R/getConfFromData.R

In babsim.hospital: Bartz & Bartz Simulation Hospital

#' @title getConfFromData
#'
#' @description  Generate a configuration list for babsimTools based on the data file and the
#' vector of resources.
#' This function returns the default configuration settings of the babsimTools functions
#' used to run \code{\link{babsimHospital}}.
#'
#' @details  Configuration \code{conf}  is a list of the following settings.
#' \describe{
#'     \item{\code{seed}}{(int) Initial seed. Default: 123}
#'     \item{\code{simRepeats}}{(int) Number of \code{\link[simmer]{simmer}} simulation runs. Default: 1}
#'     \item{\code{parallel}}{(logical) Use parallel simulations based on \code{\link[parallel]{mclapply}}. Default: FALSE}
#'     \item{\code{perCores}}{(num) Percentage of cores used, if \code{parallel == TRUE}. Default: 0.5}
#'     \item{\code{ICU}}{(logical) Use ICU (RKI) data. Default: FALSE.}
#'     \item{\code{logLevel}}{(int) 0 = no logging, >= 1 logging. Default: 0. If larger than 10, shown detailed simmer output.}
#'     \item{\code{maxCapacity}}{(num) Maximum capacity used for \code{\link{babsimHospital}} resources. Default: 1e6.}
#'     \item{\code{dataset}}{(chr)  'GA' or 'ICU'. Default: 'GA'.}
#'     \item{\code{simulationDates}}{ List with the following entries:
#'       \describe{
#'       \item{\code{StartDate}}{(chr) Start date of the simulation data (infection data used to generate
#'       arrival times), first day. Default: '2020-03-03'}
#'       \item{\code{EndDate}}{(chr) End date of the simulation data, last day. Default: '2020-06-24'}
#'     }}
#'     \item{\code{fieldDates}}{ List with the following entries:
#'       \describe{
#'       \item{\code{StartDate}}{(chr) Start date of the field (resources)  data, first day. Default: '2020-03-03'}
#'       \item{\code{EndDate}}{(chr) End date of the field data, last day. Default: '2020-06-24'}
#'     }}
#'    \item{\code{simulationData}}{(data frame) Data used for the simulation. Default \code{\link{dataCovidBeds20200624}}
#'     \describe{
#'   \item{bed}{int  2 2 3 3 3 3 3 3 4 4 ...}
#'   \item{intensiveBed}{int  0 0 0 0 0 0 0 0 0 0 ...}
#'   \item{intensiveBedVentilation}{int  0 0 0 0 0 0 0 0 0 0 ...}
#'   \item{Day}{Date, format: '2020-03-03' '2020-03-04' '2020-03-05' '2020-03-06' ...}
#'   \item{Infected}{num  5 0 0 0 0 0 0 7 2 5 ...}
#'   \item{Sick}{num  5 5 5 5 5 5 5 12 14 19 ...}
#'    }}
#'     \item{\code{fieldEvents}}{(data frame) Data used for evalution of the simulation. Default \code{\link{GABeds220200624}}
#'    \describe{
#'   \item{ressource}{chr  'bed' 'bed' 'bed' 'bed' ...}
#'   \item{time}{int  1 2 3 4 5 6 7 8 9 10 ...}
#'   \item{med}{int  2 2 3 3 3 3 3 3 4 4 ...}
#'   \item{source}{int  2 2 3 3 3 3 3 3 4 4 ...}
#'   \item{date}{Date, format: '2020-03-03' '2020-03-04' '2020-03-05' '2020-03-06' ...}
#'    }}
#'     \item{\code{resource}}{(vector) Resources used in the simulation.
#'     Default: \code{c('bed', 'intensiveBed', 'intensiveBedVentilation')}. For ICU data use:
#'     \code{c('bed', 'intensiveBedVentilation')}
#'    \describe{
#'   \item{ressource}{chr  'bed' 'bed' 'bed' 'bed' ...}
#'   \item{time}{int  1 2 3 4 5 6 7 8 9 10 ...}
#'   \item{med}{int  2 2 3 3 3 3 3 3 4 4 ...}
#'   \item{source}{int  2 2 3 3 3 3 3 3 4 4 ...}
#'   \item{date}{Date, format: '2020-03-03' '2020-03-04' '2020-03-05' '2020-03-06' ...}
#'    }}
#'   }
#'
#' @param conf Configuration. Default: \code{\link{babsimToolsConf}}
#' @param simData Simulation data. Default: \code{\link{dataCovidBeds20200624}}
#' @param fieldData Field (real) data. Default: \code{\link{dataCovidBeds20200624}}
#' @return a list
#'
#' @examples
#'
#' conf <- babsimToolsConf()
#' simData <- babsim.hospital::dataCovidBeds20200624
#' fieldData <- babsim.hospital::dataCovidBeds20200624
#' conf <- getConfFromData(
#'   conf = conf,
#'   simData = simData,
#'   fieldData = fieldData
#' )
#' # turn on parallel simulation:
#' conf$parallel <- TRUE
#' # Change the start date of the simulations
#' conf$simulationDates$StartDate <- "2020-01-01"
#' @export
#'
getConfFromData <- function(conf, simData, fieldData) {
  conf$simulationDates <- list(StartDate = min(simData$Day), EndDate = max(simData$Day))
  if (is.null(fieldData)) {
    ## fieldData can be null in the case of a continued SubSimulation
    conf$start <- conf$simulationDates$StartDate
    conf$end <- conf$simulationDates$EndDate
  } else {
    conf$fieldDates <- list(StartDate = min(fieldData$Day), EndDate = max(fieldData$Day))
    conf$start <- max(conf$simulationDates$StartDate, conf$fieldDates$StartDate)
    conf$end <- min(conf$simulationDates$EndDate, conf$fieldDates$EndDate)
  }
  return(conf)
}