R: Invokes a P-model function call

rpmodel {rpmodel}

R Documentation

Invokes a P-model function call

Description

R implementation of the P-model and its corollary predictions (Prentice et al., 2014; Han et al., 2017).

Usage

rpmodel(
  tc,
  vpd,
  co2,
  fapar,
  ppfd,
  patm = NA,
  elv = NA,
  kphio = ifelse(c4, 1, ifelse(do_ftemp_kphio, ifelse(do_soilmstress, 0.087182,
    0.081785), 0.049977)),
  beta = ifelse(c4, 146/9, 146),
  soilm = stopifnot(!do_soilmstress),
  meanalpha = 1,
  apar_soilm = 0,
  bpar_soilm = 0.733,
  c4 = FALSE,
  method_jmaxlim = "wang17",
  do_ftemp_kphio = TRUE,
  do_soilmstress = FALSE,
  returnvar = NULL,
  verbose = FALSE
)

Arguments

`tc`	Temperature, relevant for photosynthesis (deg C)
`vpd`	Vapour pressure deficit (Pa)
`co2`	Atmospheric CO2 concentration (ppm)
`fapar`	(Optional) Fraction of absorbed photosynthetically active radiation (unitless, defaults to `NA`)
`ppfd`	Incident photosynthetic photon flux density (mol m-2 d-1, defaults to `NA`). Note that the units of `ppfd` (per area and per time) determine the units of outputs `lue`, `gpp`, `vcmax`, and `rd`. For example, if `ppfd` is provided in units of mol m-2 month-1, then respective output variables are returned as per unit months.
`patm`	Atmospheric pressure (Pa). When provided, overrides `elv`, otherwise `patm` is calculated using standard atmosphere (101325 Pa), corrected for elevation (argument `elv`), using the function calc_patm.
`elv`	Elevation above sea-level (m.a.s.l.). Is used only for calculating atmospheric pressure (using standard atmosphere (101325 Pa), corrected for elevation (argument `elv`), using the function calc_patm), if argument `patm` is not provided. If argument `patm` is provided, `elv` is overridden.
`kphio`	Apparent quantum yield efficiency (unitless). Defaults to 0.081785 for `method_jmaxlim="wang17", do_ftemp_kphio=TRUE, do_soilmstress=FALSE`, 0.087182 for `method_jmaxlim="wang17", do_ftemp_kphio=TRUE, do_soilmstress=TRUE`, and 0.049977 for `method_jmaxlim="wang17", do_ftemp_kphio=FALSE, do_soilmstress=FALSE`, corresponding to the empirically fitted value as presented in Stocker et al. (2019) Geosci. Model Dev. for model setup 'BRC', 'FULL', and 'ORG' respectively, corresponding to `(a_L b_L)/4` in Eq.20 in Stocker et al. (2020) for C3 photosynthesis. For C4 photosynthesis (`c4 = TRUE`), `kphio` defaults to 1.0, corresponding to the parametrisation by Cai & Prentice (2020).
`beta`	Unit cost ratio. Defaults to 146.0 (see Stocker et al., 2019) for C3 plants and 146/9 for C4 plants.
`soilm`	(Optional, used only if `do_soilmstress==TRUE`) Relative soil moisture as a fraction of field capacity (unitless). Defaults to 1.0 (no soil moisture stress). This information is used to calculate an empirical soil moisture stress factor (calc_soilmstress) whereby the sensitivity is determined by average aridity, defined by the local annual mean ratio of actual over potential evapotranspiration, supplied by argument `meanalpha`.
`meanalpha`	(Optional, used only if `do_soilmstress==TRUE`) Local annual mean ratio of actual over potential evapotranspiration, measure for average aridity. Defaults to 1.0. Only scalar numbers are accepted. If a vector is provided, only the first element will be used.
`apar_soilm`	(Optional, used only if `do_soilmstress==TRUE`) Parameter determining the sensitivity of the empirical soil moisture stress function. Defaults to 0.0, the empirically fitted value as presented in Stocker et al. (2019) Geosci. Model Dev. for model setup 'FULL' (corresponding to a setup with `method_jmaxlim="wang17", do_ftemp_kphio=TRUE, do_soilmstress=TRUE`).
`bpar_soilm`	(Optional, used only if `do_soilmstress==TRUE`) Parameter determining the sensitivity of the empirical soil moisture stress function. Defaults to 0.7330, the empirically fitted value as presented in Stocker et al. (2019) Geosci. Model Dev. for model setup 'FULL' (corresponding to a setup with `method_jmaxlim="wang17", do_ftemp_kphio=TRUE, do_soilmstress=TRUE`).
`c4`	(Optional) A logical value specifying whether the C3 or C4 photosynthetic pathway is followed.Defaults to `FALSE`. If `TRUE`, the leaf-internal CO2 concentration is still estimated using beta but `m` (returned variable `mj`) tends to 1, and `m'` tends to 0.669 (with `c = 0.41`) to represent CO2 concentrations within the leaf. With `do_ftemp_kphio = TRUE`, a C4-specific temperature dependence of the quantum yield efficiency is used (see ftemp_kphio).
`method_jmaxlim`	(Optional) A character string specifying which method is to be used for factoring in Jmax limitation. Defaults to `"wang17"`, based on Wang Han et al. 2017 Nature Plants and (Smith 1937). Available is also `"smith19"`, following the method by Smith et al., 2019 Ecology Letters, and `"none"` for ignoring effects of Jmax limitation.
`do_ftemp_kphio`	(Optional) A logical specifying whether temperature-dependence of quantum yield efficiency is used. See ftemp_kphio for details. Defaults to `TRUE`. Only scalar numbers are accepted. If a vector is provided, only the first element will be used.
`do_soilmstress`	(Optional) A logical specifying whether an empirical soil moisture stress factor is to be applied to down-scale light use efficiency (and only light use efficiency). Defaults to `FALSE`.
`returnvar`	(Optional) A character string of vector of character strings specifying which variables are to be returned (see return below).
`verbose`	Logical, defines whether verbose messages are printed. Defaults to `FALSE`.

