=function(object){
    cpts=c(0,object@cpts)
    #	nseg=length(cpts)-1 #nseg(object)
    data=data.set(object)
    p=ncol(data)-1
    tmpbeta=matrix(NA,ncol=p,nrow=nseg(object))
    tmpsigma=rep(NA,nseg(object))
    for(j in 1:nseg(object)){
      formula=paste('-1+data[',cpts[j]+1,':',cpts[j+1],',2]',sep='')
      if(p>1){
        for(i in 2:p){
          formula=paste(formula,'+data[',(cpts[j]+1),':',cpts[j+1],',',i+1,']',sep='')
        }
      }
      tmpfit=eval(parse(text=paste('lm(data[',(cpts[j]+1),':',cpts[j+1],',1]~',formula,')',sep='')))
      tmpbeta[j,]=tmpfit$coefficients
      tmpsigma[j]=var(tmpfit$residuals)
    }
    return(list(beta=tmpbeta,sig2=tmpsigma))
  }
  if(test.stat(object)=="Normal"){
    param.est(object)<-param.norm(object)
  }
  else{
    stop("Unknown test statistic, must be 'Normal'")
  }
  return(object)
})

# summary functions
setMethod("summary","cpt",function(object){
  cat("Created Using changepoint version",object@version,'\n')
  cat("Changepoint type      : Change in",cpttype(object),'\n')
  cat("Method of analysis    :",method(object),"\n")
  cat("Test Statistic  :", test.stat(object),"\n")
  cat("Type of penalty       :", pen.type(object), "with value,",pen.value(object),"\n")
  cat("Minimum Segment Length :", minseglen(object),"\n")
  cat("Maximum no. of cpts   :", ncpts.max(object),"\n")
  if(length(cpts(object))<=20){cat("Changepoint Locations :",cpts(object),"\n")}
  else{cat("Number of changepoints:", ncpts(object),"\n")}
})

setMethod("summary","cpt.range",function(object){
  cat("Created Using changepoint version",object@version,'\n')
  cat("Changepoint type      : Change in",cpttype(object),'\n')
  cat("Method of analysis    :",method(object),"\n")
  cat("Test Statistic  :", test.stat(object),"\n")
  cat("Type of penalty       :", pen.type(object), "with value,",pen.value(object),"\n")
  cat("Minimum Segment Length :", minseglen(object),"\n")
  cat("Maximum no. of cpts   :", ncpts.max(object),"\n")
  if(length(cpts(object))<=20){cat("Changepoint Locations :",cpts(object),"\n")}
  else{cat("Number of changepoints:", ncpts(object),"\n")}
  if((nrow(cpts.full(object))<=5)&(ncol(cpts.full(object)<=20))){cat("Range of segmentations:\n");print(cpts.full(object));cat("\n For penalty values:", pen.value.full(object),"\n")}
  else{cat("Number of segmentations recorded:", nrow(cpts.full(object)), " with between ", sum(cpts.full(object)[nrow(cpts.full(object)),]>0,na.rm=T), " and ", sum(cpts.full(object)[1,]>0,na.rm=T), "changepoints.\n Penalty value ranges from:",min(pen.value.full(object))," to ",max(pen.value.full(object)))}
})

setMethod("summary","cpt.reg",function(object){
  cat("Created Using changepoint version",object@version,'\n')
  cat("Changepoint type     : Change in",cpttype(object),'\n')
  cat("Method of analysis   :",method(object),"\n")
  cat("Test Statistic :", test.stat(object),"\n")
  cat("Type of penalty      :", pen.type(object), "with value,",pen.value(object),"\n")
  cat("Maximum no. of cpts   :", ncpts.max(object),"\n")
  if(length(cpts(object))<=20){cat("Changepoint Locations :",cpts(object),"\n")}
  else{cat("Number of changepoints:", ncpts(object),"\n")}
})

