Tools for Plant Ecophysiology & Modeling

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Documentation for package ‘photosynthesis’ version 2.1.5

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.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