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Copy pathmake_periodoframe_bkp.R
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make_periodoframe_bkp.R
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####This file is an example for making PeriodoFrame: the computation part
source('prepare_data.R',local=TRUE)
source('periodoframe.R')#for PeriodoFrame
source('periodograms.R')#for other periodograms
############################################
#####PartIV: make PeriodoFrame
############################################
if(NI>0){
Inds <- 1:NI
}else{
Inds <- 0
}
lab <- FALSE
#inds <- 1:2
inds <- NULL
sig <- TRUE
RML <- TRUE
nshow <- 1
fname <- paste0('periodograms_',paste(per.types,collapse='0'),'_Ndata_',Ndata,'modeltype',model.type,'_',star,'_NI',NI,'Nma',Nma,'_Nc',Nc,'_ofac',ofac,'_opt',opt.type,'_Nap',Nap,'_res',Np.max,loading)
fname <- paste0('results/',fname)
######plot
leg.pos <- 'topright'
pdf.name <- paste0(fname,'.pdf')
if(sequential){
pdf(pdf.name,8,8)
size <- 1.0
par(mfrow=c(2,2),mar=c(4.5,4.5,1,1),cex.lab=size,cex.axis=size,cex=size)
tit <- TRUE
}else{
pdf(pdf.name,4,4)
size <- 1.0
par(mfrow=c(1,1),mar=c(4.5,4.5,1,1),cex.lab=size,cex.axis=size,cex=size)
tit <- FALSE
}
for(kk in 1:length(per.types)){
per.type <- per.types[kk]
cat('periodogram: ',per.type,'\n')
t <- tab[,1]-min(tab[,1])
y <- tab[,2]
dy <- tab[,3]
cat('\nfind 1 signal!\n')
####BFP
if(tit){
main <- paste0(per.type,'; 1 signal')
}else{
main <- ''
}
if(per.type=='BFP'){
t1 <- proc.time()
per <- BFP(tab[,1],tab[,2],tab[,3],Nma=Nma,Inds=Inds,Indices=Indices,ofac=ofac,opt.type=opt.type,model.type=model.type,fmax=fmax,progress=FALSE,quantify=quantify)
t2 <- proc.time()
dur1 <- format((t2-t1)[3],digit=3)
cat('BFP computation time:',dur1,'s\n\n')
ylim <- range(median(per$power),max(per$power),per$sig.level)
plot(per$P,per$power,xlab='Period[d]',ylab='log(BF)',type='l',log='x',ylim=ylim,main=main)
if(is.null(inds)){
inds <- which(per$power.opt>max(per$sig.level))
if(length(inds)>0) inds <- inds[1:min(nshow,length(inds))]
}
abline(h=per$sig.level,lty=2)
if(length(inds)>1 & sig){
abline(v=per$ps[inds],col='red',lty=3,lwd=2)
text(x=per$ps[inds],y=per$power.opt[inds],pos=c(2,4),labels=paste0(format(per$ps[inds],digit=3),'d'),col='red')
}else if(length(inds)==1 & sig){
abline(v=per$ps[inds],col='red',lty=3,lwd=2)
text(x=per$ps[inds],y=per$power.opt[inds],pos=4,offset=-0.1,labels=paste0(format(per$ps[inds],digit=3),'d'),col='red')
}
}
####MLP
if(per.type=='MLP'){
t1 <- proc.time()
per <- MLP(tab[,1],tab[,2],tab[,3],Nma=Nma,Inds=Inds,ofac=ofac,mar.type='part',model.type=model.type,fmax=fmax,opt.par=NULL,Indices=Indices,MLP.type=MLP.type)
if(RML){
per$sig.level <- per$sig.level-max(per$power)
per$power.opt <- per$power.opt-max(per$power)
per$power <- per$power-max(per$power)
}
t2 <- proc.time()
dur2 <- format((t2-t1)[3],digit=3)
cat('MLP computation time:',dur2,'s\n')
Nma <- per$Nma
NI <- per$NI
if(RML){
ylab <- expression('log(ML/'*ML[max]*')')
}else{
ylab <- 'log(ML)'
}
plot(per$P,per$power,xlab='Period[d]',ylab=ylab,type='l',log='x',main=main)
abline(h=per$sig.level,lty=2)
if(is.null(inds)){
inds <- which(per$power.opt>max(per$sig.level))
if(length(inds)>0) inds <- inds[1:min(nshow,length(inds))]
}
if(length(inds)>1 & sig){
abline(v=per$ps[inds],col='red',lty=3,lwd=2)
text(x=per$ps[inds],y=per$power.opt[inds],pos=c(2,4),labels=paste0(format(per$ps[inds],digit=3),'d'),col='red')
