The rpmodel package implements the P-model as described in Stocker et al. (2019) Geosci. Mod. Dev. The main function available through the package is rpmodel(), which returns a list of quantities (see ?rpmodel) for a given set of inputs. An additional set of important functions that are used within rpmodel() are also available through this package. Usage examples are given below.
Let's run the P-model, without \(J_{\text{max}}\) limitation (argument method_jmaxlim = "none"), for one point. The set of inputs, being temperature (tc), photosynthetic photon flux density (ppfd), vapour pressure deficit (vpd), ambient CO\(_2\) (co2), elevation (elv), and fraction of absorbed photosynthetically active radiation (fapar). The quantum yield efficiency parameter is provided as an argument (kphio) and corresponds to \(\widehat{\varphi_0}\) in Stocker et al. (2019) if the temperature-dependence of this parameter is ignored (argument do_ftemp_kphio = FALSE, corresponding to simulation setup 'ORG' in Stocker et al. (2019)), or to \(\widehat{c_L}\) if the temperature-dependence of the quantum yield efficiency is included (argument do_ftemp_kphio = TRUE, used in simulation setups 'BRC' and 'FULL' in Stocker et al. (2019)). By default the optional argument do_soilmstress is set to FALSE, meaning that the empirical soil moisture stress function is not included. The unit cost ratio (\(\beta\) in Stocker et al. (2019)) is given by argument beta.
To run the rpmodel() function we can do:
library(rpmodel)
out_pmodel <- rpmodel(
tc = 20, # temperature, deg C
vpd = 1000, # Pa,
co2 = 400, # ppm,
fapar = 1, # fraction ,
ppfd = 300, # mol/m2/d,
elv = 0, # m.a.s.l.,
kphio = 0.05, # quantum yield efficiency,
beta = 146, # unit cost ratio a/b,
method_optci = "prentice14",
method_jmaxlim = "none",
do_ftemp_kphio = FALSE,
do_soilmstress = FALSE,
verbose = TRUE
)
## Warning: Atmospheric pressure (patm) not provided. Calculating it as a
## function of elevation (elv), assuming standard atmosphere (101325 Pa at sea
## level).
print(out_pmodel)
## $ca
## [1] 40.53
##
## $gammastar
## [1] 3.339251
##
## $kmm
## [1] 46.09928
##
## $ns_star
## [1] 1.125361
##
## $chi
## [1] 0.694352
##
## $mj
## [1] 0.7123038
##
## $mc
## [1] 0.3340838
##
## $ci
## [1] 28.14209
##
## $lue
## [1] 0.4277633
##
## $gpp
## [1] 128.329
##
## $iwue
## [1] 7.742446
##
## $gs
## [1] 0.8624985
##
## $vcmax
## [1] 31.98167
##
## $vcmax25
## [1] 50.20073
##
## $rd
## [1] 0.50805
Here, we specified the model paramters (arguments beta and kphio). This overrides the defaults, where rpmodel() uses the parameters as calibrated by Stocker et al. (2019), depending on the choices for arguments do_ftemp_kphio and do_soilmstress:
kphio = ifelse(do_ftemp_kphio, ifelse(do_soilmstress, 0.087182, 0.081785), 0.049977)
beta = 146.0
apar_soilm = 0.0
bpar_soilm = 0.73300
The function returns a list of variables (see also man page by ?rpmodel), including \(V_{\mathrm{cmax}}\), \(g_s\), and all the parameters of the photosynthesis model (\(K\), \(\Gamma^{\ast}\)), which are all internally consistent, as can be verified for…
\[
c_i = c_a - A / g_s = \chi c_a
\]
c_molmass <- 12.0107 # molecular mass of carbon
kphio <- 0.05 # quantum yield efficiency, value as used in the function call to rpmodel()
ppfd <- 300 # mol/m2/d, value as used in the function call to rpmodel()
fapar <- 1 # fraction, value as used in the function call to rpmodel()
print( out_pmodel$ci )
## [1] 28.14209
print( out_pmodel$ca - (out_pmodel$gpp / c_molmass) / out_pmodel$gs )
## [1] 28.14209
print( out_pmodel$ca * out_pmodel$chi )
## [1] 28.14209
Yes.
