R/obsSim_consistency.R

In SticsRPacks/CroptimizR: A Package to Estimate Parameters of Crop Models

#' @title Try to make observation and simulation lists consistent if possible
#'
#' @param sim_list List of simulated values
#' @param obs_list List of observed values
#'
#' @return A list containing consistent obs and sim lists
#'
#' @details This function checks and fix the homogeneity of types of obs and sim
#'  Date columns
#'
#' @keywords internal
#'
make_obsSim_consistent <- function(sim_list, obs_list) {

  # Check homogeneity of types of obs and sim Date columns
  # ------------------------------------------------------

  isPosixObs <- sapply(
    obs_list,
    function(x) lubridate::is.POSIXct(x$Date)
  )
  isAllPosixObs <- all(isPosixObs)
  isDateObs <- sapply(
    obs_list,
    function(x) lubridate::is.Date(x$Date)
  )
  isAllDateObs <- all(isDateObs)
  isPosixSim <- sapply(
    sim_list,
    function(x) lubridate::is.POSIXct(x$Date)
  )
  isAllPosixSim <- all(isPosixSim)
  isDateSim <- sapply(
    sim_list,
    function(x) lubridate::is.Date(x$Date)
  )
  isAllDateSim <- all(isDateSim)

  if (!all(isPosixObs | isDateObs)) {
    stop(paste(
  "Error: incorrect format for Date column of observation list for situations",
      paste(names(obs_list)[!(isPosixObs | isDateObs)], collapse = ", "),
      ". \n Date columns should be of type Date or POSIXct."
    ))
  }
  if (!all(isPosixSim | isDateSim)) {
    stop(paste(
    "Error: incorrect format for Date column of simulation list for situations",
      paste(names(sim_list)[!(isPosixSim | isDateSim)], collapse = ", "),
      ". \n Date columns should be of type Date or POSIXct."
    ))
  }

  # if types of obs$*$Date are not homogeneous => convert obs$*$Date to the
  # format of sim$*$Date
  if (!isAllPosixObs && !isAllDateObs) {
    if (isAllPosixSim) {
      sapply(
        names(obs_list),
        function(x) {
          obs_list[[x]]$Date <<- as.POSIXct(as.character(obs_list[[x]]$Date),
            tz = "UTC"
          )
        }
      )
      isAllPosixObs <- TRUE
    } else if (isAllDateSim) {
      sapply(
        names(obs_list),
        function(x) obs_list[[x]]$Date <<- as.Date(obs_list[[x]]$Date)
      )
      isAllDateObs <- TRUE
    } else {
      sapply(
        names(obs_list),
        function(x) {
          obs_list[[x]]$Date <<- as.POSIXct(as.character(obs_list[[x]]$Date),
            tz = "UTC"
          )
        }
      )
      isAllPosixObs <- TRUE
    }
  }

  # if types of sim$*$Date are not homogeneous => convert sim$*$Date
  # to the format of obs$*$Date
  if (!isAllPosixSim && !isAllDateSim) {
    if (isAllPosixObs) {
      sapply(
        names(sim_list),
        function(x) {
          sim_list[[x]]$Date <<- as.POSIXct(as.character(sim_list[[x]]$Date),
            tz = "UTC"
          )
        }
      )
      isAllPosixSim <- TRUE
    } else if (isAllDateObs) {
      sapply(
        names(sim_list),
        function(x) sim_list[[x]]$Date <<- as.Date(sim_list[[x]]$Date)
      )
      isAllDateSim <- TRUE
    }
  }

  # if types of Date in Sim and Obs are different => convert obs$*$Date
  # to the format of sim$*$Date
  if (isAllPosixSim && isAllDateObs) {
    sapply(
      names(obs_list),
      function(x) {
        obs_list[[x]]$Date <<- as.POSIXct(as.character(obs_list[[x]]$Date),
          tz = "UTC"
        )
      }
    )
  } else if (isAllDateSim && isAllPosixObs) {
    sapply(
      names(obs_list),
      function(x) obs_list[[x]]$Date <<- as.Date(obs_list[[x]]$Date)
    )
  }

  return(list(obs_list = obs_list, sim_list = sim_list))
}


#' @title Check the consistency of observation and simulation lists
#'
#' @param sim_list List of simulated values
#' @param obs_list List of observed values
#'
#' @details This function checks:
#' (i) that Date columns in obs and sim are either in Date or POSIXct formats
#' (ii) that variables in obs and sim list have same types and are numeric
#'
#' @keywords internal
#'
check_obsSim_consistency <- function(sim_list, obs_list) {

