runread_pmodel_f function

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).

Returns

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

c("$\\beta(\\theta) = \\frac{\\beta_0 - 1}{{\\theta^{*}}^2} \n$", "$(\\theta - \\theta^{*})^2 + 1$") 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)
output_vcmax25 <- rsofun::runread_pmodel_f(
  drivers = rsofun::p_model_drivers_vcmax25,
  par = params_modl)