And for… \[ A = V_{\text{cmax}} \frac{c_i-\Gamma^{\ast}}{c_i + K} = \phi_0 I_{\text{abs}} \frac{c_i-\Gamma^{\ast}}{c_i + 2 \Gamma^{\ast}} = g_s (c_a - c_i) \]
print( out_pmodel$gpp / c_molmass )
## [1] 10.68456
print( out_pmodel$vcmax * (out_pmodel$ci - out_pmodel$gammastar) / (out_pmodel$ci + out_pmodel$kmm ))
## [1] 10.68456
print( out_pmodel$gs * (out_pmodel$ca - out_pmodel$ci) )
## [1] 10.68456
print( kphio * ppfd * fapar * (out_pmodel$ci - out_pmodel$gammastar) / (out_pmodel$ci + 2 * out_pmodel$gammastar ))
## [1] 10.68456
Yes.
Above, atmospheric pressure (patm) was not provided as an argument, but elevation (elv) was. Hence the warning was printed (only when verbose = TRUE), saying: Atmospheric pressure (patm) not provided. Calculating it as a function of elevation (elv), Assuming standard atmosphere (101325 Pa at sea level).. Alternatively, we can provide atmospheric pressure (patm) as input, which overrides the argument elv.
The rpmodel() function can also be invoked for time series, where tc, vpd, co2, fapar, patm, and ppfd are vectors.
out_ts_pmodel <- rpmodel(
tc = 20 + rnorm(5, mean = 0, sd = 5),
vpd = 1000 + rnorm(5, mean = 0, sd = 50),
co2 = rep(400, 5),
fapar = rep(1, 5),
ppfd = 300 + rnorm(5, mean = 0, sd = 30),
elv = 0,
kphio = 0.05,
beta = 146,
method_optci = "prentice14",
method_jmaxlim = "none",
do_ftemp_kphio = FALSE,
verbose = FALSE
)
print(out_ts_pmodel$gpp)
## [1] 131.3053 138.9738 119.8071 137.4992 129.6590 131.3053 138.9738
## [8] 119.8071 137.4992 129.6590 131.3053 138.9738 119.8071 137.4992
## [15] 129.6590 131.3053 138.9738 119.8071 137.4992 129.6590 131.3053
## [22] 138.9738 119.8071 137.4992 129.6590
Note that gpp (as well as all other returned variables) are now vectors of the same length as the vectors provided as inputs.
We can create a data frame (in tidyverse this is a tibble) and apply the rpmodel() function to each row.
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(purrr)
df <- tibble(
tc = 20 + rnorm(5, mean = 0, sd = 5),
vpd = 1000 + rnorm(5, mean = 0, sd = 50),
co2 = rep(400, 5),
fapar = rep(1, 5),
ppfd = 300 + rnorm(5, mean = 0, sd = 30)
) %>%
mutate( out_pmodel = purrr::pmap(., rpmodel,
elv = 0,
kphio = 0.05,
beta = 146,
method_optci = "prentice14",
method_jmaxlim = "none",
do_ftemp_kphio = FALSE
) )
print(df)
## # A tibble: 5 x 6
## tc vpd co2 fapar ppfd out_pmodel
## <dbl> <dbl> <dbl> <dbl> <dbl> <list>
## 1 25.1 1032. 400 1 252. <named list [15]>
## 2 18.4 997. 400 1 303. <named list [15]>
## 3 22.1 891. 400 1 337. <named list [15]>
## 4 26.2 1087. 400 1 270. <named list [15]>
## 5 23.6 1016. 400 1 331. <named list [15]>
Note that the new column out_pmodel now contains the list returned as output of the rpmodel() function applied to each row separately. Additional (constant) arguments are just passed to purrr::pmap as arguments.
If you prefer the elements of these lists to be in separate columns of df, use tidyr to do:
library(tidyr)
df <- df %>%
mutate( out_pmodel = purrr::map(out_pmodel, ~as_tibble(.))) %>%
unnest(out_pmodel)
print(df)
## # A tibble: 5 x 20
## tc vpd co2 fapar ppfd ca gammastar kmm ns_star chi mj
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 25.1 1032. 400 1 252. 40.5 4.36 71.7 0.997 0.752 0.666
## 2 18.4 997. 400 1 303. 40.5 3.06 40.0 1.17 0.674 0.725
## 3 22.1 891. 400 1 337. 40.5 3.72 55.0 1.07 0.731 0.699
## 4 26.2 1087. 400 1 270. 40.5 4.61 78.6 0.973 0.759 0.654
## 5 23.6 1016. 400 1 331. 40.5 4.03 62.8 1.03 0.736 0.681
## # … with 9 more variables: mc <dbl>, ci <dbl>, lue <dbl>, gpp <dbl>,
## # iwue <dbl>, gs <dbl>, vcmax <dbl>, vcmax25 <dbl>, rd <dbl>
A number of auxiliary functions, which are used within rpmodel(), are available (public) through the package.
