Additional Code/OPTIMA_TEST.R

In benenns/OUD-Model: Semi-Markov Decision Model

library(dplyr)    # to manipulate data
library(reshape2) # to transform data
library(ggplot2)  # for nice looking plots
library(tidyverse)

# Call model setup functions
# To-do: Move into package eventually
source("R/OPTIMA_00_input_parameter_functions.R")
source("R/OPTIMA_01_model_setup_functions.R")

# Load parameters
# BNX scenario
l_params_BUP <- load_all_params(file.init = "data/init_params.csv",
                                file.init_dist = "data/init_dist_bup.csv", # Change initial distributions (100% in BUP)
                                file.mort = "data/all_cause_mortality.csv",
                                file.death_hr = "data/death_hr.csv",
                                file.frailty = "data/frailty.csv",
                                file.weibull_scale = "data/weibull_scale.csv",
                                file.weibull_shape = "data/weibull_shape.csv",
                                file.unconditional = "data/unconditional.csv",
                                file.overdose = "data/overdose.csv",
                                file.hiv = "data/hiv_sero.csv",
                                file.hcv = "data/hcv_sero.csv",
                                file.costs = "data/costs.csv",
                                file.crime_costs = "data/crime_costs.csv",
                                file.qalys = "data/qalys.csv")

# Methadone scenario
l_params_MET <- load_all_params(file.init = "data/init_params.csv",
                                file.init_dist = "data/init_dist_met.csv", # Change initial distributions (100% in MET)
                                file.mort = "data/all_cause_mortality.csv",
                                file.death_hr = "data/death_hr.csv",
                                file.frailty = "data/frailty.csv",
                                file.weibull_scale = "data/weibull_scale.csv",
                                file.weibull_shape = "data/weibull_shape.csv",
                                file.unconditional = "data/unconditional.csv",
                                file.overdose = "data/overdose.csv",
                                file.hiv = "data/hiv_sero.csv",
                                file.hcv = "data/hcv_sero.csv",
                                file.costs = "data/costs.csv",
                                file.crime_costs = "data/crime_costs.csv",
                                file.qalys = "data/qalys.csv")

### Main deterministic model outputs ###
# Run Markov model and return outputs
MET <- l_out_markov <- markov_model(l_params_all = l_params_MET, err_stop = FALSE, verbose = TRUE)
BUP  <- l_out_markov <- markov_model(l_params_all = l_params_BUP, err_stop = FALSE, verbose = TRUE)