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photosynthesis
View on CRAN: Click
here
Download and install photosynthesis package within the R console
Install from CRAN:
install.packages("photosynthesis")
Install from Github:
library("remotes")
install_github("cran/photosynthesis")
Install by package version:
library("remotes")
install_version("photosynthesis", "2.1.4")
Attach the package and use:
library("photosynthesis")
Maintained by
Chris Muir
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-05-09
Latest Update: 2023-08-15
Description:
Contains modeling and analytical tools for plant ecophysiology.
MODELING: Simulate C3 photosynthesis using the Farquhar, von Caemmerer,
Berry (1980) model as described in Buckley and
Diaz-Espejo (2015) . It uses units to ensure that
parameters are properly specified and transformed before calculations.
Temperature response functions get automatically "baked" into all
parameters based on leaf temperature following Bernacchi et al. (2002)
. The package includes boundary layer, cuticular,
stomatal, and mesophyll conductances to CO2, which each can vary on the
upper and lower portions of the leaf. Use straightforward functions to
simulate photosynthesis over environmental gradients such as Photosynthetic
Photon Flux Density (PPFD) and leaf temperature, or over trait gradients
such as CO2 conductance or photochemistry.
ANALYTICAL TOOLS: Fit ACi (Farquhar et al. (1980) )
and AQ curves (Marshall & Biscoe (1980) ),
temperature responses (Heskel et al. (2016) ;
Kruse et al. (2008) , Medlyn et al.
(2002) , Hobbs et al. (2013)
), respiration in the light (Kok (1956)
, Walker & Ort (2015) ,
Yin et al. (2009) , Yin et al. (2011)
), mesophyll conductance (Harley et al. (1992)
), pressure-volume curves (Koide et al. (2000)
, Sack et al. (2003)
, Tyree et al. (1972)
), hydraulic vulnerability curves (Ogle et al. (2009)
, Pammenter et al. (1998)
), and tools for running sensitivity
analyses particularly for variables with uncertainty (e.g. g_mc(), gamma_star(),
R_d()).
How to cite:
Chris Muir (2019). photosynthesis: Tools for Plant Ecophysiology & Modeling. R package version 2.1.4, https://cran.r-project.org/web/packages/photosynthesis
Previous versions and publish date:
Other packages that cited photosynthesis R package
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Other R packages that photosynthesis depends,
imports, suggests or enhances
Functions, R codes and Examples using
the photosynthesis R package
Some associated functions: A_supply . CO2_conductance . FvCB . J . analyze_sensitivity . aq_response . bake . bake_par . baked-class . calculated-parameters . compile_data . compute_sensitivity . constants . enviro_par . fit_PV_curve . fit_aci_response . fit_aq_response . fit_aq_response2 . fit_g_mc_variableJ . fit_gs_model . fit_hydra_vuln_curve . fit_many . fit_photosynthesis . fit_r_light . fit_r_light2 . fit_t_response . gs_models . j_calculations . leaf_par . make_parameters . models . parameter_names . photo_parameters . photosynthesis-package . photosynthesis . ppm2pa . print_graphs . read_li6800 . read_licor . required_variables . simulate_error . t_functions .
Some associated R codes: FvCB.R . analyze_sensitivity.R . aq_response.R . bake-par.R . bake.R . calculated-parameters.R . compile_data.R . compute_sensitivity.R . conductance.R . constants.R . data.R . enviro-par.R . fit_PV_curve.R . fit_aci_response.R . fit_aq_response.R . fit_g_mc_variableJ.R . fit_gs_model.R . fit_hyrda_vuln_curve.R . fit_many.R . fit_photosynthesis.R . fit_r_light.R . fit_t_response.R . gs_models.R . j_calculations.R . leaf-par.R . make_parameters.R . models.R . parameter_names.R . photosynthesis-package.R . photosynthesis.R . print_graphs.R . read_licor.R . simulate_error.R . t_functions.R . utils.R . Full photosynthesis package functions and examples
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