R/ComputeConfidenceIntervalAllId.R

In sistm/SEIRcovid19: Interface Monolix for multilevel modeling of epidemic dynamics

#' @export
ComputeConfidenceIntervalAllId <- function(ode_list, nb_mc, is_global, TimeDependantParameter=c()){
  # Get the optimisation result

  indivParams  <- read.table(paste(here::here(), '/MonolixFile/', "/outputMonolix/", ode_list[[1]]$nameproject, "/IndividualParameters/estimatedIndividualParameters.txt",
                                   sep=""),
                             header=TRUE, sep=",")
  popParams <- read.table(paste(here::here(), '/MonolixFile/', "/outputMonolix/", ode_list[[1]]$nameproject, "/populationParameters.txt",
                                sep=""),
                          header=TRUE, sep=",")
  data <- read.table(ode_list[[1]]$DataInfo$File,
                     sep = ode_list[[1]]$DataInfo$Sep,
                     header = TRUE)
  InputNames <- colnames(data)
  timename <- InputNames[ode_list[[1]]$DataInfo$HeaderType == "time"]
  for (index_id in 1:length(indivParams$id)){
    # Compute CI for each ID and set result
    ode_list[[index_id]] <- ComputeConfidenceInterval(ode_list[[index_id]],
                                                      indivParams, popParams,
                                                      index_id, nb_mc, is_global,
                                                      timename, TimeDependantParameter)
  }
  return (ode_list)
}