cost_rmse_pmodel: Cost function computing RMSE for calibration of P-model...

In stineb/rsofun: The P-Model and BiomeE Modelling Framework

Cost function computing RMSE for calibration of P-model parameters

Description

The cost function performs a P-model run for the input drivers and parameter values, and compares the output to observations of various targets by computing the root mean squared error (RMSE).

Usage

cost_rmse_pmodel(
  par,
  obs,
  drivers,
  targets,
  par_fixed = NULL,
  target_weights = NULL,
  parallel = FALSE,
  ncores = 2
)

Arguments

par	A vector of values for the parameters to be calibrated (a subset of those described in runread_pmodel_f, in order).
obs	A nested data.frame of observations, with columns 'sitename' and 'data' (see p_model_validation or p_model_validation_vcmax25 to check their structure).
drivers	A nested data.frame of driver data. See p_model_drivers for a description of the data structure.
targets	A character vector indicating the target variables for which the optimization will be done and the RMSE computed. This string must be a column name of the data data.frame belonging to the validation nested data.frame (for example 'gpp').
par_fixed	A named list of model parameter values to keep fixed during the calibration. These should complement the input par such that all model parameters are passed on to runread_pmodel_f.
target_weights	A vector of weights to be used in the computation of the RMSE if using several targets. By default (target_weights = NULL) the RMSE is computed separately for each target and then averaged. The provided weights are used to compute a weighted average of RMSE across targets.
parallel	A logical specifying whether simulations are to be parallelised (sending data from a certain number of sites to each core). Defaults to FALSE.
ncores	An integer specifying the number of cores used for parallel computing. Defaults to 2.

Details

To run the P-model, all model parameters must be given. The cost function uses arguments par and par_fixed such that, in the calibration routine, par can be updated by the optimizer and par_fixed are kept unchanged throughout calibration.

If the validation data contains a "date" column (fluxes), the simulated target time series is compared to the observed values on those same dates (e.g. for GPP). Otherwise, there should only be one observed value per site (leaf traits), and the outputs (averaged over the growing season, weighted by predicted GPP) will be compared to this single value representative of the site (e.g. Vcmax25). As an exception, when the date of a trait measurement is available, it will be compared to the trait value predicted on that date.

Value

The root mean squared error (RMSE) between observed values and P-model predictions. The RMSE is computed for each target separately and then aggregated (mean or weighted average).

Examples

# Compute RMSE for a set
# of model parameter values
# and example data
cost_rmse_pmodel(
 par = c(0.05, -0.01, 0.5),  # kphio related parameters
 obs = p_model_validation,
 drivers = p_model_drivers,
 targets = c('gpp'),
 par_fixed = list(
  soilm_thetastar    = 0.6 * 240,  # old setup with soil moisture stress
  soilm_betao        = 0.0,
  beta_unitcostratio = 146.0,
  rd_to_vcmax        = 0.014,      # from Atkin et al. 2015 for C3 herbaceous
  tau_acclim         = 30.0,
  kc_jmax            = 0.41
 )
)

stineb/rsofun documentation built on April 29, 2024, 1:29 p.m.