}else if(length(inds)==1 & sig){
text(x=per$ps[inds],y=per$power.opt[inds],pos=4,offset=-0.1,labels=paste0(format(per$ps[inds],digit=3),'d'),col='red')
}
if(lab) legend(leg.pos,legend=c('MLP',paste0(dur2,'s')),bty='n')
}
#####BGLS
if(per.type=='BGLS'){
t1 <- proc.time()
per <- bgls(tab[,1],tab[,2],tab[,3],ofac=ofac,fmax=fmax)
if(RML){
per$sig.level <- per$sig.level-max(per$power)
per$power.opt <- per$power.opt-max(per$power)
per$power <- per$power-max(per$power)
}
t2 <- proc.time()
dur3 <- format((t2-t1)[3],digit=3)
plot(per$P,per$power,xlab='Period[d]',ylab='Relative probability',type='l',log='x',main=main)
if(is.null(inds)){
inds <- which(per$power.opt>max(per$sig.level))
if(length(inds)>0) inds <- inds[1:min(nshow,length(inds))]
}
abline(h=per$sig.level,lty=2)
if(length(inds)>1 & sig){
abline(v=per$ps[inds],col='red',lty=3,lwd=2)
text(x=per$ps[inds],y=per$power.opt[inds],pos=c(2,4),labels=paste0(format(per$ps[inds],digit=3),'d'),col='red')
}else if(length(inds)==1 & sig){
abline(v=per$ps[inds],col='red',lty=3,lwd=2)
text(x=per$ps[inds],y=per$power.opt[inds],pos=4,offset=-0.1,labels=paste0(format(per$ps[inds],digit=3),'d'),col='red')
}
if(lab) legend(leg.pos,legend=c('BGLS',paste0(dur3,'s')),bty='n')
}
#####GLS
if(per.type=='GLS'){
t1 <- proc.time()
per <- gls(tab[,1],tab[,2],tab[,3],ofac=ofac,fmax=fmax)
t2 <- proc.time()
plot(per$P,per$power,xlab='Period[d]',ylab='Power',type='l',log='x',main=main)
if(is.null(inds)){
inds <- which(per$power.opt>max(per$sig.level))
if(length(inds)>0) inds <- inds[1:min(nshow,length(inds))]
}
abline(h=per$sig.level,lty=2)
if(length(inds)>1 & sig){
abline(v=per$ps[inds],col='red',lty=3,lwd=2)
text(x=per$ps[inds],y=per$power.opt[inds],pos=c(2,4),labels=paste0(format(per$ps[inds],digit=3),'d'),col='red')
}else if(length(inds)==1 & sig){
abline(v=per$ps[inds],col='red',lty=3,lwd=2)
text(x=per$ps[inds],y=per$power.opt[inds],pos=4,offset=-0.1,labels=paste0(format(per$ps[inds],digit=3),'d'),col='red')
}
if(lab) legend(leg.pos,legend=c('GLS',paste0(dur3,'s')),bty='n')
}
####GLST
if(per.type=='GLST'){
t1 <- proc.time()
per <- glst(tab[,1],tab[,2],tab[,3],ofac=ofac,fmax=fmax)
t2 <- proc.time()
dur <- format((t2-t1)[3],digit=3)
plot(per$P,per$power,xlab='Period[d]',ylab='Power',type='l',log='x',main=main)
abline(h=per$sig.level,lty=2)
abline(v=per$ps[inds],col='red',lty=3,lwd=2)
if(length(inds)>1 & sig){
text(x=per$ps[inds],y=per$power.opt[inds],pos=c(2,4),labels=paste0(format(per$ps[inds],digit=3),'d'),col='red')
}else if(length(inds)==1 & sig){
text(x=per$ps[inds],y=per$power.opt[inds],pos=4,offset=-0.1,labels=paste0(format(per$ps[inds],digit=3),'d'),col='red')
}
if(lab) legend(leg.pos,legend=c('GLST',paste0(dur,'s')),bty='n')
}
if(per.type=='LS'){
t1 <- proc.time()
per <- lsp(times=tab[,1]-min(tab[,1]),x=y,ofac=ofac,from=NULL,to=fmax,alpha=c(0.1,0.01,0.001))
t2 <- proc.time()
dur <- format((t2-t1)[3],digit=3)
plot(per$P,per$power,xlab='Period[d]',ylab='Power',type='l',log='x',main=main)
if(is.null(inds)){
inds <- which(per$power.opt>max(per$sig.level))
if(length(inds)>0) inds <- inds[1:min(nshow,length(inds))]
}
abline(h=per$sig.level,lty=2)
if(length(inds)>1 & sig){
abline(v=per$ps[inds],col='red',lty=3,lwd=2)
text(x=per$ps[inds],y=per$power.opt[inds],pos=c(2,4),labels=paste0(format(per$ps[inds],digit=3),'d'),col='red')
}else{
