Run the P-model

Runs the P-model and loads output in once.

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 \(^o\)C.

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).

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.

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.

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)