R/get_pars_surf.R
In smildiner/simHMM: Execute simulation study with mHMMbayes
Defines functions
get_pars_surf
Documented in
get_pars_surf
#' Load simulation parameters
#'
#' @export
get_pars_surf <- function(pars, baseline) {
# Legend
# pars[1] = sample_size
# pars[2] = n_t
# pars[3] = n_dep
# pars[4] = noisiness
# pars[5] = overlapping
# pars[6] = iter
# pars[7] = burnin
# pars[8] = repetitions
# pars[9] = scenario_uid
# pars[10] = uid
# pars[11:17] = .Random.seed
# Specify the correct gamma, emiss and eps_str
if(baseline == TRUE) {
gamma_sim <- matrix(c(0.9, 0.05, 0.05,
0.1, 0.7, 0.2,
0.2, 0.3, 0.5), ncol = 3, byrow = TRUE)
gamma_var <- matrix(c(1.12, 1.12,
0.16, 0.16,
0.13, 0.13), nrow = 3, byrow = TRUE)
} else {
gamma_sim <- matrix(c(0.9, 0.05, 0.05,
0.1, 0.7, 0.2,
0.2, 0.3, 0.5), ncol = 3, byrow = TRUE)
gamma_var <- matrix(c(1.12, 1.12,
0.16, 0.16,
0.13, 0.13), nrow = 3, byrow = TRUE)
# gamma_sim <- matrix(c(0.96, 0.02, 0.02,
# 0.03, 0.94, 0.03,
# 0.04, 0.04, 0.92), ncol = 3, byrow = TRUE)
}
emiss_sim <- list("low" = list(matrix(c(0.95, 0.02, 0.01, 0.01, 0.01,
0.02, 0.48, 0.48, 0.01, 0.01,
0.02, 0.01, 0.01, 0.48, 0.48), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.01, 0.01, 0.48, 0.48,
0.95, 0.02, 0.01, 0.01, 0.01,
0.02, 0.48, 0.48, 0.01, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.48, 0.48, 0.01, 0.01,
0.02, 0.01, 0.01, 0.48, 0.48,
0.95, 0.02, 0.01, 0.01, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.01, 0.48, 0.01, 0.48,
0.95, 0.02, 0.01, 0.01, 0.01,
0.02, 0.48, 0.01, 0.48, 0.01), nrow = 3, ncol = 5, byrow = T)),
"moderate" = list(matrix(c(0.95, 0.02, 0.01, 0.01, 0.01,
0.02, 0.48, 0.48, 0.01, 0.01,
0.02, 0.01, 0.48, 0.48, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.01, 0.01, 0.48, 0.48,
0.95, 0.02, 0.01, 0.01, 0.01,
0.02, 0.01, 0.48, 0.48, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.48, 0.01, 0.01, 0.48,
0.02, 0.01, 0.01, 0.48, 0.48,
0.95, 0.02, 0.01, 0.01, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.01, 0.48, 0.01, 0.48,
0.95, 0.02, 0.01, 0.01, 0.01,
0.02, 0.48, 0.01, 0.01, 0.48), nrow = 3, ncol = 5, byrow = T)),
"high" = list(matrix(c(0.02, 0.95, 0.01, 0.01, 0.01,
0.02, 0.48, 0.48, 0.01, 0.01,
0.02, 0.01, 0.48, 0.48, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.01, 0.01, 0.48, 0.48,
0.02, 0.01, 0.01, 0.01, 0.95,
0.02, 0.01, 0.48, 0.48, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.48, 0.01, 0.01, 0.48,
0.02, 0.01, 0.01, 0.48, 0.48,
0.02, 0.01, 0.01, 0.95, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.01, 0.48, 0.01, 0.48,
0.02, 0.01, 0.95, 0.01, 0.01,
0.02, 0.48, 0.01, 0.01, 0.48), nrow = 3, ncol = 5, byrow = T)))
eps_str <- list("low" = list(matrix(c(-4*1, 1, 1, 1, 1,
1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
-4*1, 1, 1, 1, 1,
1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
-4*1, 1, 1, 1, 1), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, -3/2*1/1.5,
-4*1, 1, 1, 1, 1,
1/1.5, -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T)),
"moderate" = list(matrix(c(-4*1, 1, 1, 1, 1,
1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
-4*1, 1, 1, 1, 1,
1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5,
1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
-4*1, 1, 1, 1, 1), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, -3/2*1/1.5,
-4*1, 1, 1, 1, 1,
1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T)),
"high" = list(matrix(c(1, -4*1, 1, 1, 1,
1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
1, 1, 1, 1, -4*1,
1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5,
1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