Value

A named list of numeric values (including temperature and pressure dependent parameters of the photosynthesis model, P-model predictions, including all its corollary). This includes :

ca: Ambient CO2 expressed as partial pressure (Pa)
gammastar: Photorespiratory compensation point \Gamma*, (Pa), see calc_gammastar.
kmm: Michaelis-Menten coefficient K for photosynthesis (Pa), see calc_kmm.
ns_star: Change in the viscosity of water, relative to its value at 25 deg C (unitless).

\eta* = \eta(T) / \eta(25 deg C)

This is used to scale the unit cost of transpiration. Calculated following Huber et al. (2009).
chi: Optimal ratio of leaf internal to ambient CO2 (unitless). Derived following Prentice et al.(2014) as:

\chi = \Gamma* / ca + (1- \Gamma* / ca) \xi / (\xi + \sqrt D )

with

\xi = \sqrt (\beta (K+ \Gamma*) / (1.6 \eta*))

\beta is given by argument beta, K is kmm (see calc_kmm), \Gamma* is gammastar (see calc_gammastar). \eta* is ns_star. D is the vapour pressure deficit (argument vpd), ca is the ambient CO2 partial pressure in Pa (ca).
ci: Leaf-internal CO2 partial pressure (Pa), calculated as (\chi ca).
lue: Light use efficiency (g C / mol photons), calculated as

LUE = \phi(T) \phi0 m' Mc

where \phi(T) is the temperature-dependent quantum yield efficiency modifier (ftemp_kphio) if do_ftemp_kphio==TRUE, and 1 otherwise. \phi 0 is given by argument kphio. m'=m if method_jmaxlim=="none", otherwise

m' = m \sqrt( 1 - (c/m)^(2/3) )

with c=0.41 (Wang et al., 2017) if method_jmaxlim=="wang17". Mc is the molecular mass of C (12.0107 g mol-1). m is given returned variable mj. If do_soilmstress==TRUE, LUE is multiplied with a soil moisture stress factor, calculated with calc_soilmstress.
mj: Factor in the light-limited assimilation rate function, given by

m = (ci - \Gamma*) / (ci + 2 \Gamma*)

where \Gamma* is given by calc_gammastar.
mc: Factor in the Rubisco-limited assimilation rate function, given by

mc = (ci - \Gamma*) / (ci + K)

where K is given by calc_kmm.
gpp: Gross primary production (g C m-2), calculated as

GPP = Iabs LUE

where Iabs is given by fapar*ppfd (arguments), and is NA if fapar==NA or ppfd==NA. Note that gpp scales with absorbed light. Thus, its units depend on the units in which ppfd is given.
iwue: Intrinsic water use efficiency (iWUE, Pa), calculated as

iWUE = ca (1-\chi)/(1.6)
gs: Stomatal conductance (gs, in mol C m-2 Pa-1), calculated as

gs = A / (ca (1-\chi))

where A is gpp/Mc.
vcmax: Maximum carboxylation capacity Vcmax (mol C m-2) at growth temperature (argument tc), calculated as

