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reboot.slme <-function(fit, B=10, display=FALSE, metodo=1, frac=1, it.max=6, it.max.b=5, seed=NULL, start=NULL, msg=TRUE){
#metodo: viene passato alla funzione logL. Se 1 la logL che viene calcolata e' quella della componente
# fit$lme.fit.noG, namely the logLik from the lme fit without the G variables..
#bootRestart for slme4
#fit: un oggetto di classe "segmented.lme" (anche proveniente da un altra "bootsegMix" call)
#frac: size of the boot resample..
#start : un vettor con i nomi (se non fornito gli starting values sono presi da fit)
#-----------------------
extract.psi<-function(obj){
#questa funzione restituisce i "kappa", ovvero i coeff di psi..
nomiG<-obj$namesGZ$nomiG
b<-fixef(obj[[1]])[c("G0",nomiG)]
b
}
#-----------------------
update.lme.call<-function (old.call, fixed., ..., evaluate=FALSE) {
call <- old.call
extras <- match.call(expand.dots = FALSE)$...
if (!missing(fixed.)) call$fixed <- update.formula(call$fixed, fixed.)
if (length(extras) > 0) {
existing <- !is.na(match(names(extras), names(call)))
for (a in names(extras)[existing]) call[[a]] <- extras[[a]]
if (any(!existing)) {
call <- c(as.list(call), extras[!existing])
call <- as.call(call)
}
}
if (evaluate) eval(call, parent.frame()) else call
}
#---------
#---------
startKappa00<-extract.psi(fit)[1]
Z <- fit$Z #segmented covariate
rangeZ<-quantile(Z, c(.05,.95), names=FALSE)
#quanti soggetti? Attenzione se ci sono nested re, sotto non funziona, o meglio da i livelli del outermost group
#idLevels <- levels(fit$lme.fit$groups[,ncol(fit$lme.fit$groups)])
#N<- length(idLevels)
newData<-fit$lme.fit$data
nomeRispo<-all.vars(formula(fit$lme.fit))[1]
#AGGIUSTA la risposta
newData[,nomeRispo]<-newData[,nomeRispo] + fit$Off
nome.id <-names(fit$lme.fit$groups)[ncol(fit$lme.fit$groups)] #name of the innermost grouping variable
newData[, nome.id]<- factor(newData[, nome.id])
var.id<-newData[, nome.id]
idLevels<-levels(var.id)
N<- length(idLevels)
o.b<-fit$boot.call
#old: start.psi<-extract.psi(fit)
#old: est.psi<-start.psi["G0"]
#old: call.b<-update(object=fit, obj=o.b, data=newD, psi=est.psi, display=FALSE, evaluate=FALSE)
call.b<-update(object=fit, obj=o.b, data=newD, it.max=it.max.b,
start=list(kappa0=startKappa0,kappa=startingKappa), display=FALSE, evaluate=FALSE)
call.b$random <- fit$randomCALL
o.ok<-update.lme.call(o.b, fixed.=paste(nomeRispo,"~."), evaluate=FALSE)
#o.ok<-update.lme.call(o.b, fixed.=y~., evaluate=FALSE)
#mycall$data=quote(gh)
#o.ok<-update.lme.call(o.b, fixed.=y~.,evaluate=FALSE)
#old: call.ok<-update(object=fit, obj=o.ok, data=newData, psi=est.psi.b, display=FALSE, evaluate=FALSE)
#o.ok$fixed<- update.formula(o.ok$fixed, paste(nomeRispo,"~."))