1, 1, 1, -4*1, 1), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, -3/2*1/1.5,
1, 1, -4*1, 1, 1,
1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T)))
emiss_var <- list("low" = list("low" = list(matrix(c(1.01, 1.01, 1.01, 1.01,
0.11, 0.11, 0.11, 0.11,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
1.01, 1.01, 1.01, 1.01,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
0.11, 0.11, 0.11, 0.11,
1.01, 1.01, 1.01, 1.01), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
1.01, 1.01, 1.01, 1.01,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T)),
"moderate" = list(matrix(c(0.60, 0.60, 0.60, 0.60,
0.14, 0.14, 0.14, 0.14,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.60, 0.60, 0.60, 0.60,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.14, 0.14, 0.14, 0.14,
0.60, 0.60, 0.60, 0.60), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.60, 0.60, 0.60, 0.60,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T)),
"high" = list(matrix(c(0.82, 0.82, 0.82, 0.82,
0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.82, 0.82, 0.82, 0.82,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17,
0.82, 0.82, 0.82, 0.82), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.82, 0.82, 0.82, 0.82,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T))),
"moderate" = list("low" = list(matrix(c(1.01, 1.01, 1.01, 1.01,
0.11, 0.11, 0.11, 0.11,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
1.01, 1.01, 1.01, 1.01,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
0.11, 0.11, 0.11, 0.11,
1.01, 1.01, 1.01, 1.01), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
1.01, 1.01, 1.01, 1.01,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T)),
"moderate" = list(matrix(c(0.60, 0.60, 0.60, 0.60,
0.14, 0.14, 0.14, 0.14,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.60, 0.60, 0.60, 0.60,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.14, 0.14, 0.14, 0.14,
0.60, 0.60, 0.60, 0.60), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.60, 0.60, 0.60, 0.60,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T)),
"high" = list(matrix(c(0.82, 0.82, 0.82, 0.82,
0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.82, 0.82, 0.82, 0.82,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17,
0.82, 0.82, 0.82, 0.82), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.82, 0.82, 0.82, 0.82,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T))),
"high" = list("low" = list(matrix(c(0.35, 0.35, 0.35, 0.35,
0.11, 0.11, 0.11, 0.11,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
0.35, 0.35, 0.35, 0.35,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
0.11, 0.11, 0.11, 0.11,
0.35, 0.35, 0.35, 0.35), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
0.35, 0.35, 0.35, 0.35,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T)),
"moderate" = list(matrix(c(0.15, 0.15, 0.15, 0.15,
0.14, 0.14, 0.14, 0.14,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.15, 0.15, 0.15, 0.15,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.14, 0.14, 0.14, 0.14,
0.15, 0.15, 0.15, 0.15), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.15, 0.15, 0.15, 0.15,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T)),
"high" = list(matrix(c(0.18, 0.18, 0.18, 0.18,
0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.18, 0.18, 0.18, 0.18,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17,
0.18, 0.18, 0.18, 0.18), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.18, 0.18, 0.18, 0.18,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T))))
# emiss_sim <- list("low" = list(matrix(c(0.96, 0.01, 0.01, 0.01, 0.01,
# 0.02, 0.47, 0.47, 0.02, 0.02,
# 0.02, 0.02, 0.02, 0.47, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.02, 0.47, 0.47, 0.02, 0.02,
# 0.96, 0.01, 0.01, 0.01, 0.01,
# 0.02, 0.02, 0.02, 0.47, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.96, 0.01, 0.01, 0.01,
# 0.47, 0.02, 0.47, 0.02, 0.02,
# 0.02, 0.02, 0.02, 0.47, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.47, 0.02, 0.47, 0.02, 0.02,
# 0.02, 0.02, 0.02, 0.47, 0.47,
# 0.01, 0.96, 0.01, 0.01, 0.01), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.01, 0.96, 0.01, 0.01,
# 0.47, 0.47, 0.02, 0.02, 0.02,
# 0.02, 0.02, 0.02, 0.47, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.01, 0.01, 0.96, 0.01,
# 0.02, 0.47, 0.47, 0.02, 0.02,
# 0.47, 0.02, 0.02, 0.02, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.02, 0.47, 0.47, 0.02, 0.02,
# 0.47, 0.02, 0.02, 0.02, 0.47,
# 0.01, 0.01, 0.01, 0.96, 0.01), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.01, 0.01, 0.01, 0.96,
# 0.02, 0.47, 0.47, 0.02, 0.02,
# 0.47, 0.02, 0.02, 0.47, 0.02), nrow = 3, ncol = 5, byrow = T)),
#
# "moderate" = list(matrix(c(0.96, 0.01, 0.01, 0.01, 0.01,
# 0.02, 0.47, 0.47, 0.02, 0.02,
# 0.02, 0.02, 0.47, 0.47, 0.02), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.02, 0.47, 0.47, 0.02, 0.02,
# 0.96, 0.01, 0.01, 0.01, 0.01,
# 0.02, 0.47, 0.02, 0.02, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.96, 0.01, 0.01, 0.01,
# 0.47, 0.02, 0.47, 0.02, 0.02,
# 0.02, 0.47, 0.02, 0.02, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.47, 0.02, 0.02, 0.02, 0.47,
# 0.02, 0.02, 0.02, 0.47, 0.47,
# 0.01, 0.96, 0.01, 0.01, 0.01), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.01, 0.96, 0.01, 0.01,
# 0.47, 0.02, 0.47, 0.02, 0.02,
# 0.02, 0.47, 0.02, 0.02, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.01, 0.01, 0.96, 0.01,
# 0.02, 0.47, 0.02, 0.02, 0.47,
# 0.47, 0.02, 0.02, 0.02, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.47, 0.47, 0.02, 0.02, 0.02,
# 0.47, 0.02, 0.02, 0.47, 0.02,
# 0.01, 0.01, 0.01, 0.01, 0.96), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.02, 0.47, 0.47, 0.02, 0.02,
# 0.01, 0.01, 0.01, 0.01, 0.96,
# 0.47, 0.02, 0.02, 0.02, 0.47), nrow = 3, ncol = 5, byrow = T)),
#
# "high" = list(matrix(c(0.01, 0.96, 0.01, 0.01, 0.01,
# 0.02, 0.47, 0.47, 0.02, 0.02,
# 0.02, 0.47, 0.47, 0.02, 0.02), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.02, 0.47, 0.02, 0.02, 0.47,
# 0.01, 0.01, 0.01, 0.01, 0.96,
# 0.02, 0.47, 0.02, 0.02, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.01, 0.96, 0.01, 0.01,
# 0.47, 0.02, 0.47, 0.02, 0.02,
# 0.47, 0.02, 0.47, 0.02, 0.02), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.02, 0.02, 0.02, 0.47, 0.47,
# 0.02, 0.02, 0.02, 0.47, 0.47,
# 0.01, 0.01, 0.01, 0.96, 0.01), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.02, 0.47, 0.02, 0.47, 0.02,
# 0.01, 0.01, 0.01, 0.96, 0.01,
# 0.02, 0.47, 0.02, 0.47, 0.02), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.47, 0.02, 0.47, 0.02, 0.02,
# 0.47, 0.02, 0.47, 0.02, 0.02,
# 0.96, 0.01, 0.01, 0.01, 0.01), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.47, 0.47, 0.02, 0.02, 0.02,
# 0.47, 0.47, 0.02, 0.02, 0.02,
# 0.01, 0.96, 0.01, 0.01, 0.01), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.47, 0.02, 0.47, 0.02, 0.02,
# 0.01, 0.01, 0.96, 0.01, 0.01,
# 0.47, 0.02, 0.47, 0.02, 0.02), nrow = 3, ncol = 5, byrow = T)))
#
# eps_str <- list("low" = list(matrix(c(-4*1, 1, 1, 1, 1,
# 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -4*1, 1, 1, 1, 1,
# 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, -4*1, 1, 1, 1,
