This is suitable for n=1, and doesn't matter if warmup>0 armax.sim works fine, but hydromad treats length(init)>1 as an unspecified parameter. armax.sim(U=c(1,rep(0,20)),a_1=0.1,a_2=0.1,b_0=1,init=as.numeric(Murrindindi$Q[1:2])) armax.sim(U=c(1,rep(0,20)),a_1=0.1,a_2=0.1,b_0=1,init=as.numeric(Murrindindi$Q[1]))