rpmodel: An R repository from xiajz

Purpose

rpmodel provides an implementation of the P-model (Prentice et al., 2014; Wang et al., 2017; Stocker et al., 2020) for predicting acclimated photosynthetic parameters, assimilation, and dark respiration rates as a function of the environment. The main function is rpmodel() which returns a list of variables that are mutually consistent within the theory of the P-model (see Usage ). Further functions used within rpmodel() are also provided through the package.

Usage

This loads the rpmodel package and executes the rpmodel() function without $J_{\text{max}}$ limitation (argument method_jmaxlim = "none"), and with a temperature-independent quantum yield efficiency (argument do_ftemp_kphio = FALSE):

library(rpmodel)
out_pmodel <- rpmodel( 
  tc             = 20           # temperature, deg C
  vpd            = 1000         # Pa,
  co2            = 400          # ppm,
  elv            = 0            # m.a.s.l.,
  kphio          = 0.05         # quantum yield efficiency,
  beta           = 146,         # unit cost ratio a/b,
  fapar          = 1            # fraction  ,
  ppfd           = 300          # mol/m2/d,
  method_optci   = "prentice14",
  method_jmaxlim = "none",
  do_ftemp_kphio = FALSE 
  )

For more information and examples see Usage.

Installation

Stable release

rpmodel is available on CRAN here. To install and load, run the following commands in your R terminal:

install.packages("rpmodel")
library(rpmodel)

Development release

To install and load the latest version of the rpmodel package (development release, not yet on CRAN) run the following command in your R terminal:

if(!require(devtools)){install.packages(devtools)}
devtools::install_github( "stineb/rpmodel", build_vignettes = TRUE )
library(rpmodel)

Author and contact

Benjamin Stocker benjamin.stocker@gmail.com

References

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., 13, 1545–1581, https://doi.org/10.5194/gmd-13-1545-2020, 2020.

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.

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

Acknowledgement

This project was funded by Marie Sklodowska-Curie fellowship H2020-MSCA-IF-2015, project FIBER, grant number 701329.

xiajz/rpmodel