# -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(-3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
# 1, -4*1, 1, 1, 1), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, 1, -4*1, 1, 1,
# -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5,
# 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, 1, 1, -4*1, 1,
# 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5,
# 1, 1, 1, -4*1, 1), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, 1, 1, 1, -4*1,
# 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T)),
#
# "moderate" = list(matrix(c(-4*1, 1, 1, 1, 1,
# 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -4*1, 1, 1, 1, 1,
# 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, -4*1, 1, 1, 1,
# -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(-3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5,
# 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
# 1, -4*1, 1, 1, 1), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, 1, -4*1, 1, 1,
# -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, 1, 1, -4*1, 1,
# 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5,
# -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(-3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5,
# -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5,
# 1, 1, 1, 1, -4*1), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1, 1, 1, 1, -4*1,
# -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T)),
#
# "high" = list(matrix(c(1, -4*1, 1, 1, 1,
# 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5,
# 1, 1, 1, 1, -4*1,
# 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, 1, -4*1, 1, 1,
# -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
# 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
# 1, 1, 1, -4*1, 1), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1/1.5, -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5,
# 1, 1, 1, -4*1, 1,
# 1/1.5, -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(-3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -4*1, 1, 1, 1, 1), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(-3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5,
# -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5,
# 1, -4*1, 1, 1, 1), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(-3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1, 1, -4*1, 1, 1,
# -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T)))
# Set the correct ones
emiss_sim <- emiss_sim[[as.character(pars[5])]]
eps_str <- eps_str[[as.character(pars[5])]]
# Set emission distribution with noisiness
eps <- as.numeric(pars[4])
emiss_sim <- lapply(seq_along(emiss_sim),function(e, emiss_sim, eps_str, eps) {emiss_sim[[e]] + eps_str[[e]]*eps}, emiss_sim, eps_str, eps)
# Set marker for noisiness
if(as.numeric(pars[4]) == 0.03){
noise <- "low"
} else if(as.numeric(pars[4]) == 0.09){
noise <- "moderate"
} else if(as.numeric(pars[4]) == 0.15){
noise <- "high"
}
# Return model parameters
return(list(sample_size = as.numeric(pars[1]),
n_t = as.numeric(pars[2]),
m = 3,
n_dep = as.numeric(pars[3]),
q_emiss = rep(5, as.numeric(pars[3])),
# gamma_var = 1,
# emiss_var = rep(1, as.numeric(pars[3])),
gamma_var = gamma_var,
emiss_var = emiss_var[[as.character(pars[5])]][[noise]],
noisiness = as.numeric(pars[4]),
overlapping = as.character(pars[5]),
iter = as.numeric(pars[6]),
burnin = as.numeric(pars[7]),
repetitions = as.numeric(pars[8]),
scenario_uid = pars[9],
uid = pars[10],
save_all = FALSE,
gamma_sim = gamma_sim,
emiss_sim = emiss_sim[1:as.numeric(pars[3])]))
}
smildiner/simHMM documentation built on July 17, 2022, 2 p.m.
