run_pmodel_f_bysite: R wrapper for SOFUN P-model
In rsofun: The P-Model and BiomeE Modelling Framework

run_pmodel_f_bysite

R Documentation

R wrapper for SOFUN P-model

Description

Call to the Fortran P-model

Usage

run_pmodel_f_bysite(
  sitename,
  params_siml,
  site_info,
  forcing,
  params_modl,
  makecheck = TRUE,
  verbose = TRUE
)

Arguments

`sitename`	Site name.
`params_siml`	Simulation parameters. spinup A logical value indicating whether this simulation does spin-up. spinupyears Number of spin-up years. recycle Length of standard recycling period, in years. outdt An integer indicating the output periodicity. ltre A logical value, `TRUE` if evergreen tree. ltne A logical value, `TRUE` if evergreen tree and N-fixing. ltrd A logical value, `TRUE` if deciduous tree. ltnd A logical value, `TRUE` if deciduous tree and N-fixing. lgr3 A logical value, `TRUE` if grass with C3 photosynthetic pathway. lgn3 A logical value, `TRUE` if grass with C3 photosynthetic pathway and N-fixing. lgr4 A logical value, `TRUE` if grass with C4 photosynthetic pathway.
`site_info`	A list of site meta info. Required: lon Longitude of the site location. lat Latitude of the site location. elv Elevation of the site location, in meters. whc A numeric value for the total root zone water holding capacity (in mm), used for simulating the soil water balance.
`forcing`	A data frame of forcing climate data, used as input (see `p_model_drivers` for a detailed description of its structure and contents).
`params_modl`	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 and model parameters. `TRUE` by default.
`verbose`	A logical specifying whether to print warnings. Defaults to `TRUE`.

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

Model output is provided as a tidy dataframe, with columns:

date: Date of the observation in YYYY-MM-DD format.
year_dec: Decimal representation of year and day of the year (for example, 2007.000 corresponds to 2007-01-01 and 2007.003 to 2007-01-02.
fapar: Fraction of photosynthetic active radiation (fAPAR), taking values between 0 and 1.
gpp: Gross Primary Productivity (GPP) for each time stamp (in gC m^{-2} d^{-1}).
aet: Actual evapotranspiration (AET), calculated by SPLASH following Priestly-Taylor (in mm d^{-1}).
le: Latent heat flux (in J m^{-2} d^{-1}).
pet: Potential evapotranspiration (PET), calculated by SPLASH following Priestly-Taylor (in mm d^{-1}).
vcmax: Maximum rate of RuBisCO carboxylation (Vcmax) (in mol C m^{-2} d^{-1}).
jmax: Maximum rate of electron transport for RuBP regeneration (in mol CO_2 m^{-2} s^{-1}).
vcmax25: Maximum rate of carboxylation (Vcmax), normalised to 25^oC (in mol C m^{-2} d^{-1}).
jmax25: Maximum rate of electron transport, normalised to 25^oC (in mol C m^{-2} s^{-1}).
gs_accl: Acclimated stomatal conductance (in mol C m^{-2} d^{-1} Pa^{-1}).
wscal: Relative soil water content, between 0 (permanent wilting point, PWP) and 1 (field capacity, FC).
chi: Ratio of leaf-internal to ambient CO_{2}, ci:ca (unitless).
iwue: Intrinsic water use efficiency (iWUE) (in Pa).
rd: Dark respiration (Rd) in gC m^{-2} d^{-1}.
tsoil: Soil temperature, in ^{o}C.
netrad: Net radiation, in W m^{-2}. WARNING: this is currently ignored as a model forcing. Instead, net radiation is internally calculated by SPLASH.
wcont: Soil water content, in mm.
snow: Snow water equivalents, in mm.
cond: Water input by condensation, in mm d^{-1}

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 Fortran P-model 
mod_output <- run_pmodel_f_bysite(
  # unnest drivers example data
  sitename = p_model_drivers$sitename[1],
  params_siml = p_model_drivers$params_siml[[1]],
  site_info = p_model_drivers$site_info[[1]],
  forcing = p_model_drivers$forcing[[1]],
  params_modl = params_modl
 )

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