Vcmax = \phi(T) \phi0 Iabs n

where n is given by n=m'/mc.
vcmax25: Maximum carboxylation capacity Vcmax (mol C m-2) normalised to 25 deg C following a modified Arrhenius equation, calculated as Vcmax25 = Vcmax / fv, where fv is the instantaneous temperature response by Vcmax and is implemented by function ftemp_inst_vcmax.
jmax: The maximum rate of RuBP regeneration () at growth temperature (argument tc), calculated using

A_J = A_C
rd: Dark respiration Rd (mol C m-2), calculated as

Rd = b0 Vcmax (fr / fv)

where b0 is a constant and set to 0.015 (Atkin et al., 2015), fv is the instantaneous temperature response by Vcmax and is implemented by function ftemp_inst_vcmax, and fr is the instantaneous temperature response of dark respiration following Heskel et al. (2016) and is implemented by function ftemp_inst_rd.

Additional variables are contained in the returned list if argument method_jmaxlim=="smith19"

omega: Term corresponding to \omega, defined by Eq. 16 in Smith et al. (2019), and Eq. E19 in Stocker et al. (2019).
omega_star: Term corresponding to \omega^\ast, defined by Eq. 18 in Smith et al. (2019), and Eq. E21 in Stocker et al. (2019).

patm

References

Bernacchi, C. J., Pimentel, C., and Long, S. P.: In vivo temperature response func-tions of parameters required to model RuBP-limited photosynthesis, Plant Cell Environ., 26, 1419–1430, 2003

and their drivers: analysis and modelling at flux-site and global scales, Environ. Res. Lett. 15 124050 https://doi.org/10.1088/1748-9326/abc64e, 2020 Heskel, M., O’Sullivan, O., Reich, P., Tjoelker, M., Weerasinghe, L., Penillard, A.,Egerton, J., Creek, D., Bloomfield, K., Xiang, J., Sinca, F., Stangl, Z., Martinez-De La Torre, A., Griffin, K., Huntingford, C., Hurry, V., Meir, P., Turnbull, M.,and Atkin, O.: Convergence in the temperature response of leaf respiration across biomes and plant functional types, Proceedings of the National Academy of Sciences, 113, 3832–3837, doi:10.1073/pnas.1520282113,2016.

Huber, M. L., Perkins, R. A., Laesecke, A., Friend, D. G., Sengers, J. V., Assael,M. J., Metaxa, I. N., Vogel, E., Mares, R., and Miyagawa, K.: New international formulation for the viscosity of H2O, Journal of Physical and Chemical ReferenceData, 38, 101–125, 2009

Prentice, I. C., Dong, N., Gleason, S. M., Maire, V., and Wright, I. J.: Balancing the costs of carbon gain and water transport: testing a new theoretical frameworkfor plant functional ecology, Ecology Letters, 17, 82–91, 10.1111/ele.12211,http://dx.doi.org/10.1111/ele.12211, 2014.

Wang, H., Prentice, I. C., Keenan, T. F., Davis, T. W., Wright, I. J., Cornwell, W. K.,Evans, B. J., and Peng, C.: Towards a universal model for carbon dioxide uptake by plants, Nat Plants, 3, 734–741, 2017. Atkin, O. K., et al.: Global variability in leaf respiration in relation to climate, plant func-tional types and leaf traits, New Phytologist, 206, 614–636, doi:10.1111/nph.13253, https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.13253.

Smith, N. G., Keenan, T. F., Colin Prentice, I. , Wang, H. , Wright, I. J., Niinemets, U. , Crous, K. Y., Domingues, T. F., Guerrieri, R. , Yoko Ishida, F. , Kattge, J. , Kruger, E. L., Maire, V. , Rogers, A. , Serbin, S. P., Tarvainen, L. , Togashi, H. F., Townsend, P. A., Wang, M. , Weerasinghe, L. K. and Zhou, S. (2019), Global photosynthetic capacity is optimized to the environment. Ecol Lett, 22: 506-517. doi:10.1111/ele.13210

Stocker, B. et al. Geoscientific Model Development Discussions (in prep.)

Examples

## Not run: 
 rpmodel(
  tc = 20,
  vpd = 1000,
  co2 = 400,
  ppfd = 30,
  elv = 0)

## End(Not run)

[Package rpmodel version 1.2.3 Index]