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Defines functions get_pars_surf
Documented in get_pars_surf
#' Load simulation parameters
#'
#' @export
get_pars_surf <- function(pars, baseline) {
# Legend
# pars[1] = sample_size
# pars[2] = n_t
# pars[3] = n_dep
# pars[4] = noisiness
# pars[5] = overlapping
# pars[6] = iter
# pars[7] = burnin
# pars[8] = repetitions
# pars[9] = scenario_uid
# pars[10] = uid
# pars[11:17] = .Random.seed
# Specify the correct gamma, emiss and eps_str
if(baseline == TRUE) {
gamma_sim <- matrix(c(0.9, 0.05, 0.05,
0.1, 0.7, 0.2,
0.2, 0.3, 0.5), ncol = 3, byrow = TRUE)
gamma_var <- matrix(c(1.12, 1.12,
0.16, 0.16,
0.13, 0.13), nrow = 3, byrow = TRUE)
} else {
gamma_sim <- matrix(c(0.9, 0.05, 0.05,
0.1, 0.7, 0.2,
0.2, 0.3, 0.5), ncol = 3, byrow = TRUE)
gamma_var <- matrix(c(1.12, 1.12,
0.16, 0.16,
0.13, 0.13), nrow = 3, byrow = TRUE)
# gamma_sim <- matrix(c(0.96, 0.02, 0.02,
# 0.03, 0.94, 0.03,
# 0.04, 0.04, 0.92), ncol = 3, byrow = TRUE)
}
emiss_sim <- list("low" = list(matrix(c(0.95, 0.02, 0.01, 0.01, 0.01,
0.02, 0.48, 0.48, 0.01, 0.01,
0.02, 0.01, 0.01, 0.48, 0.48), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.01, 0.01, 0.48, 0.48,
0.95, 0.02, 0.01, 0.01, 0.01,
0.02, 0.48, 0.48, 0.01, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.48, 0.48, 0.01, 0.01,
0.02, 0.01, 0.01, 0.48, 0.48,
0.95, 0.02, 0.01, 0.01, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.01, 0.48, 0.01, 0.48,
0.95, 0.02, 0.01, 0.01, 0.01,
0.02, 0.48, 0.01, 0.48, 0.01), nrow = 3, ncol = 5, byrow = T)),
"moderate" = list(matrix(c(0.95, 0.02, 0.01, 0.01, 0.01,
0.02, 0.48, 0.48, 0.01, 0.01,
0.02, 0.01, 0.48, 0.48, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.01, 0.01, 0.48, 0.48,
0.95, 0.02, 0.01, 0.01, 0.01,
0.02, 0.01, 0.48, 0.48, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.48, 0.01, 0.01, 0.48,
0.02, 0.01, 0.01, 0.48, 0.48,
0.95, 0.02, 0.01, 0.01, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.01, 0.48, 0.01, 0.48,
0.95, 0.02, 0.01, 0.01, 0.01,
0.02, 0.48, 0.01, 0.01, 0.48), nrow = 3, ncol = 5, byrow = T)),
"high" = list(matrix(c(0.02, 0.95, 0.01, 0.01, 0.01,
0.02, 0.48, 0.48, 0.01, 0.01,
0.02, 0.01, 0.48, 0.48, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.01, 0.01, 0.48, 0.48,
0.02, 0.01, 0.01, 0.01, 0.95,
0.02, 0.01, 0.48, 0.48, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.48, 0.01, 0.01, 0.48,
0.02, 0.01, 0.01, 0.48, 0.48,
0.02, 0.01, 0.01, 0.95, 0.01), nrow = 3, ncol = 5, byrow = T),
matrix(c(0.02, 0.01, 0.48, 0.01, 0.48,
0.02, 0.01, 0.95, 0.01, 0.01,
0.02, 0.48, 0.01, 0.01, 0.48), nrow = 3, ncol = 5, byrow = T)))
eps_str <- list("low" = list(matrix(c(-4*1, 1, 1, 1, 1,
1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
-4*1, 1, 1, 1, 1,
1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
-4*1, 1, 1, 1, 1), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, -3/2*1/1.5,
-4*1, 1, 1, 1, 1,
1/1.5, -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T)),
"moderate" = list(matrix(c(-4*1, 1, 1, 1, 1,
1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
-4*1, 1, 1, 1, 1,
1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5,
1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
-4*1, 1, 1, 1, 1), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, -3/2*1/1.5,
-4*1, 1, 1, 1, 1,
1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T)),
"high" = list(matrix(c(1, -4*1, 1, 1, 1,
1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
1, 1, 1, 1, -4*1,
1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5,
1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
1, 1, 1, -4*1, 1), nrow = 3, ncol = 5, byrow = T),
