R/complete_soilphys.R

In valentingar/ConFluxPro: A toolkit for soil gas analysis

#' @title (Re-)calculate soil physical parameters
#'
#' @description This function completes the soilphys dataset by calculating
#'   different parameters if necessary, as long as all required parameters are
#'   available. Diffusion coefficients, as well as the air density are
#'   calculated if missing.
#'
#' @param soilphys (dataframe) the soilphys dataframe
#' @param DSD0_formula (character) A character vector defining the way DSD0
#'   should be calculated. Must refer to existing columns in soilphys. See
#'   examples below.
#' @param gases (character) A character vector defining the gases for which to
#'   calculate D0 and DS.
#' @param overwrite (logical) If true, already existing columns are overwritten.
#'
#' @param quiet (logical) Suppress messages.
#'
#' @examples soilphys <- complete_soilphys(soilphys, DSD0_formula = "a*AFPS^b")
#'
#'
#' @seealso D0_massman
#'
#' @family soilphys
#' @export
#'

complete_soilphys <- function(soilphys,
                              DSD0_formula = NULL,
                              gases = NULL,
                              overwrite = TRUE,
                              quiet = FALSE){

  if (quiet){
    soilphys <- suppressMessages(do_complete_soilphys(
      soilphys = soilphys,
      DSD0_formula =DSD0_formula,
      gases = gases,
      overwrite = overwrite))
  } else{
    soilphys <- do_complete_soilphys(soilphys = soilphys,
                                     DSD0_formula =DSD0_formula,
                                     gases = gases,
                                     overwrite = overwrite)
  }

  soilphys

}


do_complete_soilphys <- function(soilphys,
                                 DSD0_formula = NULL,
                                 gases = NULL,
                                 overwrite = TRUE){
  df_names <- names(soilphys)
  if (all(c("depth","upper","lower","TPS","SWC","t","p") %in% df_names)==FALSE){
    stop("there are essential parameters missing. please run check_soilphys()")
  }

  stopifnot("Must provide a valid DSD0_formula!" = (!is.null(DSD0_formula)))

  gas_present_flag <- "gas" %in% names(soilphys)
  AFPS_flag <- !("AFPS" %in% df_names)
  DSD0_flag <- !("DSD0" %in% df_names)
  DS_flag <- !("DS" %in% df_names)
  D0_flag <- !("D0" %in% df_names)
  c_air_flag <- !("c_air" %in% df_names)

  if (AFPS_flag == TRUE | overwrite == TRUE ){
    soilphys$AFPS <- soilphys$TPS - soilphys$SWC
  }
  if (DSD0_flag == TRUE | overwrite == TRUE){

    soilphys <- soilphys %>%
      dplyr::select(!dplyr::any_of("DSD0")) %>%
      dplyr::mutate(DSD0 = !!(rlang::parse_expr(DSD0_formula)))

    if (any_negative_values(soilphys$DSD0)){
      message("Negative DSD0 calculated, setting NA!")
      soilphys$DSD0[soilphys$DSD0 < 0] <- NA
    }
  }
  if (D0_flag == TRUE | overwrite == TRUE){



    if(is.null(gases) & !gas_present_flag){
      stop("No gases argument provided and 'gas' column missing in soilphys!")
    }

    # if gases is already present, no need to apply new ones!
    if(gas_present_flag){
      if (!is.null(gases)){
        message("gas-column found in soilphys, ignoring 'gases' argument.")
      }
    } else {

      #otherwise: for each row, add new gases
      soilphys <- soilphys %>%
        dplyr::cross_join(data.frame(gas = gases))
    }

    # then calculate D0 based on that.
    soilphys$D0 <- D0_massman(soilphys$gas,
                              soilphys$t,
                              soilphys$p)

    if (any_negative_values(soilphys$D0)){
      message("Negative D0 calculated, setting NA!")
      soilphys$D0[soilphys$D0 < 0] <- NA
    }

  }

  if(DS_flag == TRUE | overwrite == TRUE){
    soilphys$DS <- soilphys$DSD0 * soilphys$D0

    if (any_negative_values(soilphys$DS)){
      message("Negative DS calculated, setting NA!")
      soilphys$DS[soilphys$DS < 0] <- NA
    }

  }

  if(c_air_flag == TRUE | overwrite == TRUE){
    soilphys$c_air <-  (soilphys$p*100 / (8.314 * (273.15 + soilphys$t)))

    if (any_negative_values(soilphys$c_air)){
      message("Negative c_air calculated, setting NA!")
      soilphys$c_air[soilphys$c_air < 0] <- NA
    }
  }

  col_names <-
    c("AFPS",
      "DSD0",
      "D0",
      "DS",
      "c_air")

  col_added <-
    c(AFPS_flag,
      DSD0_flag,
      D0_flag,
      DS_flag,
      c_air_flag)

  if (any(col_added)){
    message(paste0("The following columns were added: ",
                   paste0(col_names[col_added == TRUE],
                          collapse = " ")))
  }
  if(overwrite == TRUE){
    message(paste0(("The following columns were overwritten: "),
                   paste0(col_names[col_added == FALSE],
                          collapse = " ")))

  }
  soilphys
}