# spectrum of recruits Splus

rec_scan("E:\\Stat207\\Class\\Examples\\Ch2\\recruit.dat")

help(spec.pgram) # to get details
# see the difference
par(mfrow=c(2,2))
spec.pgram(rec, spans=1, taper=0.1, pad=0, detrend=F, demean=T, plot=T)
spec.pgram(rec, spans=3, taper=0.1, pad=0, detrend=F, demean=T, plot=T)
spec.pgram(rec, spans=c(3,3), taper=0.1, pad=0, detrend=F, demean=T, plot=T)
spec.pgram(rec, spans=c(3,5), taper=0.1, pad=0, detrend=F, demean=T, plot=T)
# note spectrum() does the same thing as spec.pgram

# AR spectral estimate for recruits
rec.ar <- ar(rec)      # Fit an AR model using AIC
rec.ar$aic             # to see which model is chosen (p=13)
par(mfrow=c(1,1))
rec.arspec <- spec.ar(rec.ar,plot=T) 	#  superimpose the AR spectrum for this
rec.per <- spec.pgram(rec)          	# data and its periodogram.  
spec.plot(rec.per, add=T)

# Coherency between SOI and Recruits
x1_matrix(soi)
x2_matrix(rec)
x_cbind(x1,x2)
spec_spec.pgram(x, spans=c(3,5), taper=0.1, pad=0, detrend=F, demean=T, plot=T)
rho_spec$coh
length(rho)
length(x1)
freq_(1:length(rho)-1)/length(x1)
plot(freq,rho,type="l")