matrix(c(1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, -3/2*1/1.5,
1, 1, -4*1, 1, 1,
1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T)))
emiss_var <- list("low" = list("low" = list(matrix(c(1.01, 1.01, 1.01, 1.01,
0.11, 0.11, 0.11, 0.11,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
1.01, 1.01, 1.01, 1.01,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
0.11, 0.11, 0.11, 0.11,
1.01, 1.01, 1.01, 1.01), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
1.01, 1.01, 1.01, 1.01,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T)),
"moderate" = list(matrix(c(0.60, 0.60, 0.60, 0.60,
0.14, 0.14, 0.14, 0.14,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.60, 0.60, 0.60, 0.60,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.14, 0.14, 0.14, 0.14,
0.60, 0.60, 0.60, 0.60), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.60, 0.60, 0.60, 0.60,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T)),
"high" = list(matrix(c(0.82, 0.82, 0.82, 0.82,
0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.82, 0.82, 0.82, 0.82,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17,
0.82, 0.82, 0.82, 0.82), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.82, 0.82, 0.82, 0.82,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T))),
"moderate" = list("low" = list(matrix(c(1.01, 1.01, 1.01, 1.01,
0.11, 0.11, 0.11, 0.11,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
1.01, 1.01, 1.01, 1.01,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
0.11, 0.11, 0.11, 0.11,
1.01, 1.01, 1.01, 1.01), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
1.01, 1.01, 1.01, 1.01,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T)),
"moderate" = list(matrix(c(0.60, 0.60, 0.60, 0.60,
0.14, 0.14, 0.14, 0.14,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.60, 0.60, 0.60, 0.60,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.14, 0.14, 0.14, 0.14,
0.60, 0.60, 0.60, 0.60), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.60, 0.60, 0.60, 0.60,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T)),
"high" = list(matrix(c(0.82, 0.82, 0.82, 0.82,
0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.82, 0.82, 0.82, 0.82,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17,
0.82, 0.82, 0.82, 0.82), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.82, 0.82, 0.82, 0.82,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T))),
"high" = list("low" = list(matrix(c(0.35, 0.35, 0.35, 0.35,
0.11, 0.11, 0.11, 0.11,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
0.35, 0.35, 0.35, 0.35,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
0.11, 0.11, 0.11, 0.11,
0.35, 0.35, 0.35, 0.35), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.11, 0.11, 0.11, 0.11,
0.35, 0.35, 0.35, 0.35,
0.11, 0.11, 0.11, 0.11), nrow = 3, ncol = 4, byrow = T)),
"moderate" = list(matrix(c(0.15, 0.15, 0.15, 0.15,
0.14, 0.14, 0.14, 0.14,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.15, 0.15, 0.15, 0.15,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.14, 0.14, 0.14, 0.14,
0.15, 0.15, 0.15, 0.15), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.14, 0.14, 0.14, 0.14,
0.15, 0.15, 0.15, 0.15,
0.14, 0.14, 0.14, 0.14), nrow = 3, ncol = 4, byrow = T)),
"high" = list(matrix(c(0.18, 0.18, 0.18, 0.18,
0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.18, 0.18, 0.18, 0.18,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.17, 0.17, 0.17, 0.17,
0.18, 0.18, 0.18, 0.18), nrow = 3, ncol = 4, byrow = T),
matrix(c(0.17, 0.17, 0.17, 0.17,
0.18, 0.18, 0.18, 0.18,
0.17, 0.17, 0.17, 0.17), nrow = 3, ncol = 4, byrow = T))))
