R/get_pars.R
In smildiner/simHMM: Execute simulation study with mHMMbayes
Defines functions
get_pars
Documented in
get_pars
#' Load simulation parameters
#'
#' @export
get_pars <- function(uid) {
# Check that log file exists
# Load log
scenario <- readRDS("inputs/scenarios_log.rds")
# if(surf == TRUE){
# scenario <- readRDS("scenarios_log.rds")
# } else {
# scenario <- readRDS("inputs/scenarios_log.rds")
# }
# Select the incumbent scenario
scenario <- scenario[which(scenario[["uid"]] == uid),]
# Specify the correct gamma, emiss and eps_str
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(0.96, 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[[scenario[["overlapping"]]]]
eps_str <- eps_str[[scenario[["overlapping"]]]]
# Set emission distribution with noisiness
eps <- scenario[["noisiness"]]
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)
# Return model parameters
return(list(sample_size = scenario[["sample_size"]],
n_t = scenario[["n_t"]],
m = scenario[["m"]],
n_dep = scenario[["n_dep"]],
q_emiss = rep(scenario[["q_emiss"]], scenario[["n_dep"]]),
gamma_var = scenario[["gamma_var"]],
emiss_var = rep(scenario[["emiss_var"]], scenario[["n_dep"]]),
noisiness = scenario[["noisiness"]],
overlapping = scenario[["overlapping"]],
iter = scenario[["iter"]],
burnin = scenario[["burnin"]],
repetitions = scenario[["repetitions"]],
scenario_uid = scenario[["scenario_uid"]],
uid = scenario[["uid"]],
save_all = scenario[["save_all"]],
gamma_sim = gamma_sim,
emiss_sim = emiss_sim[1:scenario[["n_dep"]]]))
}
smildiner/simHMM documentation built on July 17, 2022, 2 p.m.
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Defines functions get_pars
Documented in get_pars
#' Load simulation parameters
#'
#' @export
get_pars <- function(uid) {
# Check that log file exists
# Load log
scenario <- readRDS("inputs/scenarios_log.rds")
# if(surf == TRUE){
# scenario <- readRDS("scenarios_log.rds")
# } else {
# scenario <- readRDS("inputs/scenarios_log.rds")
# }
# Select the incumbent scenario
scenario <- scenario[which(scenario[["uid"]] == uid),]
# Specify the correct gamma, emiss and eps_str
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(0.96, 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[[scenario[["overlapping"]]]]
eps_str <- eps_str[[scenario[["overlapping"]]]]
# Set emission distribution with noisiness
eps <- scenario[["noisiness"]]
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)
# Return model parameters
return(list(sample_size = scenario[["sample_size"]],
n_t = scenario[["n_t"]],
m = scenario[["m"]],
n_dep = scenario[["n_dep"]],
q_emiss = rep(scenario[["q_emiss"]], scenario[["n_dep"]]),
gamma_var = scenario[["gamma_var"]],
emiss_var = rep(scenario[["emiss_var"]], scenario[["n_dep"]]),
noisiness = scenario[["noisiness"]],
overlapping = scenario[["overlapping"]],
iter = scenario[["iter"]],
burnin = scenario[["burnin"]],
repetitions = scenario[["repetitions"]],
scenario_uid = scenario[["scenario_uid"]],
uid = scenario[["uid"]],
save_all = scenario[["save_all"]],
gamma_sim = gamma_sim,
emiss_sim = emiss_sim[1:scenario[["n_dep"]]]))
}
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