NHMSAR (version 1.4)

Cond.prob.MSAR:

Description

Computes, for each time \(t\), the conditional probabilities for MSAR models \(P(Y_t|y_{1:(t-1)},y_{(t+1):T})\) where \(Y\) is the observed process and \(y\) the observed time series.

Usage

Cond.prob.MSAR(data, theta, yrange = NULL, covar.emis = NULL, covar.trans = NULL)

Arguments

data

observed time series, array of dimension T*N.samples*d

theta

object of class MSAR including the model's parameter and description. See init.theta.MSAR for more details.

yrange

values at which to compute the conditional probabilities

covar.emis

emission covariate if any.

covar.trans

transition covariate if any.

Value

a list including

..$yrange

values at which the conditional probabilities are computed

..$prob

conditional probabilities for each time t and each values of yrange

..$Yhat

mode of the conditinal distribution for each time t

See Also

predict.MSAR

Examples

data(lynx)
data = array(log10(lynx),c(length(lynx),1,1))
T = length(data)
theta.init = init.theta.MSAR(data,M=2,order=2,label="HH")
mod.lynx.hh = fit.MSAR(data,theta.init,verbose=TRUE,MaxIter=200)
ex = 100:114
lex = length(ex)
tps = (1821:1934)[ex] 
CP = Cond.prob.MSAR(array(data[ex,,],c(lex,1,1)), mod.lynx.hh$theta)
par(mfrow=c(2,1))
plot(tps,data[ex],typ="l",main="Homogeneous MSAR model",xlab="Time",ylab="Captured")
lines(tps,CP$Yhat,col="red")
alpha = .05
IC.emp = matrix(0,2,lex)
for (k in 1:lex) {
	tmp = cumsum(CP$prob[,k,])/sum(CP$prob[,k,])
	IC.emp[1,k] = CP$yrange[max(c(which(tmp<alpha/2),1))]
	IC.emp[2,k] = CP$yrange[min(max(which(tmp<(1-alpha/2))),length(CP$yrange))]
}
lines(tps,IC.emp[1,],lty=2,col="red")
lines(tps,IC.emp[2,],lty=2,col="red")

## Not run
#order = 2
#theta.init = init.theta.MSAR(data,M=2,order=2,label="NH",nh.transitions="logistic")
#theta.init$A0 = mod.lynx.hh$theta$A0
#theta.init$A = mod.lynx.hh$theta$A
#theta.init$sigma = mod.lynx.hh$theta$sigma
#theta.init$transmat = mod.lynx.hh$theta$transmat
#theta.init$prior = mod.lynx.hh$theta$prior
Y = array(data[2:T,,],c(T-1,1,1))
Z = array(data[1:(T-1),,],c(T-1,1,1))
#mod.lynx = fit.MSAR(array(Y,theta.init,covar.trans=Z)
Y.ex = array(data[ex,,],c(lex,1,1))
Z.ex = array(data[ex-1,,],c(lex,1,1))
#CPnh = Cond.prob.MSAR(Y.ex,mod.lynx$theta,covar.trans = Z.ex)
#
#plot(tps,data[ex],typ="l",main="Non Homogeneous MSAR model",xlab="Time",ylab="Captured")
#lines(tps,CPnh$Yhat,col="red")
#IC.emp = matrix(0,2,lex)
#for (k in 1:lex) {
#	tmp = cumsum(CPnh$prob[,k,])/sum(CPnh$prob[,k,])
#	IC.emp[1,k] = CPnh$yrange[max(c(which(tmp<alpha/2),1))]
#	IC.emp[2,k] = CPnh$yrange[min(max(which(tmp<(1-alpha/2))),length(CP$yrange))]
#}
#lines(tps,IC.emp[1,],lty=2,col="red")
#lines(tps,IC.emp[2,],lty=2,col="red")