Generate a BioCro model definition
write_model.RdTo facilitate the creation and validation of new BioCro models,
write_model stores the contents of a BioCro crop model definition
(see crop_model_definitions) in an R script to make its
modules and parameter values human-readable.
Usage
write_model(
name,
direct_modules,
differential_modules,
initial_values,
parameters,
ode_solver
)Arguments
- name
A string specifying a name for the model.
- direct_modules
A list or vector of fully-qualified direct module names that can be passed to
run_biocroas itsdirect_module_namesinput argument.- differential_modules
A list or vector of fully-qualified differential module names that can be passed to
run_biocroas itsdifferential_module_namesinput argument.- initial_values
A list of named elements that can be passed to
run_biocroas itsinitial_valuesinput argument.- parameters
A list of named elements that can be passed to
run_biocroas itsparametersinput argument.- ode_solver
A list of named elements that can be passed to
run_biocroas itsode_solverinput argument.
Details
This function returns a string and has no file I/O. Use
writeLines to print the output to console, or to save the
output. See examples below. Note that it is customary to name the R script
file as name.R, where name is the value provided to the function
itself.
Examples
if (require(BioCro)) {
# Create a definition string for Soybean-BioCro
out <- with(BioCro::soybean, {write_model(
'test_soybean_model',
direct_modules,
differential_modules,
initial_values,
parameters,
ode_solver
)})
# Use writeLines to print to console
writeLines(out)
if (interactive()) {
# Use writeLines to save as a `.R` file
writeLines(out, "./test_soybean_model.h")
}
}
#> test_soybean_model <- list(
#> direct_modules = list(
#> "BioCro:format_time",
#> "BioCro:stomata_water_stress_linear",
#> "BioCro:sla_linear",
#> "BioCro:parameter_calculator",
#> "BioCro:soybean_development_rate_calculator",
#> "BioCro:leaf_water_stress_exponential",
#> "BioCro:partitioning_coefficient_logistic",
#> "BioCro:soil_evaporation",
#> "BioCro:solar_position_michalsky",
#> "BioCro:shortwave_atmospheric_scattering",
#> "BioCro:incident_shortwave_from_ground_par",
#> "BioCro:height_from_lai",
#> "BioCro:canopy_gbw_thornley",
#> "BioCro:stefan_boltzmann_longwave",
#> "BioCro:ten_layer_canopy_properties",
#> "BioCro:ten_layer_c3_canopy",
#> "BioCro:ten_layer_canopy_integrator",
#> "BioCro:no_leaf_resp_neg_assim_partitioning_growth_calculator",
#> "BioCro:senescence_coefficient_logistic",
#> "BioCro:carbon_assimilation_to_biomass"
#> ),
#> differential_modules = list(
#> "BioCro:senescence_logistic",
#> "BioCro:maintenance_respiration",
#> "BioCro:partitioning_growth",
#> "BioCro:two_layer_soil_profile",
#> "BioCro:development_index",