# show functions
setMethod("show","cpt",function(object){
  cat("Class 'cpt' : Changepoint Object\n")
  cat("       ~~   : S4 class containing", length(attributes(object))-1, "slots with names\n")
  cat("             ", names(attributes(object))[1:(length(attributes(object))-1)], "\n\n")
  cat("Created on  :", object@date, "\n\n")
  cat("summary(.)  :\n----------\n")
  summary(object)
})
setMethod("show","cpt.reg",function(object){
  cat("Class 'cpt.reg' : Changepoint Regression Object\n")
  cat("       ~~   : S4 class containing", length(attributes(object))-1, "slots with names\n")
  cat("             ", names(attributes(object))[1:(length(attributes(object))-1)], "\n\n")
  cat("Created on  :", object@date, "\n\n")
  cat("summary(.)  :\n----------\n")
  summary(object)
})

# plot functions
setMethod("plot","cpt",function(x,cpt.col='red',cpt.width=1,cpt.style=1,...){
  if (cpttype(x)!="nonparametric (empirical_distribution)"){
    if(length(param.est(x))==0){# i.e. parameter.estimates=FALSE in call
      cat('Calculating parameter estimates...')
      object=param(x)
      cat('done.\n')
    }
  }
  plot(data.set.ts(x),...)
  if(cpttype(x)=="variance" || cpttype(x)=="nonparametric (empirical_distribution)"){
    abline(v=index(data.set.ts(x))[cpts(x)],col=cpt.col,lwd=cpt.width,lty=cpt.style)
  }
  else if(cpttype(x)=="mean"  ||  cpttype(x)=="mean and variance"){
    #nseg=length(cpts(x))+1
    cpts=c(0,x@cpts)
    if((test.stat(x)=="Normal")||(test.stat(x)=="CUSUM")){
      means=param.est(x)$mean
    }
    else if(test.stat(x)=="Gamma"){
      means=param.est(x)$scale*param.est(x)$shape
    }
    else if(test.stat(x)=="Exponential"){
      means=1/param.est(x)$rate
    }
    else if(test.stat(x)=="Poisson"){
      means=param.est(x)$lambda
    }
    else{
      stop('Invalid Changepoint test statistic')
    }
    for(i in 1:nseg(x)){
      segments(index(data.set.ts(x))[cpts[i]+1],means[i],index(data.set.ts(x))[cpts[i+1]],means[i],col=cpt.col,lwd=cpt.width,lty=cpt.style)
    }
  }
  else if(cpttype(x)=="trend"){
    cpts=c(0,x@cpts)
    intercept=rep(param.est(x)$thetaS,x@cpts-c(0,cpts(x)))
    slope=rep(param.est(x)$thetaT-param.est(x)$thetaS,x@cpts-c(0,cpts(x)))/rep(x@cpts-c(0,cpts(x)),x@cpts-c(0,cpts(x)))
    cptn=rep(c(0,cpts(x)),x@cpts-c(0,cpts(x)))
    n=length(data.set(x))
    means=intercept+slope*((1:n)-cptn)
    for(i in 1:nseg(x)){
      segments(index(data.set.ts(x))[cpts[i]+1],means[cpts[i]+1],index(data.set.ts(x))[cpts[i+1]],means[cpts[i+1]],col=cpt.col,lwd=cpt.width,lty=cpt.style)
    }
  }
  else{
    stop('Invalid Changepoint Type for plotting.\n Can only plot mean, variance, mean and variance')
  }
})

