periCosinor <-
function(data,adjmean=TRUE,plot=TRUE){
op <- par(no.readonly = TRUE) # the whole list of settable par's.
if(adjmean==TRUE) adjust<-mean(data) else adjust<-0
n<-length(data)
nfft<-(n/2)+1
#browser()
if (n%%2!=0) {data<-c(data,mean(data))} # taper odd length series with mean of data
first<-fft(data-adjust)/(n/2) # Fast Fourier Transform
realpart<-Re(first[1:nfft])
imagpart<- -Im(first[1:nfft])
peri<-(n/2)*(realpart^2+imagpart^2) # Periodogram
f<-(0:(n/2))*pi*2/n # Frequencies in radians
c<-pi*2/f # Frequencies in cycles
c[1]<-NA
amp<-sqrt(realpart^2+imagpart^2)
phase<-vector(mode="numeric",length=nfft) # phase in scale [0,2pi]
# phase in [0,2pi]
for (j in 2:(nfft-1)){
if (imagpart[j]==0 && realpart[j]==0){
ph<-1
} else {
ph<-atan(imagpart[j]/realpart[j])
}
if (realpart[j]>=0) {phase[j]<-ph}
if (realpart[j]<0&imagpart[j]>=0) {phase[j]<-ph+pi}
if (realpart[j]<0&imagpart[j]<0) {phase[j]<-ph-pi}
# Refinetti calcs for 4th condition -- poorer results
#if (imagpart[j]>0&realpart[j]>=0) {phase[j]<-ph}
#if (realpart[j]<0&imagpart[j]>=0) {phase[j]<ph-pi}
#if (realpart[j]<=0&imagpart[j]<0) {phase[j]<-ph-pi}
#if (imagpart[j]<=0&realpart[j]>0) {phase[j]<- -2*pi+ph}
# put in 0 to 2pi range
if (phase[j]<0) { phase[j]<-phase[j]+(2*pi)}
if (phase[j]>(2*pi)) { phase[j]<-phase[j]-(2*pi)}
}
#print(phase)
## Plot
if(plot==TRUE){
par(mfrow=c(3,1))
plot(f,peri,ylab='Periodogram',xlab='Frequency (radians)',type='h',xaxp=c(0,pi,4))
plot(c[2:nfft],peri[2:nfft],ylab='Periodogram',xlab='Cycles',type='h')
}
return(list(peri=peri,f=f,c=c,amp=amp,phase=phase,realpart=realpart,imagpart=imagpart,nfft=nfft))
#remove read only list components
op$cin<-NULL
op$cra<-NULL
op$csi<-NULL
op$cxy<-NULL
op$din<-NULL
op$page<-NULL
par(op) # restore graphic settings
}
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