Different instantaneous temperature scaling functions are applied for \(V_\text{cmax}\) and dark respiration (\(R_d\)).
calc_ftemp_inst_vcmax() calculates the instantaneous temperature response of \(V_\text{cmax}\). Let's run the P-model for tc = 10 (degrees C). The ratio of \(V_\text{cmax}/V_\text{cmax25}\) should equal the instantaneous temperature scaling function for \(V_\text{cmax}\) at 10 degrees C (calculated by calc_ftemp_inst_vcmax(10)):out_pmodel <- rpmodel(
tc = 10, # temperature, deg C
vpd = 1000, # Pa,
co2 = 400, # ppm,
fapar = 1, # fraction ,
ppfd = 300, # mol/m2/d,
elv = 0, # m.a.s.l.,
kphio = 0.05, # quantum yield efficiency,
beta = 146, # unit cost ratio a/b,
method_optci = "prentice14",
method_jmaxlim = "none",
do_ftemp_kphio = FALSE,
verbose = TRUE
)
## Warning: Atmospheric pressure (patm) not provided. Calculating it as a
## function of elevation (elv), assuming standard atmosphere (101325 Pa at sea
## level).
print(paste("Ratio Vcmax/Vcmax25 :", out_pmodel$vcmax/out_pmodel$vcmax25))
## [1] "Ratio Vcmax/Vcmax25 : 0.260975632963417"
print(paste("calc_ftemp_inst_vcmax(10):", calc_ftemp_inst_vcmax(10)))
## [1] "calc_ftemp_inst_vcmax(10): 0.260975632963417"
calc_ftemp_arrh() Calculates the Arrhenius-type temperature response and is used inside calc_ftemp_inst_vcmax().
calc_ftemp_inst_rd() calculates the temperature response of dark respiration (\(R_d\)), which is slightly less steep than that for \(V_\text{cmax}\):
print(paste("calc_ftemp_inst_rd(10):", calc_ftemp_inst_rd(10)))
## [1] "calc_ftemp_inst_rd(10): 0.284933345928884"
calc_gammastar() calculates the CO\(_2\) compensation point (\(\Gamma^\ast\)) in the Farquhar-von Caemmerer-Berry model as a function of temperature (argument tc) and atmospheric pressure (argument patm). This is returned by the rpmodel() function and by the separate auxiliary function calc_gammastar(). calc_gammastar() requires atmospheric pressure (patm) to be given as an argument (in addition to temperature). Corresponding to the rpmodel() call above, let's calculate this using the auxiliary function calc_patm() with 0 metres above sea level, and assuming standard atmospheric pressure (101325 Pa at 0 m a.s.l.):print(paste("From rpmodel call :", out_pmodel$gammastar))
## [1] "From rpmodel call : 1.93016150706341"
print(paste("calc_gammastar(10):", calc_gammastar(10, patm = calc_patm(elv = 0))))
## [1] "calc_gammastar(10): 1.93016150706341"
calc_kmm() calculates the Michaelis Menten coefficient for Rubisco-limited photosynthesis as a function of temperature (argument tc) and atmospheric pressure (argument patm). As above, calc_kmm() requires atmospheric pressure to be given as an argument (in addition to temperature). Corresponding to the rpmodel() call above, let's calculate this using the auxiliary function calc_patm() with 0 metres above sea level, and assuming standard atmospheric pressure (101325 Pa at 0 m a.s.l.):print(paste("From rpmodel call:", out_pmodel$kmm))
## [1] "From rpmodel call: 19.6242174524746"
print(paste("calc_kmm(10) :", calc_kmm(10, patm = calc_patm(elv = 0))))
## [1] "calc_kmm(10) : 19.6242174524746"
The temperature dependence of quantum yield efficiency is modelled following Bernacchi et al. (2003), if the argument to the rpmodel() call do_ftemp_kphio = TRUE. This affects several quantities returned by the rpmodel() call (GPP, LUE, Vcmax), and can be calculated direction using calc_ftemp_kphio().