setMethod("plot","cpt.range",function(x,ncpts=NA,diagnostic=FALSE,cpt.col='red',cpt.width=1,cpt.style=1,...){
  if(diagnostic==TRUE){
    return(plot(apply(cpts.full(x),1,function(x){sum(x>0,na.rm=TRUE)}),pen.value.full(x),type='l',xlab='Number of Changepoints',ylab='Difference in Test Statistic',...))
  }
  plot(data.set.ts(x),...)
  if(is.na(ncpts)){
    if(pen.type(x)=="CROPS"){
      stop('CROPS does not supply an optimal set of changepoints, set ncpts to the desired segmentation to plot or use diagnostic=TRUE to identify an appropriate number of changepoints')
    }
    cpts.to.plot=cpts(x)
    param.est=x
  }
  else{
    ncpts.full=apply(cpts.full(x),1,function(x){sum(x>0,na.rm=TRUE)})
    row=which(ncpts.full==ncpts)
    if(length(row)==0){
      stop(paste("Your input object doesn't have a segmentation with the requested number of changepoints.\n Possible ncpts are: "),paste(ncpts.full,collapse=','))
    }
    cpts.to.plot=cpts.full(x)[row,1:ncpts]
    if(cpttype(x)!="nonparametric (empirical_distribution)"){
      if(test.stat(x)=="Gamma"){
        param.est=param(x,ncpts,shape=param.est(x)$shape)
      }
      else{
        param.est=param(x,ncpts)
      }
    }
  }
  if(cpttype(x)=="variance"||(cpttype(x)=="nonparametric (empirical_distribution)")){
    abline(v=index(data.set.ts(x))[cpts.to.plot],col=cpt.col,lwd=cpt.width,lty=cpt.style)
  }
  else if(cpttype(x)=="mean"  ||  cpttype(x)=="mean and variance"){
    if((test.stat(x)=="Normal")||(test.stat(x)=="CUSUM")){
      means=param.est(param.est)$mean
    }
    else if(test.stat(x)=="Gamma"){
      means=param.est(param.est)$scale*param.est(param.est)$shape
    }
    else if(test.stat(x)=="Exponential"){
      means=1/param.est(param.est)$rate
    }
    else if(test.stat(x)=="Poisson"){
      means=param.est(param.est)$lambda
    }
    else{
      stop('Invalid Changepoint test statistic')
    }
    nseg=length(means)
    cpts.to.plot=c(0,cpts.to.plot,length(data.set(x)))
    for(i in 1:nseg){
      segments(index(data.set.ts(x))[cpts.to.plot[i]+1],means[i],index(data.set.ts(x))[cpts.to.plot[i+1]],means[i],col=cpt.col,lwd=cpt.width,lty=cpt.style)
    }
  }
  else{
    stop('Invalid Changepoint Type for plotting.\n Can only plot mean, variance, mean and variance')
  }
})

setMethod("plot","cpt.reg",function(x,cpt.col='red',cpt.width=1,cpt.style=1,...){
  if(length(param.est(x))==0){# i.e. parameter.estimates=FALSE in call
    cat('Calculating parameter estimates...')
    object=param(x)
    cat('done.\n')
  }
  plot(data.set(x)[,1],type='l',...)
  if(test.stat(x)=="Normal"){
    cpts=c(0,x@cpts)
    betas=param.est(x)$beta
    for(i in 1:nseg(x)){
      lines((cpts[i]+1):cpts[i+1],betas[i,]%*%t(data.set(x)[(cpts[i]+1):cpts[i+1],-1]),col=cpt.col,lwd=cpt.width,lty=cpt.style)
    }
  }
  else{
    stop('Invalid Changepoint test statistic')
  }
})