# emiss_sim <- list("low" = list(matrix(c(0.96, 0.01, 0.01, 0.01, 0.01,
# 0.02, 0.47, 0.47, 0.02, 0.02,
# 0.02, 0.02, 0.02, 0.47, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.02, 0.47, 0.47, 0.02, 0.02,
# 0.96, 0.01, 0.01, 0.01, 0.01,
# 0.02, 0.02, 0.02, 0.47, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.96, 0.01, 0.01, 0.01,
# 0.47, 0.02, 0.47, 0.02, 0.02,
# 0.02, 0.02, 0.02, 0.47, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.47, 0.02, 0.47, 0.02, 0.02,
# 0.02, 0.02, 0.02, 0.47, 0.47,
# 0.01, 0.96, 0.01, 0.01, 0.01), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.01, 0.96, 0.01, 0.01,
# 0.47, 0.47, 0.02, 0.02, 0.02,
# 0.02, 0.02, 0.02, 0.47, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.01, 0.01, 0.96, 0.01,
# 0.02, 0.47, 0.47, 0.02, 0.02,
# 0.47, 0.02, 0.02, 0.02, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.02, 0.47, 0.47, 0.02, 0.02,
# 0.47, 0.02, 0.02, 0.02, 0.47,
# 0.01, 0.01, 0.01, 0.96, 0.01), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.01, 0.01, 0.01, 0.96,
# 0.02, 0.47, 0.47, 0.02, 0.02,
# 0.47, 0.02, 0.02, 0.47, 0.02), nrow = 3, ncol = 5, byrow = T)),
#
# "moderate" = list(matrix(c(0.96, 0.01, 0.01, 0.01, 0.01,
# 0.02, 0.47, 0.47, 0.02, 0.02,
# 0.02, 0.02, 0.47, 0.47, 0.02), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.02, 0.47, 0.47, 0.02, 0.02,
# 0.96, 0.01, 0.01, 0.01, 0.01,
# 0.02, 0.47, 0.02, 0.02, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.96, 0.01, 0.01, 0.01,
# 0.47, 0.02, 0.47, 0.02, 0.02,
# 0.02, 0.47, 0.02, 0.02, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.47, 0.02, 0.02, 0.02, 0.47,
# 0.02, 0.02, 0.02, 0.47, 0.47,
# 0.01, 0.96, 0.01, 0.01, 0.01), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.01, 0.96, 0.01, 0.01,
# 0.47, 0.02, 0.47, 0.02, 0.02,
# 0.02, 0.47, 0.02, 0.02, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.01, 0.01, 0.96, 0.01,
# 0.02, 0.47, 0.02, 0.02, 0.47,
# 0.47, 0.02, 0.02, 0.02, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.47, 0.47, 0.02, 0.02, 0.02,
# 0.47, 0.02, 0.02, 0.47, 0.02,
# 0.01, 0.01, 0.01, 0.01, 0.96), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.02, 0.47, 0.47, 0.02, 0.02,
# 0.01, 0.01, 0.01, 0.01, 0.96,
# 0.47, 0.02, 0.02, 0.02, 0.47), nrow = 3, ncol = 5, byrow = T)),
#
# "high" = list(matrix(c(0.01, 0.96, 0.01, 0.01, 0.01,
# 0.02, 0.47, 0.47, 0.02, 0.02,
# 0.02, 0.47, 0.47, 0.02, 0.02), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.02, 0.47, 0.02, 0.02, 0.47,
# 0.01, 0.01, 0.01, 0.01, 0.96,
# 0.02, 0.47, 0.02, 0.02, 0.47), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.01, 0.01, 0.96, 0.01, 0.01,
# 0.47, 0.02, 0.47, 0.02, 0.02,
# 0.47, 0.02, 0.47, 0.02, 0.02), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.02, 0.02, 0.02, 0.47, 0.47,
# 0.02, 0.02, 0.02, 0.47, 0.47,
# 0.01, 0.01, 0.01, 0.96, 0.01), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.02, 0.47, 0.02, 0.47, 0.02,
# 0.01, 0.01, 0.01, 0.96, 0.01,
# 0.02, 0.47, 0.02, 0.47, 0.02), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.47, 0.02, 0.47, 0.02, 0.02,
# 0.47, 0.02, 0.47, 0.02, 0.02,
# 0.96, 0.01, 0.01, 0.01, 0.01), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.47, 0.47, 0.02, 0.02, 0.02,
# 0.47, 0.47, 0.02, 0.02, 0.02,
# 0.01, 0.96, 0.01, 0.01, 0.01), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(0.47, 0.02, 0.47, 0.02, 0.02,
# 0.01, 0.01, 0.96, 0.01, 0.01,
# 0.47, 0.02, 0.47, 0.02, 0.02), nrow = 3, ncol = 5, byrow = T)))
#
# eps_str <- list("low" = list(matrix(c(-4*1, 1, 1, 1, 1,
# 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -4*1, 1, 1, 1, 1,
# 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, -4*1, 1, 1, 1,
