R/examples/Pois_twoStates.R

In pneff93/HMM: Fitting a Hidden Markov Model

##RESULTS:
#Both methods estimate the parameters with high speed and accurately



#transition matrix
gamma <- matrix(c(0.8, 0.2, 0.3, 0.7), byrow = TRUE, nrow = 2)

#initial state probabilities
delta <- c(0.3, 0.7)

#sample size
n <- 1000

x <- c()
set.seed(10)
s1 <- rpois(10000, 10)
s2 <- rpois(10000, 2)

#initial state
random_number <- runif(1, 0, 1)

if (random_number < delta[1]){
  p <- 1
  x[1] <- sample(s1, 1, replace = FALSE)
} else {
  p <- 2
  x[1] <- sample(s2, 1, replace = FALSE)
}

#sample creation
for (i in 2:n){
  random_number <- runif(1, 0, 1)
  if (random_number < gamma[p,1]){
    p <- 1
    x[i] <- sample(s1, 1, replace = FALSE)
  } else {
    p <- 2
    x[i] <- sample(s2, 1, replace = FALSE)
  }
}


#likelihoods
L1 <- function(x, lambda){
  p1 <- lambda^x / factorial(x) * exp(-lambda)
  return(p1)
}


L2 <- function(x, lambda){
  p2 <- lambda^x / factorial(x) * exp(-lambda)
  return(p2)
}


#number of states 
m <- 2

HMM(x = x, m = m, method = "EM", L1 = L1, L2 = L2)
HMM(x = x, m = m, method = "DM", L1 = L1, L2 = L2)