# likelihood functions
setMethod("logLik", "cpt", function(object) {
  if(length(param.est(object))==0){# i.e. parameter.estimates=FALSE in call
    cat('Calculating parameter estimates...')
    object=param(object)
    cat('done.\n')
  }
  if(test.stat(object)=="Normal"){
    if(cpttype(object)=="mean"){
      means=rep(param.est(object)$mean,object@cpts-c(0,cpts(object)))
      rss=sum((data.set(object)-means)^2)
      n=length(data.set(object))
      like=n*(log(2*pi)+log(rss/n)+1) # -2*loglik
      if(pen.type(object)=="MBIC"){
        like=c(like, like+(nseg(object)-2)*pen.value(object)+sum(log(cpts[-1]-cpts[-(nseg(object)+1)])))
      }else{
        like=c(like,like+(nseg(object)-1)*pen.value(object))
      }
    }
    else if(cpttype(object)=="variance"){
      rss=c(0,cumsum((data.set(object)-param.est(object)$mean)^2))
      cpts=c(0,object@cpts)
      n=length(data.set(object))
      seglen=seg.len(object)
      sigmas=(rss[cpts[-1]+1]-rss[cpts[-length(cpts)]+1])/seglen
      like=n*log(2*pi)+sum(seglen*log(sigmas))+n
      if(pen.type(object)=="MBIC"){
        like=c(like, like+(nseg(object)-2)*pen.value(object)+sum(log(seglen)))
      }else{
        like=c(like,like+(nseg(object)-1)*pen.value(object))
      }
    }
    else if(cpttype(object)=="mean and variance"){
      means=rep(param.est(object)$mean,object@cpts-c(0,cpts(object)))
      rss=sum((data.set(object)-means)^2)
      n=length(data.set(object))
      cpts=c(0,object@cpts)
      seglen=seg.len(object)
      sigmas=param.est(object)$variance
      like=n*log(2*pi)+sum(seglen*log(sigmas))+n
      if(pen.type(object)=="MBIC"){
        like=c(like,like+(nseg(object)-2)*pen.value(object)+sum(log(seglen)))
      }else{
        like=c(like,like+(nseg(object)-1)*pen.value(object))
      }
    }
    else if(cpttype(object)=="trend"){
      intercept=rep(param.est(object)$thetaS,object@cpts-c(0,cpts(object)))
      slope=rep(param.est(object)$thetaT-param.est(object)$thetaS,object@cpts-c(0,cpts(object)))/rep(object@cpts-c(0,cpts(object)),object@cpts-c(0,cpts(object)))
      cptn=rep(c(0,cpts(object)),object@cpts-c(0,cpts(object)))
      n=length(data.set(object))
      means=intercept+slope*((1:n)-cptn)
      rss=sum((data.set(object)-means)^2)
      like=n*(log(2*pi)+log(rss/n)+1) # -2*loglik
      if(pen.type(object)=="MBIC"){
        like=c(like, like+(nseg(object)-2)*pen.value(object)+sum(log(seg.len(object))))
      }else{
        like=c(like,like+(nseg(object)-1)*pen.value(object))
      }
    }
    else if(cpttype(object)=="trendar"){
      seglen=seg.len(object)
      intercept=rep(param.est(object)$thetaj,seglen)
      slope=rep(param.est(object)$thetajpo-param.est(object)$thetaj,seglen)/rep(seglen,seglen)
      ar=rep(param.est(object)$beta,seglen)
      cptn=rep(c(0,cpts(object)),seglen)
      n=length(data.set(object))
      means=NULL;means[1]=0
      for(i in 2:n){means[i]=intercept+slope*((1:n)-cptn)+ar*means[i-1]}
      means=means[-1]
      rss=sum((data.set(object)[-1]-means)^2)
      like=n*(log(2*pi)+log(rss/n)+1) # -2*loglik
      if(pen.type(object)=="MBIC"){
        like=c(like, like+(nseg(object)-2)*pen.value(object)+sum(log(seg.len(object))))
      }else{
        like=c(like,like+(nseg(object)-1)*pen.value(object))
      }
    }
    else if(cpttype(object)=="meanar"){
