R/GetR0AtSpecificDate.R

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

#' @import xtable
#' @export

GetR0AtSpecificDate <- function(ode_list, dateR0, popsize_name, NationalName){

  R0 <- as.data.frame(matrix(NA, length(ode_list)+1, 2))
  colnames(R0) <- c("Reg", "R0")
  indivParams  <- read.table(paste(here::here(), '/MonolixFile/', "/outputMonolix/", ode_list[[1]]$nameproject, "/IndividualParameters/estimatedIndividualParameters.txt", sep=""),
                           header=TRUE, sep=",")
  popsize_per_id <- rep(0, length(ode_list))
  R0$Reg <- c(as.character(indivParams$id), NationalName)
  dateR0 <- as.Date(dateR0)
  Rt <- as.data.frame(matrix(NA, length(ode_list), 1))
  Rtmin <- as.data.frame(matrix(NA, length(ode_list), 1))
  Rtmax <- as.data.frame(matrix(NA, length(ode_list), 1))

  for (id in 1:length(ode_list)){
    popsize_per_id[id] <- ode_list[[id]]$parameter[names(ode_list[[id]]$parameter)==popsize_name]
    Rt[id, 1] <- ode_list[[id]]$R0[which((as.Date(ode_list[[id]]$R0[, "date"])==dateR0) & (ode_list[[id]]$R0[, "obs_id"]==2)), "R0"]
    Rtmin[id, 1] <- ode_list[[id]]$R0[which((as.Date(ode_list[[id]]$R0[, "date"])==dateR0) & (ode_list[[id]]$R0[, "obs_id"]==2)), "R0_min"]
    Rtmax[id, 1] <- ode_list[[id]]$R0[which((as.Date(ode_list[[id]]$R0[, "date"])==dateR0) & (ode_list[[id]]$R0[, "obs_id"]==2)), "R0_max"]
    R0$R0[id] <- paste(format(round(Rt[id, 1], 2), nsmall=0), " [",
                     format(round(Rtmin[id, 1], 2), nsmall=0), ";",
                     format(round(Rtmax[id, 1], 2), nsmall=0), "]", sep="")
  }
  R0$R0[length(ode_list)+1] <- paste(format(round(sum(Rt[, 1]*(popsize_per_id))/sum(popsize_per_id), 2), nsmall=2), " [",
                                   format(round(sum(Rtmin[, 1]*(popsize_per_id))/sum(popsize_per_id), 2), nsmall=2), ";",
                                   format(round(sum(Rtmax[, 1]*(popsize_per_id))/sum(popsize_per_id), 2), nsmall=2), "]", sep="")

  print(xtable(R0), include.rownames = FALSE,
        file = paste(here::here(), '/MonolixFile/', "/outputMonolix/", ode_list[[1]]$nameproject, "/R0_", as.character(dateR0), ".txt", sep=""))
  return(R0)
}