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R3744/HCV_model_exeAllCases.R
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HCV_model_exeAllCases.R
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#############Executable file ######################################
#########################################
### Scenario: We need to choose the treatment scenario that we want to apply
### Simulation starts at time of HCV infection
### This file include all the required packages, and call all the required sources
### In this file the Cohort Size and the duration of simulation are defined.
#####################################################################
cat("\014")
cat('\n')
cat('***********************************************************\n')
cat('Mathematical Modeling of Hepatitis C Virus Progression Disease\n')
cat('\t \t 2017')
cat('\n')
cat('\n \t Version: 10')
cat('\n Requires files: \n')
cat('simulate_cohort.R: To do the simulation \n')
cat('baseline.R: Identify the baseline chracteristics \n')
cat('hazard_fun.R: Calls file specifying the hazard functions \n')
cat('params_cov.R: To choose parameters file \n')
cat('scenario_treatFx.R: To choose the treatment scenario \n')
cat('simulate_cohort.R: To do the simulation \n')
cat('TransitionTime.R: Shows all the possible transitions\n')
cat('***********************************************************\n')
#############################################################
rm(list = ls())
wd = getwd()
######################### Required Packages #################
require(MASS)
require(msm)
require(mstate)
require(survival)
require(splines)
require(plyr)
require(gems)
#########################################################
start.time <- Sys.time()
current_dir = getwd()
###############################################################
### The parameters that we can change to have different scenarios!
###############################################################
cohortSize <- 50 # specify how many patients to simulate
maxTime <- 100 # specify duration of simulation in years
#diag_ind <- readline(prompt = "Please enter the screening scenario: 1.Baseline,2.Birth, 3.IDU, 4.ex_IDU")
diag_ind = 1
#ans <- readline(prompt="Please enter the treatment scenario you are interested to study: Treating patients in (and after) stage F0, F1, F2, F3, F4 or BL (baseline) \t")
ans <- "All"
FP_scenario <- 1
########################################################
data <- read.table("baseline_data.txt", header = T)
all_cases = matrix(NA,1,52 + 13)
diag_scenario = c("Baseline","Birth","IDU", "ex_IDU")
#################################################################
for (case in 1:nrow(data))
{
print(case)
#####################Source Codes ###########################
source("baseline.R") # call file specifying baseline characteristics
source(sprintf("scenario_treat%s.R",ans))
source("hazard_fun.R") # call file specifying the hazard functions
source("params_cov.R") #choose parameters file
source("TransitionTime.R")
source("sim_cohort.R") # call the cohort simulator
######################################################
#setwd(wd)
# setwd("../Tables")
#########################################################
mainDir <- wd
today <- Sys.Date()
dd = format(today, format = "%B%d%Y")
subDir <- sprintf("outputDirectoryTreat_%s_%s_%s",diag_scenario[diag_ind],ans,dd)
dir.create(file.path(mainDir, subDir), showWarnings = FALSE)
wd = setwd(file.path(mainDir, subDir))
mainDir <- wd
setwd(file.path(mainDir, subDir))
write.table(cohort@time.to.state, sprintf("treat%s%s_%s",ans,case, dd))
########################################################
write.table(cbind(cohort@time.to.state, bl), sprintf("treat%s_baseline%s_%s_%s",ans,case,diag_scenario[diag_ind], dd))
all_cases = rbind(as.matrix(all_cases),as.matrix(read.table(sprintf("treat%s_baseline%s_%s_%s",ans,case,diag_scenario[diag_ind], dd))))
setwd(current_dir)
}
#####################################
end.time <- Sys.time()
cat('***********************************************************\n')
print("Required time: ")
print(end.time - start.time)
cat('***********************************************************\n')
cat('You can find all the required data in the Table "all_cases"!! \n')
cat('all_cases are saved in Required_Data folder with suffix of date \n')
today <- Sys.Date()
dd = format(today, format = "%B%d%Y")
write.table(all_cases, sprintf("All_casestreat%s_%s_%s_%s",ans,case,diag_scenario[diag_ind], dd))
write.table(all_cases, sprintf("All_casestreat%s_%s_%s_%s.csv",ans,case,diag_scenario[diag_ind], dd))
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