      seglen=seg.len(object)
      intercept=rep(param.est(object)$beta1,seglen)
      ar=rep(param.est(object)$beta2,seglen)
      cptn=rep(c(0,cpts(object)),seglen)
      n=length(data.set(object))
      means[1]=0;for(i in 2:n){means[i]=intercept+ar*means[i-1]}
      means=means[-1]
      rss=sum((data.set(object)[-1]-means)^2)
      like=n*(log(2*pi)+log(rss/n)+1) # -2*loglik
      if(pen.type(object)=="MBIC"){
        like=c(like, like+(nseg(object)-2)*pen.value(object)+sum(log(seg.len(object))))
      }else{
        like=c(like,like+(nseg(object)-1)*pen.value(object))
      }
    }
    else{
      stop("Unknown changepoint type, must be 'mean', 'variance', 'mean and variance', 'trend', 'meanar' or 'trendar'")
    }
  }
  else if(test.stat(object)=="Gamma"){
    if(cpttype(object)!="mean and variance"){
      stop("Unknown changepoint type for test.stat='Gamma', must be 'mean and variance'")
    }
    else{
      warning("Not changed to be -2*logLik")
      mll.meanvarg=function(x,n,shape){
        return(n*shape*log(n*shape)-n*shape*log(x))
      }
      y=c(0,cumsum(data.set(object)))
      shape=param.est(object)$shape
      cpts=c(0,object@cpts)
      #nseg=length(cpts)-1
      tmplike=0
      for(j in 1:nseg(object)){
        tmplike=tmplike+mll.meanvarg(y[cpts[j+1]+1]-y[cpts[j]+1],cpts[j+1]-cpts[j],shape)
      }
      if(pen.type(object)=="MBIC"){
        like=c(tmplike, tmplike+(nseg(object)-2)*pen.value(object)+sum(log(seg.len(object))))
      }else{
        like=c(tmplike,tmplike+(nseg(object)-1)*pen.value(object))
      }
    }
  }
  else if(test.stat(object)=="Exponential"){
    if(cpttype(object)!="mean and variance"){
      stop("Unknown changepoint type for test.stat='Exponential', must be 'mean and variance'")
    }
    else{
      warning("Not changed to be -2*logLik")
      mll.meanvare=function(x,n){
        return(n*log(n)-n*log(x))
      }
      y=c(0,cumsum(data.set(object)))
      cpts=c(0,object@cpts)
      #nseg=length(cpts)-1
      tmplike=0
      for(j in 1:nseg(object)){
        tmplike=tmplike+mll.meanvare(y[cpts[j+1]+1]-y[cpts[j]+1],cpts[j+1]-cpts[j])
      }
      if(pen.type(object)=="MBIC"){
        like=c(tmplike, tmplike+(nseg(object)-2)*pen.value(object)+sum(log(seg.len(object))))
      }else{
        like=c(tmplike,tmplike+(nseg(object)-1)*pen.value(object))
      }
    }
  }
  else if(test.stat(object)=="Poisson"){
    if(cpttype(object)!="mean and variance"){
      stop("Unknown changepoint type for test.stat='Poisson', must be 'mean and variance'")
    }
    else{
      warning("Not changed to be -2*logLik")
      mll.meanvarp=function(x,n){
        return(x*log(x)-x*log(n))
      }
      y=c(0,cumsum(data.set(object)))
      cpts=c(0,object@cpts)
      #nseg=length(cpts)-1
      tmplike=0
      for(j in 1:nseg(object)){
        tmplike=tmplike+mll.meanvarp(y[cpts[j+1]+1]-y[cpts[j]+1],cpts[j+1]-cpts[j])
      }
      if(pen.type(object)=="MBIC"){
        like=c(tmplike, tmplike+(nseg(object)-2)*pen.value(object)+sum(log(seg.len(object))))
      }else{
        like=c(tmplike,tmplike+(nseg(object)-1)*pen.value(object))
      }
    }
  }
  else{stop("logLik is only valid for distributional assumptions, not CUSUM or CSS")}
  names(like)=c("-2*logLik","-2*Loglike+pen")
  return(like)
})