# -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(-3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
# 1, -4*1, 1, 1, 1), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, 1, -4*1, 1, 1,
# -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5,
# 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, 1, 1, -4*1, 1,
# 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5,
# 1, 1, 1, -4*1, 1), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, 1, 1, 1, -4*1,
# 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T)),
#
# "moderate" = list(matrix(c(-4*1, 1, 1, 1, 1,
# 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -4*1, 1, 1, 1, 1,
# 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, -4*1, 1, 1, 1,
# -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(-3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5,
# 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
# 1, -4*1, 1, 1, 1), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, 1, -4*1, 1, 1,
# -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, 1, 1, -4*1, 1,
# 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5,
# -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(-3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5,
# -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5,
# 1, 1, 1, 1, -4*1), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1, 1, 1, 1, -4*1,
# -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T)),
#
# "high" = list(matrix(c(1, -4*1, 1, 1, 1,
# 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1/1.5, -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5,
# 1, 1, 1, 1, -4*1,
# 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1, 1, -4*1, 1, 1,
# -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
# 1/1.5, 1/1.5, 1/1.5, -3/2*1/1.5, -3/2*1/1.5,
# 1, 1, 1, -4*1, 1), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(1/1.5, -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5,
# 1, 1, 1, -4*1, 1,
# 1/1.5, -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(-3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# -4*1, 1, 1, 1, 1), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(-3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5,
# -3/2*1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5, 1/1.5,
# 1, -4*1, 1, 1, 1), nrow = 3, ncol = 5, byrow = T),
#
# matrix(c(-3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5,
# 1, 1, -4*1, 1, 1,
# -3/2*1/1.5, 1/1.5, -3/2*1/1.5, 1/1.5, 1/1.5), nrow = 3, ncol = 5, byrow = T)))
# Set the correct ones
emiss_sim <- emiss_sim[[as.character(pars[5])]]
eps_str <- eps_str[[as.character(pars[5])]]
# Set emission distribution with noisiness
eps <- as.numeric(pars[4])
emiss_sim <- lapply(seq_along(emiss_sim),function(e, emiss_sim, eps_str, eps) {emiss_sim[[e]] + eps_str[[e]]*eps}, emiss_sim, eps_str, eps)
# Set marker for noisiness
if(as.numeric(pars[4]) == 0.03){
noise <- "low"
} else if(as.numeric(pars[4]) == 0.09){
noise <- "moderate"
} else if(as.numeric(pars[4]) == 0.15){
noise <- "high"
}
# Return model parameters
return(list(sample_size = as.numeric(pars[1]),
n_t = as.numeric(pars[2]),
m = 3,
n_dep = as.numeric(pars[3]),
q_emiss = rep(5, as.numeric(pars[3])),
# gamma_var = 1,
# emiss_var = rep(1, as.numeric(pars[3])),
gamma_var = gamma_var,
emiss_var = emiss_var[[as.character(pars[5])]][[noise]],
noisiness = as.numeric(pars[4]),
overlapping = as.character(pars[5]),
iter = as.numeric(pars[6]),
burnin = as.numeric(pars[7]),
repetitions = as.numeric(pars[8]),
scenario_uid = pars[9],
uid = pars[10],
save_all = FALSE,
gamma_sim = gamma_sim,
emiss_sim = emiss_sim[1:as.numeric(pars[3])]))
}
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