  # Check homogeneity of types of obs and sim Date columns
  # ------------------------------------------------------

  isPosixObs <- sapply(
    obs_list,
    function(x) lubridate::is.POSIXct(x$Date)
  )
  isDateObs <- sapply(
    obs_list,
    function(x) lubridate::is.Date(x$Date)
  )
  isPosixSim <- sapply(
    sim_list,
    function(x) lubridate::is.POSIXct(x$Date)
  )
  isDateSim <- sapply(
    sim_list,
    function(x) lubridate::is.Date(x$Date)
  )

  if (!all(isPosixObs | isDateObs)) {
    stop(paste(
  "Error: incorrect format for Date column of observation list for situations",
      paste(names(obs_list)[!(isPosixObs | isDateObs)], collapse = ", "),
      ". \n Date columns should be of type Date or POSIXct."
    ))
  }
  if (!all(isPosixSim | isDateSim)) {
    stop(paste(
    "Error: incorrect format for Date column of simulation list for situations",
      paste(names(sim_list)[!(isPosixSim | isDateSim)], collapse = ", "),
      ". \n Date columns should be of type Date or POSIXct."
    ))
  }

  # Check that variables in obs and sim list have same types
  # --------------------------------------------------------

  situations <- intersect(names(obs_list), names(sim_list))
  nonCoherent_sit <- NULL
  nonNumeric_sit <- NULL
  for (situation in situations) {
    var_names <- intersect(
      names(obs_list[[situation]]),
      names(sim_list[[situation]])
    )
    var_names <- setdiff(var_names, c("Date", "Plant"))
    is_num_obs <- sapply(
      var_names,
      function(x) is.numeric(obs_list[[situation]][[x]])
    )
    is_num_sim <- sapply(
      var_names,
      function(x) is.numeric(sim_list[[situation]][[x]])
    )
    if (!all(is_num_obs) | !all(is_num_sim)) {
      nonNumeric_sit <- c(nonNumeric_sit, situation)
    }
    if (!all(is_num_obs == is_num_sim)) {
      nonCoherent_sit <- c(nonCoherent_sit, situation)
    }
  }
  if (!is.null(nonCoherent_sit)) {
    stop(paste(
      "Error: some variables in observation and simulation lists have different types for situations",
      paste(nonCoherent_sit, collapse = ",")
    ))
  }
  if (!is.null(nonNumeric_sit)) {
    warning(paste(
      "some variables in observation and simulation lists are non numeric for situations",
      paste(nonNumeric_sit, collapse = ",")
    ))
  }
}


#' @title Check if sim contains inf/na values when there are observations
#'
#' @param sim_list List of simulated values
#' @param obs_list List of observed values
#' @param param_values vector of input parameters used in the simulations
#'
#' @keywords internal
#'
is_sim_inf_or_na <- function(sim_list, obs_list, param_values) {

  res <- FALSE
  mess <- ""

  # check presence of Inf/NA in simulated results where obs is not NA
  for (sit in names(sim_list)) {

    var_list <- lapply(names(sim_list[[sit]]), function(x) {
      if (any(is.infinite(sim_list[[sit]][!is.na(obs_list[[sit]][,x]),][[x]])) ||
          any(is.na(sim_list[[sit]][!is.na(obs_list[[sit]][,x]),][[x]]))) {
        return(list(sim_list[[sit]]$Date[(is.infinite(sim_list[[sit]][[x]]) &
                                                        !is.na(obs_list[[sit]][,x])) |
                                           (is.na(sim_list[[sit]][[x]]) &
                                                    !is.na(obs_list[[sit]][,x]))]))
      }  else {
        return(NULL)
      }
    })

    names(var_list) <- names(sim_list[[sit]])

    if (!is.null(unlist(var_list))) {
      mess <- paste(mess,
        paste("\n  for situation ",sit,
        ", variable(s):",
        paste(sapply(names(var_list), function(x) {
          if (!is.null(var_list[[x]])) {
            paste("\n    o",x," at date(s) ",
                  paste(var_list[[x]][[1]], collapse = ", "))
          } else {
            return("")
          }
        }),collapse="")
      ))
      res <- TRUE
    }

  }
  if (res) {
    warning("\n\nSimulated values are NA or Inf," ,mess, ",\nwhen using input parameters: ",
            paste(names(param_values), collapse = ", "), ", with values: ",
            paste(param_values, collapse = ", "))
  }
  return(res)

}