tests/testthat/test-vit_mHMM.R

In mHMMbayes: Multilevel Hidden Markov Models Using Bayesian Estimation

context("obtaining state sequence using Viterbi")

## general properties tested model
n_t <- 100
n <- 10
m <- 3
J = 11
burn_in = 5
n_dep <- 2
q_emiss <- c(4,2)

gamma <- matrix(c(0.8, 0.1, 0.1,
                  0.2, 0.6, 0.2,
                  0.1, 0.2, 0.7), ncol = m, byrow = TRUE)
emiss_distr <- list(matrix(c(0.45, 0.45, 0.05, 0.05,
                             0.1, 0.05, 0.8, 0.05,
                             0.1, 0.1, 0.2, 0.6), nrow = m, ncol = q_emiss[1], byrow = TRUE),
                    matrix(c(0.7, 0.3,
                             0.9, 0.1,
                             0.8, 0.2), nrow = m, ncol = q_emiss[2], byrow = TRUE)
)

set.seed(4231)
data_sim <- sim_mHMM(n_t = n_t, n = n, gen = list(m= m, n_dep = n_dep, q_emiss = q_emiss), gamma = gamma,
                     emiss_distr = emiss_distr, var_gamma = .5, var_emiss = c(.5, 0.5))
colnames(data_sim$obs) <- c("subj", "output_1", "output_2")

# Fit the mHMM on 2 dep variable data
set.seed(3523)
out_2st_simb <- mHMM(s_data = data_sim$obs,
                     gen = list(m = m, n_dep = n_dep, q_emiss = q_emiss),
                     start_val = c(list(gamma), emiss_distr),
                     mcmc = list(J = J, burn_in = burn_in), show_progress = FALSE)


####################
## TESTING
###############

test_that("expected errors viterbi", {
  expect_error(vit_mHMM(out_2st_simb, s_data = data_sim$obs, burn_in = 10), "burn in period should be at least 2 points smaller")
  ab <- c(2,3,4)
  expect_error(vit_mHMM(ab, s_data = data_sim$obs), "should be from the class mHMM")
  expect_error(vit_mHMM(out_2st_simb, s_data = data_sim$obs[1:200,]), "number of subjects in the datasets")
})

test_that("output viterbi", {
  states1 <- vit_mHMM(out_2st_simb, s_data = data_sim$obs)
  expect_equal(dim(states1), c(n_t * n, 2))
  expect_equal(sort(unique(states1[,2])), c(1:m))
  expect_equal(sum(states1[,2]), 1890)
})