runread_pmodel_f: Run the P-model

In rsofun: The P-Model and BiomeE Modelling Framework

Run the P-model

Description

Runs the P-model and loads output in once.

Usage

runread_pmodel_f(drivers, par, makecheck = TRUE, parallel = FALSE, ncores = 1)

Arguments

drivers	A nested data frame with one row for each site and columns named according to the arguments of function run_pmodel_f_bysite, namely sitename, params_siml, site_info and forcing.
par	A named list of free (calibratable) model parameters. kphio The quantum yield efficiency at optimal temperature \varphi_0, in mol mol^{-1}. When temperature dependence is used, it corresponds to the multiplicative parameter c (see Details). kphio_par_a The shape parameter a of the temperature-dependency of quantum yield efficiency (see Details). To disable the temperature dependence, set kphio_par_a = 0. kphio_par_b The optimal temperature parameter b of the temperature dependent quantum yield efficiency (see Details), in ^oC. soilm_thetastar The threshold parameter \theta^{*} in the soil moisture stress function (see Details), given in mm. To turn off the soil moisture stress, set soilm_thetastar = 0. soilm_betao The intercept parameter \beta_{0} in the soil moisture stress function (see Details). This is the parameter calibrated in Stocker et al. 2020 GMD. beta_unitcostratio The unit cost of carboxylation, corresponding to \beta = b / a' in Eq. 3 of Stocker et al. 2020 GMD. rd_to_vcmax Ratio of Rdark (dark respiration) to Vcmax25. tau_acclim Acclimation time scale of photosynthesis, in days. kc_jmax Parameter for Jmax cost ratio (corresponding to c^* in Stocker et al. 2020 GMD).
makecheck	A logical specifying whether checks are performed to verify forcings. Defaults to TRUE.
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 (by default ncores = 2).

Details

Depending on the input model parameters, it's possible to run the different P-model setups presented in Stocker et al. 2020 GMD. The P-model version implemented in this package allows more flexibility than the one presented in the paper, with the following functions:

The temperature dependence of the quantum yield efficiency is given by:
\varphi_0 (T) = c (1 + a (T - b)^2 ) if 0 < c (1 + a (T - b)^2 ) < 1,
\varphi_0 (T) = 0 if c (1 + a (T - b)^2 ) \leq 0, and
\varphi_0 (T) = 1 if c (1 + a (T - b)^2 ) \geq 1.
The ORG setup can be reproduced by setting kphio_par_a = 0 and calibrating the kphio parameter only. The BRC setup (which calibrates c_L = \frac{a_L b_L}{4} in Eq. 18) is more difficult to reproduce, since the temperature-dependency has been reformulated and a custom cost function would be necessary for calibration. The new parameters are related to c_L as follows:
a = -0.0004919819
b = 32.35294
c = 0.6910823 c_L

The soil moisture stress is implemented as
\beta(\theta) = \frac{\beta_0 - 1}{{\theta^{*}}^2} (\theta - \theta^{*})^2 + 1 if 0 \leq \theta \leq \theta^{*} and
\beta(\theta) = 1 if \theta > \theta^{*}.
In Stocker et al. 2020 GMD, the threshold plant-available soil water is set as \theta^{*} = 0.6 * whc where whc is the site's water holding capacity. Also, the \beta reduction at low soil moisture (\beta_0 = \beta(0)) was parameterized as a linear function of mean aridity (Eq. 20 in Stocker et al. 2020 GMD) but is considered a constant model parameter in this package. Hence, the FULL calibration setup cannot be exactly replicated.

Value

A data frame (tibble) with one row for each site, site information stored in the nested column site_info and outputs stored in the nested column data. See run_pmodel_f_bysite for a detailed description of the outputs.

Examples

# Define model parameter values from previous work
params_modl <- list(
  kphio              = 0.04998,    # setup ORG in Stocker et al. 2020 GMD
  kphio_par_a        = 0.0,        # disable temperature-dependence of kphio
  kphio_par_b        = 1.0,
  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
)

# Run the model for these parameters and the example drivers
output <- rsofun::runread_pmodel_f(
  drivers = rsofun::p_model_drivers,
  par = params_modl)
output_vcmax25 <- rsofun::runread_pmodel_f(
  drivers = rsofun::p_model_drivers_vcmax25,
  par = params_modl)

rsofun documentation built on April 4, 2025, 1:07 a.m.