abline(v=per$ps[inds],col='red',lty=3,lwd=2)
text(x=per$ps[inds],y=per$power.opt[inds],pos=4,offset=-0.1,labels=paste0(format(per$ps[inds],digit=3),'d'),col='red')
}
if(lab) legend(leg.pos,legend=c('GLST',paste0(dur,'s')),bty='n')
}
############################
####find additional signals
############################
if(sequential){
for(jj in 1:Np.max){
cat('\nfind',jj+1,'signal!\n')
###make another BFP for data subtracted by the signal
if(jj==1){
rr <- y
}else{
if(is.matrix(per$res)){
rr <- per$res[1,]
}else{
rr <- per$res
}
}
# cat('head(rr)=',head(rr),'\n')
if(per.type=='BFP'){
per <- BFP(tab[,1],rr,tab[,3],Nma=Nma,Inds=Inds,Indices=Indices,ofac=ofac,opt.type=opt.type,model.type=model.type,fmax=fmax,progress=FALSE,quantify=quantify)
ylim <- range(min(median(per$power),0),1.1*max(per$power),5)
ylab <- 'log(BF)'
}
if(per.type=='MLP'){
per <- MLP(tab[,1],rr,tab[,3],Nma=Nma,Inds=Inds,ofac=ofac,mar.type='part',model.type=model.type,fmax=fmax,opt.par=NULL,Indices=Indices,MLP.type=MLP.type)
ylim <- range(min(median(per$power),0),1.1*max(per$power))
if(RML){
ylab <- expression('log(ML/'*ML[max]*')')
}else{
ylab <- 'log(ML)'
}
}
if(per.type=='GLS'){
per <- gls(tab[,1],rr,tab[,3],ofac=ofac,fmax=fmax)
ylim <- range(median(per$power),max(per$power)+0.1*(max(per$power)-min(per$power)),per$sig.level)
# ylim <- c(min(median(per$power),0),1.1*max(per$power))
ylab <- 'Power'
}
if(per.type=='BGLS'){
per <- bgls(tab[,1],rr,tab[,3],ofac=ofac,fmax=fmax)
ylim <- range(median(per$power),max(per$power)+0.1*(max(per$power)-min(per$power)),per$sig.level)
if(RML){
ylab <- expression('log(ML/'*ML[max]*')')
}else{
ylab <- 'log(ML)'
}
}
if(per.type=='GLST'){
per <- glst(tab[,1],rr,tab[,3],ofac=ofac,fmax=fmax)
ylim <- range(median(per$power),max(per$power)+0.1*(max(per$power)-min(per$power)),per$sig.level)
ylab <- 'Power'
}
if(per.type=='LS'){
per <- lsp(times=tab[,1]-min(tab[,1]),x=rr,ofac=ofac,from=NULL,to=fmax,alpha=c(0.1,0.01,0.001))
ylim <- range(median(per$power),max(per$power)+0.1*(max(per$power)-min(per$power)),per$sig.level)
ylab <- 'Power'
}
# if(sd(rr)<sd(per$res)) break()
if(per.type=='MLP' | per.type=='BFP'){
plot(per$P,per$power,xlab='Period[d]',ylab=ylab,type='l',log='x',ylim=ylim,main=main)
}else{
plot(per$P,per$power,xlab='Period[d]',ylab=ylab,type='l',log='x',ylim=ylim,main=main)
}
if(is.null(inds)){
inds <- which(per$power.opt>max(per$sig.level))
if(length(inds)>0) inds <- inds[1:min(nshow,length(inds))]
}
abline(h=per$sig.level,lty=2)
if(length(inds)>0){
abline(v=per$ps[inds],col='red',lty=3,lwd=2)
text(x=per$ps[inds],y=per$power.opt[inds],pos=c(2,4),labels=paste0(format(per$ps[inds],digit=3),'d'),col='red')
}else{
abline(v=per$ps[inds],col='red',lty=3,lwd=2)
text(x=per$ps[inds],y=per$power.opt[inds],pos=4,offset=-0.1,labels=paste0(format(per$ps[inds],digit=3),'d'),col='red')
}
# if(per.type=='BFP' | per.type=='MLP'){
# if(per.type=='BFP' & all(per$power.opt<log(150)))
# break()
# if(per.type=='MLP' & all(per$power.opt<log(1000)))
# break()
# }else{
# if(max(per$power) < max(per$sig.level))
# break()
# }
}
}
}
################################################
#####PartV: save the data and plot periodograms
################################################
###save data
#obj.name <- paste0(fname,'.Robj')
#cat(obj.name,'\n')
#save(list = ls(all.names = TRUE),file=obj.name)
####output pdf
cat('output pdf:\n')
cat(pdf.name,'\n')
dev.off()