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Run the FraNchEstYN crop–disease simulation or calibration

Source: R/franchestyn_batch.R
franchestyn_batch.Rd

Runs the FraNchEstYN model. The function prepares inputs (weather, management, parameters, reference) and launches the executable. Users do not manage paths or config files manually.

Usage

franchestyn_batch(
  weather_data,
  management_data,
  cropParameters = NULL,
  diseaseParameters = NULL,
  fungicideParameters = NULL,
  start_end = c(2000, 2025),
  ...,
  out_folder
)

Arguments

weather_data

A data frame of daily or hourly weather for one site only. The function will detect if input is daily or hourly. Column names are matched case-insensitively, ignoring spaces, underscores, and dashes.

Date columns (mandatory):

Provide the combination of year, month, day (and optionally hour for hourly data).

Meteorological variables:

Mandatory:

  • Daily inputs: tmax, tx, t2mmax, maxtemp (max temperature, °C), tmin, tn, t2mmin, mintemp (min temperature, °C), precipitation, prec, p, rainfall, rain (mm d\(^{-1}\)).

  • Hourly inputs: temp, temperature, t2m (air temperature, °C), precipitation, prec, precip, prectotcorr, rainfall, rain (mm h\(^{-1}\)).

Radiation or Latitude (one required):

  • Radiation: rad, solar, solarrad [MJ m\(^{-2}\) d\(^{-1}\)]

  • Latitude: lat, latitude, site_lat [decimal degrees]

If radiation is missing, it will be estimated from latitude and day length.

Optional variables (used if present, estimated otherwise):

  • Relative humidity: rh, humidity, relhumidity, relativehumidity (hourly), rhmax, rhx and rhmin, rhn (daily).

  • Leaf wetness: not required — computed internally from humidity > 90% or rainfall ≥ 0.2 mm/h.

management_data

A data frame with management information for the same site as weather_data. Column matching is case-insensitive; spaces/underscores/dashes are ignored and normalized to snake_case.

Required columns:

  • crop — character (e.g., "Wheat").

  • sowingDOY — integer DOY in [1, 366].

  • year — either an ISO year (YYYY) or the string "All".

Optional:

  • treatment — character with one or more fungicide dates separated by commas/semicolons (e.g., "12 Feb; 28 Feb").

cropParameters

A named list of crop parameters (see data(cropParameters)).

diseaseParameters

A named list of disease parameters (see data(diseaseParameters)).

fungicideParameters

Optional list of fungicide parameters (see data(fungicideParameters)).

start_end

Numeric vector of length 2. Start and end years for simulation (default: c(2000, 2025)).

out_folder

output folder path

Value

A list with elements: outputs, diagnostics, parameters, spooky_message.

Details

- Only one site per run. - Column names matched case-insensitively, tolerant to spaces, underscores, and dashes.

Examples

if (FALSE) { # \dontrun{
franchestyn(
  weather_data        = weather_df,
  management_data     = mgmt_df,
  reference_data      = ref_df,
  cropParameters      = cropParameters$wheat,
  diseaseParameters   = diseaseParameters$septoria,
  fungicideParameters = fungicideParameters$protectant,
  calibration         = "all",
  start_end           = c(2010, 2020),
  apikey              = "sk-or-v1-xxxx",
  franchy_message     = TRUE,
  iterations          = 200
)
} # }