setMethod("logLik", "cpt.range", function(object,ncpts=NA) {
  warning("Not changed to be -2*logLik")
  if(is.na(ncpts)){
    if(pen.type(object)=="CROPS"){
      stop('CROPS does not supply an optimal set of changepoints, set ncpts argument to the desired segmentation to plot or use diagnostic=TRUE to identify an appropriate number of changepoints')
    }
    cpts=c(0,object@cpts)
    pen.value=pen.value(object)
  }
  else{
    ncpts.full=apply(cpts.full(object),1,function(x){sum(x>0,na.rm=TRUE)})
    row=which(ncpts.full==ncpts)
    if(length(row)==0){
      stop(paste("Your input object doesn't have a segmentation with the requested number of changepoints.\n Possible ncpts are: "),paste(ncpts.full,collapse=','))
    }
    cpts=c(0,cpts.full(object)[row,1:ncpts],length(data.set(object)))
    pen.value=pen.value.full(object)[row]
  }
  nseg=length(cpts)-1
  
  if(test.stat(object)=="Normal"){
    if(cpttype(object)=="mean"){
      mll.mean=function(x2,x,n){
        return( x2-(x^2)/n)
      }
      y2=c(0,cumsum(data.set(object)^2))
      y=c(0,cumsum(data.set(object)))
      tmplike=0
      for(j in 1:nseg){
        tmplike=tmplike+mll.mean(y2[cpts[j+1]+1]-y2[cpts[j]+1],y[cpts[j+1]+1]-y[cpts[j]+1],cpts[j+1]-cpts[j])
      }
      ##c(tmplike, tmplike+(nseg-2)*pen.value(object)+sum(log(cpts[-1]-cpts[-(nseg+1)])))
      if(pen.type(object)=="MBIC"){
        like=c(tmplike, tmplike+(nseg-2)*pen.value+sum(log(seg.len(object))))
      }else{
        like=c(tmplike,tmplike+(nseg-1)*pen.value)
      }
      names(like)=c("-like","-likepen")
    }
    else if(cpttype(object)=="variance"){
      mll.var=function(x,n){
        neg=x<=0
        x[neg==TRUE]=0.00000000001    
        return( n*(log(2*pi)+log(x/n)+1))
      }
      y2=c(0,cumsum((data.set(object)-param.est(object)$mean)^2))
      tmplike=0
      for(j in 1:nseg){
        tmplike=tmplike+mll.var(y2[cpts[j+1]+1]-y2[cpts[j]+1],cpts[j+1]-cpts[j])
      }
      if(pen.type(object)=="MBIC"){
        like=c(tmplike, tmplike+(nseg-2)*pen.value+sum(log(seg.len(object))))
      }else{
        like=c(tmplike,tmplike+(nseg-1)*pen.value)
      }
      names(like)=c("-like","-likepen")
    }
    else if(cpttype(object)=="mean and variance"){
      mll.meanvar=function(x2,x,n){
        sigmasq=(1/n)*(x2-(x^2)/n)
        neg=sigmasq<=0
        sigmasq[neg==TRUE]=0.00000000001
        return( n*(log(2*pi)+log(sigmasq)+1))
      }
      y2=c(0,cumsum(data.set(object)^2))
      y=c(0,cumsum(data.set(object)))
      tmplike=0
      for(j in 1:nseg){
        tmplike=tmplike+mll.meanvar(y2[cpts[j+1]+1]-y2[cpts[j]+1],y[cpts[j+1]+1]-y[cpts[j]+1],cpts[j+1]-cpts[j])
      }
      if(pen.type(object)=="MBIC"){
        like=c(tmplike, tmplike+(nseg-2)*pen.value+sum(log(seg.len(object))))
      }else{
        like=c(tmplike,tmplike+(nseg-1)*pen.value)
      }
      names(like)=c("-like","-likepen")
    }
    else{
      stop("Unknown changepoint type, must be 'mean', 'variance' or 'mean and variance'")
    }
  }
  else if(test.stat(object)=="Gamma"){
    if(cpttype(object)!="mean and variance"){
      stop("Unknown changepoint type for test.stat='Gamma', must be 'mean and variance'")
    }
    else{
      mll.meanvarg=function(x,n,shape){
        return(n*shape*log(n*shape)-n*shape*log(x))
      }
      y=c(0,cumsum(data.set(object)))
      shape=param.est(object)$shape
      cpts=c(0,object@cpts)
      #nseg=length(cpts)-1
      tmplike=0
      for(j in 1:nseg){
        tmplike=tmplike+mll.meanvarg(y[cpts[j+1]+1]-y[cpts[j]+1],cpts[j+1]-cpts[j],shape)
      }
      if(pen.type(object)=="MBIC"){
        like=c(tmplike, tmplike+(nseg-2)*pen.value+sum(log(seg.len(object))))
      }else{
        like=c(tmplike,tmplike+(nseg-1)*pen.value)
      }
      names(like)=c("-like","-likepen")
    }
  }
  else if(test.stat(object)=="Exponential"){
    if(cpttype(object)!="mean and variance"){
      stop("Unknown changepoint type for test.stat='Exponential', must be 'mean and variance'")
    }
    else{
      mll.meanvare=function(x,n){
        return(n*log(n)-n*log(x))
      }
      y=c(0,cumsum(data.set(object)))
      cpts=c(0,object@cpts)
      #nseg=length(cpts)-1
      tmplike=0
      for(j in 1:nseg){
        tmplike=tmplike+mll.meanvare(y[cpts[j+1]+1]-y[cpts[j]+1],cpts[j+1]-cpts[j])
      }
      if(pen.type(object)=="MBIC"){
        like=c(tmplike, tmplike+(nseg-2)*pen.value+sum(log(seg.len(object))))
      }else{
        like=c(tmplike,tmplike+(nseg-1)*pen.value)
      }
      names(like)=c("-like","-likepen")
    }
  }
  else if(test.stat(object)=="Poisson"){
    if(cpttype(object)!="mean and variance"){
      stop("Unknown changepoint type for test.stat='Poisson', must be 'mean and variance'")
    }
    else{
      mll.meanvarp=function(x,n){
        return(x*log(x)-x*log(n))
      }
      y=c(0,cumsum(data.set(object)))
      cpts=c(0,object@cpts)
      #nseg=length(cpts)-1
      tmplike=0
      for(j in 1:nseg){
        tmplike=tmplike+mll.meanvarp(y[cpts[j+1]+1]-y[cpts[j]+1],cpts[j+1]-cpts[j])
      }
      if(pen.type(object)=="MBIC"){
        like=c(tmplike, tmplike+(nseg-2)*pen.value+sum(log(seg.len(object))))
      }else{
        like=c(tmplike,tmplike+(nseg-1)*pen.value)
      }
      names(like)=c("-like","-likepen")
    }
  }
  else{stop("logLik is only valid for distributional assumptions, not CUSUM or CSS")}
  return(like)
})

