R/make_some_infective.R

In IhsanKhaliq/ascotraceR: Simulate the Spread of Ascochyta Blight in Chickpea

#' Makes infected growing points sources for spore dispersal
#'
#' @param spore_packet A data.table with three variables, 'x', 'y' and
#'   'spores_per_packet'.
#' @param daily_vals A list of the current day's values and paddock `data.table`
#' @param latent_period Latent period in cumulative degree days (sum of daily
#'   temperature means) is the period between infection and production of
#'   lesions on susceptible growing points. Defaults to `200`.
#' @param cdd_at_infection Cumulative degree days when infection occurred.
#' @param susceptible_gp Represents non-infected growing points.
#' @param  infectious_gp Represents sporulating lesions.
#' @param  max_growing_points_limit Are the maximum number of growing points per
#'   square metre. Defaults to `5000`.
#' @param paddock A `data.table` detailing the growing points and infections.
#'
#' @return updated `daily_vals` list object
#' @keywords internal
#' @noRd

make_some_infective <- function(daily_vals,
                                latent_period = 200) {
  cdd_at_infection <- x <- y <- susceptible_gp <- spores_per_packet <-
    infectious_gp <-
    max_growing_points_limit <- min_growing_points <- NULL

  newly_exposed <- daily_vals[["exposed_gps"]]

  newly_infectious <-
    newly_exposed[cdd_at_infection + latent_period <= daily_vals[["cdd"]], ]


  for (i_row in seq_len(NROW(newly_infectious))) {
    # save on time data filtering
    row_index <-
      daily_vals[["paddock"]][x == newly_infectious[i_row, x] &
                                y == newly_infectious[i_row, y],
                              which = TRUE]
    paddock_vals <- daily_vals[["paddock"]][row_index, ]


    if (paddock_vals[, susceptible_gp] <
        newly_infectious[i_row, spores_per_packet]) {
      infections_new <-
        random_integer_from_real(paddock_vals[, susceptible_gp])
      daily_vals[["paddock"]][row_index, susceptible_gp := 0]
    } else{
      infections_new <- newly_infectious[i_row, spores_per_packet]
      daily_vals[["paddock"]][row_index, susceptible_gp :=
                                paddock_vals[, susceptible_gp] - infections_new]
    }

    daily_vals[["paddock"]][row_index, infectious_gp :=
                              daily_vals[["paddock"]][row_index, infectious_gp] +
                              infections_new]

  }

  daily_vals[["exposed_gps"]] <-
    newly_exposed[cdd_at_infection + latent_period > daily_vals[["cdd"]], ]

  # This line is here due to https://github.com/Rdatatable/data.table/issues/869
  daily_vals[["paddock"]]

  return(daily_vals)
}