out_pmodel_ftemp_kphio_ON <- rpmodel(
tc = 20, # temperature, deg C
vpd = 1000, # Pa,
co2 = 400, # ppm,
fapar = 1, # fraction ,
ppfd = 300, # mol/m2/d,
elv = 0, # m.a.s.l.,
do_ftemp_kphio = TRUE
)
out_pmodel_ftemp_kphio_OFF <- rpmodel(
tc = 20, # temperature, deg C
vpd = 1000, # Pa,
co2 = 400, # ppm,
fapar = 1, # fraction ,
ppfd = 300, # mol/m2/d,
elv = 0, # m.a.s.l.,
do_ftemp_kphio = FALSE
)
print(paste("LUE ftemp_ON /LUE ftemp_OFF =", out_pmodel_ftemp_kphio_ON$lue / out_pmodel_ftemp_kphio_OFF$lue))
## [1] "LUE ftemp_ON /LUE ftemp_OFF = 1.07351301598735"
print(paste("GPP ftemp_ON /GPP ftemp_OFF =", out_pmodel_ftemp_kphio_ON$gpp / out_pmodel_ftemp_kphio_OFF$gpp))
## [1] "GPP ftemp_ON /GPP ftemp_OFF = 1.07351301598735"
print(paste("Vcmax ftemp_ON /Vcmax ftemp_OFF =", out_pmodel_ftemp_kphio_ON$vcmax / out_pmodel_ftemp_kphio_OFF$vcmax))
## [1] "Vcmax ftemp_ON /Vcmax ftemp_OFF = 1.07351301598735"
print(paste("calc_ftemp_kphio(20) =", calc_ftemp_kphio(20)))
## [1] "calc_ftemp_kphio(20) = 0.656"
Similar to above (), the soil moisture dependence of LUE (and hence GPP, and Vcmax) can be calculated directly using the function calc_soilmstress() and affects several quantities returned by the rpmodel() call (GPP, LUE, Vcmax):
out_pmodel_soilmstress_OFF <- rpmodel(
tc = 20, # temperature, deg C
vpd = 1000, # Pa,
co2 = 400, # ppm,
fapar = 1, # fraction ,
ppfd = 300, # mol/m2/d,
elv = 0, # m.a.s.l.,
do_ftemp_kphio = FALSE,
do_soilmstress = TRUE
)
out_pmodel_soilmstress_ON <- rpmodel(
tc = 20, # temperature, deg C
vpd = 1000, # Pa,
co2 = 400, # ppm,
fapar = 1, # fraction ,
ppfd = 300, # mol/m2/d,
elv = 0, # m.a.s.l.,
do_ftemp_kphio = FALSE,
do_soilmstress = TRUE,
soilm = 0.2,
apar_soilm = 0.1,
bpar_soilm = 0.7,
meanalpha = 0.2
)
print(paste("LUE soilmstress_ON /LUE soilmstress_OFF =", out_pmodel_soilmstress_ON$lue / out_pmodel_soilmstress_OFF$lue))
## [1] "LUE soilmstress_ON /LUE soilmstress_OFF = 0.662222222222222"
print(paste("GPP soilmstress_ON /GPP soilmstress_OFF =", out_pmodel_soilmstress_ON$gpp / out_pmodel_soilmstress_OFF$gpp))
## [1] "GPP soilmstress_ON /GPP soilmstress_OFF = 0.662222222222222"
print(paste("Vcmax soilmstress_ON /Vcmax soilmstress_OFF =", out_pmodel_soilmstress_ON$vcmax / out_pmodel_soilmstress_OFF$vcmax))
## [1] "Vcmax soilmstress_ON /Vcmax soilmstress_OFF = 0.662222222222222"
print(paste("calc_soilmstress(0.2, apar_soilm = 0.1, bpar_soilm = 0.7, meanalpha = 0.2) =", calc_soilmstress(0.2, apar_soilm = 0.1, bpar_soilm = 0.7, meanalpha = 0.2)))
## [1] "calc_soilmstress(0.2, apar_soilm = 0.1, bpar_soilm = 0.7, meanalpha = 0.2) = 0.662222222222222"
calc_ftemp_arrh() Calculates the Arrhenius-type temperature response.
Stocker, B. D., Wang, H., Smith, N. G., Harrison, S. P., Keenan, T. F., Sandoval, D., Davis, T., and Prentice, I. C.: P-model v1.0: An optimality-based light use efficiency model for simulating ecosystem gross primary production, Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2019-200, in review, 2019.