setMethod("logLik", "cpt.reg", function(object) {
  if(length(param.est(object))==0){# i.e. parameter.estimates=FALSE in call
    cat('Calculating parameter estimates...')
    object=param(object)
    cat('done.\n')
  }
  if(test.stat(object)=="Normal"){
    cpts=c(0,object@cpts)
    seglen=seg.len(object)
    data=data.set(object)
    beta=param.est(object)$beta
    sigmas=param.est(object)$sig2
    rss=NULL
    for(i in 1:length(seglen)){
      rss[i]=sum((data[(cpts[i]+1):cpts[i+1],1]-data[(cpts[i]+1):cpts[i+1],-1]%*%beta[i,])^2)
    }
    like=sum(seglen*log(2*pi*sigmas))+sum(rss/sigmas)
    if(pen.type(object)=="MBIC"){
      like=c(like, like+(nseg(object)-2)*pen.value(object)+sum(log(seg.len(object))))
    }else{
      like=c(like,like+(nseg(object)-1)*pen.value(object))
    }
  }
  else{stop("logLik is only valid for Normal distributional assumption.")}
  return(like)
})

setGeneric("likelihood", function(object) standardGeneric("likelihood"))
setMethod("likelihood", "cpt", function(object) {
  return(logLik(object))
})

# acf functions
setGeneric("acf", function(object,...) standardGeneric("acf"))
setMethod("acf", "cpt", function(object,lag.max=NULL,...) {
  cpts=c(0,object@cpts)
  nseg=nseg(object)
  data=data.set(object)
  for(i in 1:nseg){
    stats::acf(data[(cpts[i]+1):cpts[i+1]],main=paste("Series part:",(cpts[i]+1),":",cpts[i+1]),...)
  }
})

setMethod("acf", "cpt.reg", function(object,lag.max=NULL,...) {
  cpts=c(0,object@cpts)
  nseg=nseg(object)
  data=data.set(object)[,1]
  for(i in 1:nseg){
    stats::acf(data[(cpts[i]+1):cpts[i+1]],main=paste("Series part:",(cpts[i]+1),"-",cpts[i+1]),...)
  }
})