LaMa (version 1.0.0)

forward: Forward algorithm with homogeneous transition probability matrix

Description

Forward algorithm with homogeneous transition probability matrix

Usage

forward(delta, Gamma, allprobs, trackInd = NULL)

Value

Log-likelihood for given data and parameters

Arguments

delta

Initial or stationary distribution of length N, or matrix of dimension c(k,N) for k independent tracks, if trackInd is provided

Gamma

Transition probability matrix of dimension c(N,N), or array of k transition probability matrices of dimension c(N,N,k), if trackInd is provided.

allprobs

Matrix of state-dependent probabilities/ density values of dimension c(n, N)

trackInd

Optional vector of length k containing the indices that correspond to the beginning of separate tracks. If provided, the total log-likelihood will be the sum of each track's likelihood contribution. In this case, Gamma can be a matrix, leading to the same transition probabilities for each track, or an array of dimension c(N,N,k), with one (homogeneous) transition probability matrix for each track. Furthermore, instead of a single vector delta corresponding to the initial distribution, a delta matrix of initial distributions, of dimension c(k,N), can be provided, such that each track starts with it's own initial distribution.

Examples

## generating data from homogeneous 2-state HMM
mu = c(0, 6)
sigma = c(2, 4)
Gamma = matrix(c(0.5, 0.05, 0.15, 0.85), nrow = 2, byrow = TRUE)
delta = c(0.5, 0.5)
# simulation
s = x = rep(NA, 500)
s[1] = sample(1:2, 1, prob = delta)
x[1] = rnorm(1, mu[s[1]], sigma[s[1]])
for(t in 2:500){
  s[t] = sample(1:2, 1, prob = Gamma[s[t-1],])
  x[t] = rnorm(1, mu[s[t]], sigma[s[t]])
}

## negative log likelihood function
mllk = function(theta.star, x){
  # parameter transformations for unconstraint optimization
  Gamma = tpm(theta.star[1:2])
  delta = stationary(Gamma) # stationary HMM
  mu = theta.star[3:4]
  sigma = exp(theta.star[5:6])
  # calculate all state-dependent probabilities
  allprobs = matrix(1, length(x), 2)
  for(j in 1:2){ allprobs[,j] = dnorm(x, mu[j], sigma[j]) }
  # return negative for minimization
  -forward(delta, Gamma, allprobs)
}

## fitting an HMM to the data
theta.star = c(-2,-2,0,5,log(2),log(3))
mod = stats::nlm(mllk, theta.star, x = x)