3. Preprocessing_Determine_comorbidities.R

rm(list = ls())

# Load necessary packages
library(readr)
library(jsonlite)
library(dplyr)

# Read the data from CSV files
POM_allvisits <- read_csv("M:/Documents/Projecten/Covid-19 survey/Data and analysis/PEP data/Data files/POM_allvisits.csv")
POM_precov <- read_csv("M:/Documents/Projecten/Covid-19 survey/Data and analysis/PEP data/Data files/POM_precovid_visit.csv")

# Initialize a list to store the processed data
precov <- vector("list", length = nrow(POM_precov))

# Process the data from JSON files
for (i in 1:nrow(POM_precov)) {
  sub_folder <- paste0("P:/3022026.01/pep/ClinVars4/", POM_precov$Subj_ID[i])
  visit_folder <- paste0(sub_folder, "/ses-POMVisit", POM_precov$precov[i])
  
  if (file.exists(file.path(visit_folder, "Castor.Visit", POM_precov$precov[i], 
                            "Demografische_vragenlijsten.Andere_ziekten.json"))) {
    json_file <- paste0(visit_folder, "/Castor.Visit", POM_precov$precov[i], 
                        ".Demografische_vragenlijsten.Andere_ziekten.json")
    Comorb <- fromJSON(json_file)
    precov[[i]] <- list(
      Subj_ID = POM_precov$Subj_ID[i],
      precov = POM_precov$precov[i],
      Comorb_present = as.numeric(Comorb$crf$OthSelfDisease)
    )
    
    if (precov[[i]]$Comorb_present == 1) {
      precov[[i]]$Nr_comorb <- length(Comorb$reports$ZiektenAndersDeelnemer)
    } else {
      precov[[i]]$Nr_comorb <- 0
    }
  } else {
    precov[[i]] <- list(
      Subj_ID = POM_precov$Subj_ID[i],
      precov = POM_precov$precov[i],
      Comorb_present = 0
    )
    cat("For subj.", POM_precov$Subj_ID[i], ", comorbidities are unknown.\n")
  }
}

# Convert the list to a data frame and add to pre-COVID visit data file
precov <- bind_rows(precov)
POM_precov <- cbind(POM_precov, precov[3])

# Save csv file with PPP pre-COVID visit data where comorbidies present (yes/no) is included as column
Write.csv(POM_precov,"M:/Documents/Projecten/Covid-19 survey/Data and analysis/PEP data/Data files/POM_precovid_visit.csv", row.names = FALSE)