R/data_w_no_age.R

In covid19br/nowcaster: Nowcaster

#' @title data.w_no_age
#'
#' @description Function to put the data into the format proper to the nowcasting estimation,
#' has to use the maximum of data present on the last week parsed to the estimation.
#' Makes the account of maximum days per week to be used. With no age structure.
#'
#' @param dataset dataset to be formatted as data by week
#' @param trim.data How much to trim of the data?
#' @param date_onset Column of dates of onset of the events, normally date of onset of first symptoms of cases
#' @param date_report Column of dates of report of the event, normally date of digitation of the notification of cases
#' @param use.epiweek If TRUE, it uses the CDC epiweek definition where the week starts on Sunday, if FALSE it the week ends at the weekday of the last record date.
#' @param K How much weeks to forecast ahead?
#' [Default] K is 0, no forecasting ahead
#'
#' @return Data in weeks format, with the maximum dates for the last week used
#' @export
#'
#' @examples If the last data is at a Sunday, so the week starts at Monday before.
#' If ends at Thursday, so it starts on the Friday before
data.w_no_age<-function(dataset,
                        trim.data,
                        date_onset,
                        date_report,
                        use.epiweek = FALSE,
                        K=0,
                        silent=F){
  if(!silent){
    ## Last digitation date considered
    if(missing(trim.data)){
      trim.data <-  0
      warning("Using default, no trimming out of the data")
    } else {
      warning("Using default, trimming out ",
              trim.data ,
              " days of data",
              call. = T)
    }
  }else{
    ## Trim.data
    trim.data <-  0
  }

  ## Transforming trim.data into days
  trim.data.w <- 7*trim.data

  ## K parameter of forecasting
  K.w<-7*K

  ## Maximum date to be considered on the estimation (Last day)
  DT_max <- max(dataset |>
                  dplyr::pull(var = {{date_report}}),
                na.rm = T) - trim.data.w + K.w


  ## Day of the week of the last day
  DT_max_diadasemana <- as.integer(format(DT_max, "%w"))

  ## Ignore data after the last Sunday of recording (Sunday as too)
  aux.trimming.date = ifelse( use.epiweek | DT_max_diadasemana == 6, DT_max_diadasemana + 1, 0)

  ## Accounting for the maximum of days on the last week to be used
  data_w <- dataset |>
    dplyr::rename(date_report = {{date_report}},
                  date_onset = {{date_onset}}) |>
    dplyr::filter(date_report <= DT_max - aux.trimming.date) |>
    dplyr::mutate(
      ## Onset date
      # Moving the date to sunday
      DT.sun.aux = as.integer(format(date_onset, "%w")),
      ## Altering the date for the first day of the week
      dt.aux = date_onset -
        # Last recording date (DT_max_diadasemana) is the last day of the new week format
        DT.sun.aux +
        ifelse( use.epiweek, 0, DT_max_diadasemana+1 -
                  ifelse(DT_max_diadasemana+1>DT.sun.aux,7, 0)
                ),
      date_onset = dt.aux - ifelse( date_onset < dt.aux, 7, 0),
      # Recording date
      DT.sun.aux = as.integer(format(date_report, "%w")),
      ## Altering the date for the first day of the week
      dt.aux = date_report -
        # Last recording date (DT_max_diadasemana) is the last day of the new week format
        DT.sun.aux +
        ifelse( use.epiweek, 0, DT_max_diadasemana+1 -
                  ifelse(DT_max_diadasemana+1 > DT.sun.aux,7, 0)
        ),
      date_report = dt.aux - ifelse( date_report < dt.aux, 7, 0),
      Delay = as.numeric(date_report - date_onset) / 7
      ) |>
    dplyr::select(-dt.aux, -DT.sun.aux) |>
    dplyr::filter(Delay >= 0)

  # Returning the data
  return(data_w)
}