R: Tools for Plant Ecophysiology & Modeling

# Tools for Plant Ecophysiology & Modeling

## Documentation for package ‘photosynthesis’ version 2.1.5

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

.get_gbc | Conductance to CO2 (mol / m^2 / s)
.get_gmc | Conductance to CO2 (mol / m^2 / s)
.get_gsc | Conductance to CO2 (mol / m^2 / s)
.get_gtc | Conductance to CO2 (mol / m^2 / s)
.get_guc | Conductance to CO2 (mol / m^2 / s)
analyze_sensitivity | Running 2-parameter sensitivity analyses
aq_response | Non-rectangular hyperbolic model of light responses
A_demand | CO2 supply and demand function (mol / m^2 s)
A_supply | CO2 supply and demand function (mol / m^2 s)
bake | Leaf parameter temperature responses
baked-class | S3 class baked
bake_par | S3 class bake_par
calculated-parameters | Get default functions for calculated parameters in photosynthesis
calculate_j | Inverse non-rectangular hyperbola for J_max calculation
calculate_jmax | Inverse non-rectangular hyperbola for J_max calculation
CO2_conductance | Conductance to CO2 (mol / m^2 / s)
compile_data | Compiling outputs from lists
compute_sensitivity | Computing measures of sensitivity
constants | S3 class constants
enviro_par | S3 class enviro_par
fit_aci_response | Fitting ACi curves
fit_aq_response | Fitting light responses of net CO2 assimilation
fit_aq_response2 | Fit photosynthetic light-response curves
fit_gs_model | Fitting stomatal conductance models
fit_g_mc_variableJ | Fitting mesophyll conductance with the variable J method
fit_hydra_vuln_curve | Fitting hydraulic vulnerability curves
fit_many | Fitting many functions across groups
fit_photosynthesis | Fit photosynthetic models with gas-exchange data
fit_PV_curve | Fitting pressure-volume curves
fit_r_light2 | Fit models to estimate light respiration (R_\mathrm{d})
fit_r_light_kok | Estimating light respiration
fit_r_light_WalkerOrt | Estimating light respiration
fit_r_light_yin | Estimating light respiration
fit_t_response | Fitting temperature responses
FvCB | Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis model
get_all_models | Get default model
get_default_model | Get default model
get_f_parameter | Get default functions for calculated parameters in photosynthesis
gs_mod_ballberry | Stomatal conductance models
gs_mod_leuning | Stomatal conductance models
gs_mod_opti | Stomatal conductance models
gs_mod_optifull | Stomatal conductance models
J | J: Rate of electron transport (umol/m^2/s)
leaf_par | S3 class leaf_par
make_bakepar | Make lists of parameters for 'photosynthesis'
make_constants | Make lists of parameters for 'photosynthesis'
make_enviropar | Make lists of parameters for 'photosynthesis'
make_leafpar | Make lists of parameters for 'photosynthesis'
make_parameters | Make lists of parameters for 'photosynthesis'
marshall_biscoe_1980 | Get default model
parameter_names | Get vector of parameter names
photo | Simulate C3 photosynthesis
photoinhibition | Get default model
photosynthesis | Simulate C3 photosynthesis
photo_parameters | Input parameters to simulate C3 photosynthesis using 'photosynthesis()'
ppm2pa | Convert pressure from PPM to Pascals
print_graphs | Printing graphs to system
read_li6800 | Read a LI-COR file
read_licor | Read a LI-COR file
required_variables | Variables required for *photosynthesis* models
simulate_error | Simulate gas exchange data with measurement error
temp_resp1 | Leaf parameter temperature responses
temp_resp2 | Leaf parameter temperature responses
t_response_arrhenius | Temperature response functions
t_response_arrhenius_kruse | Temperature response functions
t_response_arrhenius_medlyn | Temperature response functions
t_response_arrhenius_topt | Temperature response functions
t_response_calc_dS | Temperature response functions
t_response_calc_topt | Temperature response functions
t_response_heskel | Temperature response functions
t_response_mmrt | Temperature response functions
W_carbox | Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis model
W_regen | Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis model
W_tpu | Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis model