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400 tf24 hydraulics merge existing leaf model with tests #433

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400 tf24 hydraulics merge existing leaf model with tests #433

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183a872
add leaf mods
itowers1 Jun 28, 2024
b923dcf
remove plant::: from tests
itowers1 Jul 1, 2024
867b714
add leaf to yml, add argument descriptions
itowers1 Jul 1, 2024
a24a5f6
Create leaf_submodel_documentation.Rmd
itowers1 Jul 1, 2024
99b1e14
package build
itowers1 Jul 1, 2024
eb4b861
Vignette edits and rename
dfalster Jul 1, 2024
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1 change: 1 addition & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ export(K93_Strategy)
export(K93_fixed_environment)
export(K93_hyperpar)
export(K93_make_environment)
export(Leaf)
export(No_Disturbance)
export(NodeSchedule)
export(TF24_Environment)
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340 changes: 340 additions & 0 deletions R/RcppExports.R
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Original file line number Diff line number Diff line change
@@ -1,6 +1,346 @@
# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

Leaf__ctor <- function(vcmax_25, c, b, psi_crit, beta2, jmax_25, hk_s, a, curv_fact_elec_trans, curv_fact_colim, GSS_tol_abs, vulnerability_curve_ncontrol, ci_abs_tol, ci_niter) {
.Call('_plant_Leaf__ctor', PACKAGE = 'plant', vcmax_25, c, b, psi_crit, beta2, jmax_25, hk_s, a, curv_fact_elec_trans, curv_fact_colim, GSS_tol_abs, vulnerability_curve_ncontrol, ci_abs_tol, ci_niter)
}

Leaf__initialize_integrator <- function(obj_, integration_rule, integration_tol) {
invisible(.Call('_plant_Leaf__initialize_integrator', PACKAGE = 'plant', obj_, integration_rule, integration_tol))
}

Leaf__set_physiology <- function(obj_, rho, a_bio, PPFD, psi_soil, leaf_specific_conductance_max, atm_vpd, ca, sapwood_volume_per_leaf_area, leaf_temp, atm_o2_kpa, atm_kpa) {
invisible(.Call('_plant_Leaf__set_physiology', PACKAGE = 'plant', obj_, rho, a_bio, PPFD, psi_soil, leaf_specific_conductance_max, atm_vpd, ca, sapwood_volume_per_leaf_area, leaf_temp, atm_o2_kpa, atm_kpa))
}

Leaf__proportion_of_conductivity <- function(obj_, psi) {
.Call('_plant_Leaf__proportion_of_conductivity', PACKAGE = 'plant', obj_, psi)
}

Leaf__arrh_curve <- function(obj_, Ea, ref_value, leaf_temp) {
.Call('_plant_Leaf__arrh_curve', PACKAGE = 'plant', obj_, Ea, ref_value, leaf_temp)
}

Leaf__peak_arrh_curve <- function(obj_, Ea, ref_value, leaf_temp, H_d, d_S) {
.Call('_plant_Leaf__peak_arrh_curve', PACKAGE = 'plant', obj_, Ea, ref_value, leaf_temp, H_d, d_S)
}

Leaf__transpiration <- function(obj_, psi_stem) {
.Call('_plant_Leaf__transpiration', PACKAGE = 'plant', obj_, psi_stem)
}

Leaf__transpiration_full_integration <- function(obj_, psi_stem) {
.Call('_plant_Leaf__transpiration_full_integration', PACKAGE = 'plant', obj_, psi_stem)
}

Leaf__stom_cond_CO2 <- function(obj_, psi_stem) {
.Call('_plant_Leaf__stom_cond_CO2', PACKAGE = 'plant', obj_, psi_stem)
}

Leaf__transpiration_to_psi_stem <- function(obj_, transpiration_) {
.Call('_plant_Leaf__transpiration_to_psi_stem', PACKAGE = 'plant', obj_, transpiration_)
}

Leaf__assim_rubisco_limited <- function(obj_, ci_) {
.Call('_plant_Leaf__assim_rubisco_limited', PACKAGE = 'plant', obj_, ci_)
}

Leaf__assim_electron_limited <- function(obj_, ci_) {
.Call('_plant_Leaf__assim_electron_limited', PACKAGE = 'plant', obj_, ci_)
}

Leaf__assim_colimited <- function(obj_, ci_) {
.Call('_plant_Leaf__assim_colimited', PACKAGE = 'plant', obj_, ci_)
}

Leaf__assim_minus_stom_cond_CO2 <- function(obj_, x, psi_stem) {
.Call('_plant_Leaf__assim_minus_stom_cond_CO2', PACKAGE = 'plant', obj_, x, psi_stem)
}

Leaf__electron_transport <- function(obj_) {
.Call('_plant_Leaf__electron_transport', PACKAGE = 'plant', obj_)
}

Leaf__set_leaf_states_rates_from_psi_stem <- function(obj_, psi_stem) {
invisible(.Call('_plant_Leaf__set_leaf_states_rates_from_psi_stem', PACKAGE = 'plant', obj_, psi_stem))
}

Leaf__psi_stem_to_ci <- function(obj_, psi_stem) {
.Call('_plant_Leaf__psi_stem_to_ci', PACKAGE = 'plant', obj_, psi_stem)
}

Leaf__hydraulic_cost_Sperry <- function(obj_, psi_stem) {
.Call('_plant_Leaf__hydraulic_cost_Sperry', PACKAGE = 'plant', obj_, psi_stem)
}

Leaf__hydraulic_cost_TF <- function(obj_, psi_stem) {
.Call('_plant_Leaf__hydraulic_cost_TF', PACKAGE = 'plant', obj_, psi_stem)
}

Leaf__profit_psi_stem_Sperry <- function(obj_, psi_stem) {
.Call('_plant_Leaf__profit_psi_stem_Sperry', PACKAGE = 'plant', obj_, psi_stem)
}

Leaf__profit_Sperry_ci <- function(obj_, ci_) {
.Call('_plant_Leaf__profit_Sperry_ci', PACKAGE = 'plant', obj_, ci_)
}

Leaf__profit_psi_stem_TF <- function(obj_, psi_stem) {
.Call('_plant_Leaf__profit_psi_stem_TF', PACKAGE = 'plant', obj_, psi_stem)
}

Leaf__optimise_psi_stem_Sperry <- function(obj_) {
invisible(.Call('_plant_Leaf__optimise_psi_stem_Sperry', PACKAGE = 'plant', obj_))
}

Leaf__optimise_ci_Sperry <- function(obj_, max_ci) {
invisible(.Call('_plant_Leaf__optimise_ci_Sperry', PACKAGE = 'plant', obj_, max_ci))
}

Leaf__optimise_psi_stem_TF <- function(obj_) {
invisible(.Call('_plant_Leaf__optimise_psi_stem_TF', PACKAGE = 'plant', obj_))
}

Leaf__ci___get <- function(obj_) {
.Call('_plant_Leaf__ci___get', PACKAGE = 'plant', obj_)
}

Leaf__ci___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__ci___set', PACKAGE = 'plant', obj_, value))
}

Leaf__stom_cond_CO2___get <- function(obj_) {
.Call('_plant_Leaf__stom_cond_CO2___get', PACKAGE = 'plant', obj_)
}

Leaf__stom_cond_CO2___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__stom_cond_CO2___set', PACKAGE = 'plant', obj_, value))
}

Leaf__assim_colimited___get <- function(obj_) {
.Call('_plant_Leaf__assim_colimited___get', PACKAGE = 'plant', obj_)
}

Leaf__assim_colimited___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__assim_colimited___set', PACKAGE = 'plant', obj_, value))
}

Leaf__transpiration___get <- function(obj_) {
.Call('_plant_Leaf__transpiration___get', PACKAGE = 'plant', obj_)
}

Leaf__transpiration___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__transpiration___set', PACKAGE = 'plant', obj_, value))
}

Leaf__profit___get <- function(obj_) {
.Call('_plant_Leaf__profit___get', PACKAGE = 'plant', obj_)
}

Leaf__profit___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__profit___set', PACKAGE = 'plant', obj_, value))
}

Leaf__psi_stem__get <- function(obj_) {
.Call('_plant_Leaf__psi_stem__get', PACKAGE = 'plant', obj_)
}

Leaf__psi_stem__set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__psi_stem__set', PACKAGE = 'plant', obj_, value))
}

Leaf__lambda___get <- function(obj_) {
.Call('_plant_Leaf__lambda___get', PACKAGE = 'plant', obj_)
}

Leaf__lambda___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__lambda___set', PACKAGE = 'plant', obj_, value))
}

Leaf__lambda_analytical___get <- function(obj_) {
.Call('_plant_Leaf__lambda_analytical___get', PACKAGE = 'plant', obj_)
}

Leaf__lambda_analytical___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__lambda_analytical___set', PACKAGE = 'plant', obj_, value))
}

Leaf__electron_transport___get <- function(obj_) {
.Call('_plant_Leaf__electron_transport___get', PACKAGE = 'plant', obj_)
}

Leaf__electron_transport___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__electron_transport___set', PACKAGE = 'plant', obj_, value))
}

Leaf__gamma___get <- function(obj_) {
.Call('_plant_Leaf__gamma___get', PACKAGE = 'plant', obj_)
}

Leaf__gamma___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__gamma___set', PACKAGE = 'plant', obj_, value))
}

Leaf__ko___get <- function(obj_) {
.Call('_plant_Leaf__ko___get', PACKAGE = 'plant', obj_)
}

Leaf__ko___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__ko___set', PACKAGE = 'plant', obj_, value))
}

Leaf__kc___get <- function(obj_) {
.Call('_plant_Leaf__kc___get', PACKAGE = 'plant', obj_)
}

Leaf__kc___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__kc___set', PACKAGE = 'plant', obj_, value))
}

Leaf__km___get <- function(obj_) {
.Call('_plant_Leaf__km___get', PACKAGE = 'plant', obj_)
}

Leaf__km___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__km___set', PACKAGE = 'plant', obj_, value))
}

Leaf__R_d___get <- function(obj_) {
.Call('_plant_Leaf__R_d___get', PACKAGE = 'plant', obj_)
}

Leaf__R_d___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__R_d___set', PACKAGE = 'plant', obj_, value))
}

Leaf__leaf_specific_conductance_max___get <- function(obj_) {
.Call('_plant_Leaf__leaf_specific_conductance_max___get', PACKAGE = 'plant', obj_)
}

Leaf__leaf_specific_conductance_max___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__leaf_specific_conductance_max___set', PACKAGE = 'plant', obj_, value))
}

Leaf__vcmax___get <- function(obj_) {
.Call('_plant_Leaf__vcmax___get', PACKAGE = 'plant', obj_)
}

Leaf__vcmax___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__vcmax___set', PACKAGE = 'plant', obj_, value))
}

Leaf__jmax___get <- function(obj_) {
.Call('_plant_Leaf__jmax___get', PACKAGE = 'plant', obj_)
}

Leaf__jmax___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__jmax___set', PACKAGE = 'plant', obj_, value))
}

Leaf__rho___get <- function(obj_) {
.Call('_plant_Leaf__rho___get', PACKAGE = 'plant', obj_)
}

Leaf__rho___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__rho___set', PACKAGE = 'plant', obj_, value))
}

Leaf__a_bio___get <- function(obj_) {
.Call('_plant_Leaf__a_bio___get', PACKAGE = 'plant', obj_)
}

Leaf__a_bio___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__a_bio___set', PACKAGE = 'plant', obj_, value))
}

Leaf__PPFD___get <- function(obj_) {
.Call('_plant_Leaf__PPFD___get', PACKAGE = 'plant', obj_)
}

Leaf__PPFD___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__PPFD___set', PACKAGE = 'plant', obj_, value))
}

Leaf__atm_vpd___get <- function(obj_) {
.Call('_plant_Leaf__atm_vpd___get', PACKAGE = 'plant', obj_)
}

Leaf__atm_vpd___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__atm_vpd___set', PACKAGE = 'plant', obj_, value))
}

Leaf__ca___get <- function(obj_) {
.Call('_plant_Leaf__ca___get', PACKAGE = 'plant', obj_)
}

Leaf__ca___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__ca___set', PACKAGE = 'plant', obj_, value))
}

Leaf__psi_soil___get <- function(obj_) {
.Call('_plant_Leaf__psi_soil___get', PACKAGE = 'plant', obj_)
}

Leaf__psi_soil___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__psi_soil___set', PACKAGE = 'plant', obj_, value))
}

Leaf__leaf_temp___get <- function(obj_) {
.Call('_plant_Leaf__leaf_temp___get', PACKAGE = 'plant', obj_)
}

Leaf__leaf_temp___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__leaf_temp___set', PACKAGE = 'plant', obj_, value))
}

Leaf__atm_o2_kpa___get <- function(obj_) {
.Call('_plant_Leaf__atm_o2_kpa___get', PACKAGE = 'plant', obj_)
}

Leaf__atm_o2_kpa___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__atm_o2_kpa___set', PACKAGE = 'plant', obj_, value))
}

Leaf__atm_kpa___get <- function(obj_) {
.Call('_plant_Leaf__atm_kpa___get', PACKAGE = 'plant', obj_)
}

Leaf__atm_kpa___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__atm_kpa___set', PACKAGE = 'plant', obj_, value))
}

Leaf__hydraulic_cost___get <- function(obj_) {
.Call('_plant_Leaf__hydraulic_cost___get', PACKAGE = 'plant', obj_)
}

Leaf__hydraulic_cost___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__hydraulic_cost___set', PACKAGE = 'plant', obj_, value))
}

Leaf__opt_psi_stem___get <- function(obj_) {
.Call('_plant_Leaf__opt_psi_stem___get', PACKAGE = 'plant', obj_)
}

Leaf__opt_psi_stem___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__opt_psi_stem___set', PACKAGE = 'plant', obj_, value))
}

Leaf__opt_ci___get <- function(obj_) {
.Call('_plant_Leaf__opt_ci___get', PACKAGE = 'plant', obj_)
}

Leaf__opt_ci___set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__opt_ci___set', PACKAGE = 'plant', obj_, value))
}

Leaf__count__get <- function(obj_) {
.Call('_plant_Leaf__count__get', PACKAGE = 'plant', obj_)
}

Leaf__count__set <- function(obj_, value) {
invisible(.Call('_plant_Leaf__count__set', PACKAGE = 'plant', obj_, value))
}

Lorenz__ctor <- function(sigma, R, b) {
.Call('_plant_Lorenz__ctor', PACKAGE = 'plant', sigma, R, b)
}
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