cost_likelihood_pmodel: Cost function computing a log-likelihood for calibration of...

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

Cost function computing a log-likelihood for calibration of P-model parameters

Description

The cost function performs a P-model run for the input drivers and model parameter values, and computes the outcome's normal log-likelihood centered at the input observed values and with standard deviation given as an input parameter (calibratable).

Usage

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

Arguments

par	A vector of values for the parameters to be calibrated, including a subset of model parameters (described in runread_pmodel_f), in order, and error terms for each target variable (for example 'gpp_err'), in the same order as the targets appear in targets.
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.
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 log-likelihood of the observed target values, assuming that they are independent, normally distributed and centered on the predictions made by the P-model run with standard deviation given as input (via 'par' because the error terms are estimated through the calibration with 'BayesianTools', as shown in the "Parameter calibration and cost functions" vignette).

Examples

# Compute the likelihood for a set of 
# model parameter values involved in the
# temperature dependence of kphio 
# and example data
cost_likelihood_pmodel(
 par = c(0.05, -0.01, 1,     # model parameters
         2),                # err_gpp
 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.