tpm_phsmm {LaMa}

Build all transition probability matrices of an periodic-HSMM-approximating HMM

Description

Hidden semi-Markov models (HSMMs) are a flexible extension of HMMs. For direct numerical maximum likelhood estimation, HSMMs can be represented as HMMs on an enlarged state space (of size M) and with structured transition probabilities. This function computes the transition matrices of a periodically inhomogeneos HSMMs.

Usage

tpm_phsmm(omega, dm, eps = 1e-10)

Arguments

omega

Embedded transition probability matrix. Either a matrix of dimension c(N,N) for homogeneous conditional transition probabilities, or an array of dimension c(N,N,L) for inhomogeneous conditional transition probabilities.

dm

State dwell-time distributions arranged in a list of length(N). Each list element needs to be a matrix of dimension c(L, N_i), where each row t is the (approximate) probability mass function of state i at time t.

eps

Rounding value: If an entry of the transition probabily matrix is smaller, than it is rounded to zero.

Value

An array of dimension c(N,N,L), containing the extended-state-space transition probability matrices of the approximating HMM for each time point of the cycle.

Examples

N = 3
L = 24
# time-varying mean dwell times
Lambda = exp(matrix(rnorm(L*N, 2, 0.5), nrow = L))
sizes = c(25, 25, 25) # approximating chain with 75 states
# state dwell-time distributions
dm = list()
for(i in 1:3){
  dmi = matrix(nrow = L, ncol = sizes[i])
  for(t in 1:L){
    dmi[t,] = dpois(1:sizes[i]-1, Lambda[t,i])
  }
  dm[[i]] = dmi
}

## homogeneous conditional transition probabilites
# diagonal elements are zero, rowsums are one
omega = matrix(c(0,0.5,0.5,0.2,0,0.8,0.7,0.3,0), nrow = N, byrow = TRUE)

# calculating extended-state-space t.p.m.s
Gamma = tpm_phsmm(omega, dm)

## inhomogeneous conditional transition probabilites
# omega can be an array
omega = array(rep(omega,L), dim = c(N,N,L))
omega[1,,4] = c(0, 0.2, 0.8) # small change for inhomogeneity

# calculating extended-state-space t.p.m.s
Gamma = tpm_phsmm(omega, dm)