call.ok<-update(object=fit, obj=o.ok, data=newData, it.max=it.max,
start=list(kappa0=startKappa0.b,kappa=startingKappa.b), display=FALSE, evaluate=FALSE)
call.ok$n.boot <- call.b$n.boot<-0
call.ok$control <- call.b$control<-quote(seg.control(display=FALSE))
all.L<-all.psi<-NULL
it<-0
L0<-L.orig<-logLik(fit$lme.fit.noG)# logL(fit, metodo=metodo)
if(display){
flush.console()
cat("original data:", 0, " logLik =", formatC(as.numeric(L.orig), 3, format = "f")," psi parms:", formatC(extract.psi(fit),4,format="f"),"\n")
}
if(is.null(start)){
startingKappa<-extract.psi(fit)
startKappa0<- startingKappa[1]
startingKappa<-startingKappa[-1]
nomiKappa<-names(startingKappa)
nomiKappa<-sapply(strsplit(nomiKappa, "G\\."),function(x)x[2])
names(startingKappa) <- nomiKappa
} else {
nomiG<-sapply(strsplit(fit$namesGZ$nomiG, "G\\."),function(x)x[2])
if(length(intersect(names(start), c("G0", nomiG)))!=length(start)) stop("'start' should include all the changepoint parameters")
startKappa0<-start["G0"]
startingKappa<-start[-which("G0"%in%names(start))]
nomiKappa<-names(startingKappa)
}
if(is.null(seed)) seed<-eval(parse(text=paste(sample(0:9, size=6), collapse="")))
if(!is.numeric(seed)) stop(" 'seed' is not numeric")
set.seed(seed)
#browser()
for(i in seq(B)){
#build the boot sample
#idx<-sample(N, replace=TRUE)
#idx<-sample(1:N, size=trunc(N*frac), replace=TRUE)
idx<-sample(idLevels, size=trunc(N*frac), replace=TRUE)
newD <- do.call("rbind",lapply(idx, function(x)newData[newData[,nome.id]==x,]))
newD$y.b<- newD[,nomeRispo]
# r<-list(newD=newD, call.b=call.b)
# return(r)
#-->> CAMBIA STARTING VALUE in call.b
if(startKappa0>=rangeZ[2] | startKappa0<=rangeZ[1] ) startKappa0<- jitter(startKappa00,factor=5) #sum(rangeZ)/2
fit.b<-try(suppressWarnings(eval(call.b)), silent=TRUE) #envir=newD)
if(!is.list(fit.b)){
# fit.b<-NULL
it.b<-0
while(!is.list(fit.b)){
idx<-sample(idLevels, size=trunc(N*frac), replace=TRUE)
newD <- do.call("rbind",lapply(idx, function(x)newData[newData[,nome.id]==x,]))
newD$y.b<- newD[,nomeRispo]
startKappa0<- jitter(startKappa00,factor=5)
fit.b<-try(suppressWarnings(eval(call.b)), silent=TRUE) #envir=newD)
it.b<-it.b+1
if(it.b>=10) break
}
}
if(is.list(fit.b)){
#old: start.psi.b<-extract.psi(fit.b)
#old: est.psi.b<-start.psi.b["G0"]
startingKappa.b<-extract.psi(fit.b)
startKappa0.b<- startingKappa.b[1]
startingKappa.b<-startingKappa.b[-1]
#NB "nomiKappa" dovrebbero essere sempre gli stessi
names(startingKappa.b) <- nomiKappa
fit.ok<-try(suppressWarnings(eval(call.ok)), silent=TRUE) # data=newData)
#L1<-if(is.list(fit.ok)) logL(fit.ok, metodo=metodo) else (-Inf)
#22/05/18 aggiunto un altro tentativo... ho notato che l'insuccesso pu? dipendere dagli starting value..
if(!is.list(fit.ok)){
call.ok$start<-NULL
fit.ok<-try(suppressWarnings(eval(call.ok)), silent=TRUE)
}
L1<-if(is.list(fit.ok)) as.numeric(logLik(fit.ok)) else (-Inf)
} else {
stop("the bootstrap fit is unsuccessful")
}
if(L0<L1) {
fit<-fit.ok
L0<-L1
}
all.psi[length(all.psi)+1]<-est.psi<-extract.psi(fit)["G0"]
all.L[length(all.L)+1]<-L.ok<-max(L0,L1)
it<-it+1
if(display){
flush.console()
ll<-if(it<10) " logLik =" else " logLik ="
cat("boot resample:", it, ll, formatC(L.ok, 3, format = "f")," psi parms:", formatC(extract.psi(fit),4,format="f"),"\n")
}
startingKappa<-extract.psi(fit)
startKappa0<- startingKappa[1]
startingKappa<-startingKappa[-1]
nomiKappa<-names(startingKappa)
nomiKappa<-sapply(strsplit(nomiKappa, "G\\."),function(x)x[2])
names(startingKappa) <- nomiKappa
} #end boot replicates
fit$history.boot.restart<-cbind(b=1:length(all.psi),psi=all.psi, logL=all.L)
fit$seed<-seed
#r<-list(seg.lme.fit=fit, history=cbind(b=1:length(all.psi),psi=all.psi, logL=all.L) )
if(msg) cat(" New solution(s) found:", length(unique(all.psi))-1, "\n")
fit
}
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