#> "BioCro:thermal_time_linear"
#> ),
#> ode_solver = list(
#> type = "boost_rkck54",
#> output_step_size = 1.000000,
#> adaptive_rel_error_tol = 1.000000e-04,
#> adaptive_abs_error_tol = 1.000000e-04,
#> adaptive_max_steps = 200
#> ),
#> initial_values = list(
#> "Leaf" = 0.06312,
#> "Stem" = 0.00789,
#> "Root" = 0.00789,
#> "Grain" = 1e-05,
#> "Shell" = 1e-05,
#> "LeafLitter" = 0,
#> "RootLitter" = 0,
#> "StemLitter" = 0,
#> "soil_water_content" = 0.32,
#> "cws1" = 0.32,
#> "cws2" = 0.32,
#> "DVI" = -1,
#> "TTc" = 0,
#> "Rhizome" = 1e-07,
#> "RhizomeLitter" = 0
#> ),
#> parameters = list(
#> "soil_air_entry" = -2.6,
#> "soil_b_coefficient" = 5.2,
#> "soil_bulk_density" = 1.35,
#> "soil_clay_content" = 0.34,
#> "soil_field_capacity" = 0.32,
#> "soil_sand_content" = 0.32,
#> "soil_saturated_conductivity" = 6.4e-05,
#> "soil_saturation_capacity" = 0.52,
#> "soil_silt_content" = 0.34,
#> "soil_wilting_point" = 0.2,
#> "iSp" = 3.5,
#> "Sp_thermal_time_decay" = 0,
#> "LeafN" = 2,
#> "LeafN_0" = 2,
#> "vmax_n_intercept" = 0,
#> "vmax1" = 110,
#> "alphab1" = 0,
#> "alpha1" = 0,
#> "maturity_group" = 3,
#> "Tbase_emr" = 10,
#> "TTemr_threshold" = 60,
#> "Rmax_emrV0" = 0.199,
#> "Tmin_emrV0" = 5,
#> "Topt_emrV0" = 31.5,
#> "Tmax_emrV0" = 45,
#> "Tmin_R0R1" = 5,
#> "Topt_R0R1" = 31.5,
#> "Tmax_R0R1" = 45,
#> "Tmin_R1R7" = 0,
#> "Topt_R1R7" = 21.5,
#> "Tmax_R1R7" = 38.7,
#> "sowing_fractional_doy" = 0,
#> "alphaLeaf" = 23.8895,
#> "alphaStem" = 24.8248,
#> "betaLeaf" = -18.0851,
#> "betaStem" = -18.5214,
#> "alphaRoot" = 36.967,
#> "betaRoot" = -40.1915,
#> "alphaShell" = 13.5955,
#> "betaShell" = -9.9809,
#> "kRhizome_emr" = 0,
#> "rsec" = 0.2,
#> "soil_clod_size" = 0.04,
#> "soil_reflectance" = 0.2,
#> "soil_transmission" = 0.01,
#> "specific_heat_of_air" = 1010,
#> "lat" = 40,
#> "longitude" = -88,
#> "atmospheric_pressure" = 101325,
#> "atmospheric_transmittance" = 0.6,
#> "atmospheric_scattering" = 0.3,
#> "par_energy_fraction" = 0.5,
#> "par_energy_content" = 0.219,
#> "heightf" = 6,
#> "min_gbw_canopy" = 0.005,
#> "dry_biomass_per_carbon" = 30.026,
#> "emissivity_sky" = 1,
#> "chil" = 0.81,
#> "k_diffuse" = 0.7,
#> "kpLN" = 0,
#> "leaf_reflectance_nir" = 0.42,
#> "leaf_reflectance_par" = 0.1,
#> "leaf_transmittance_nir" = 0.42,
#> "leaf_transmittance_par" = 0.05,
#> "lnfun" = 0,
#> "Gstar_c" = 19.02,
#> "Gstar_Ea" = 37830,
#> "Jmax_c" = 17.57,
#> "Jmax_Ea" = 43540,
#> "Kc_c" = 38.05,
#> "Kc_Ea" = 79430,
#> "Ko_c" = 20.3,
#> "Ko_Ea" = 36380,
#> "phi_PSII_0" = 0.352,
#> "phi_PSII_1" = 0.022,
#> "phi_PSII_2" = -0.00034,
#> "Rd_c" = 18.72,
#> "Rd_Ea" = 46390,
#> "theta_0" = 0.76,
#> "theta_1" = 0.018,
#> "theta_2" = -0.00037,
#> "Tp_c" = 19.77399,
#> "Tp_Ha" = 62990,
#> "Tp_Hd" = 182140,
#> "Tp_S" = 588,
#> "Vcmax_c" = 26.35,
#> "Vcmax_Ea" = 65330,
#> "jmax" = 195,
#> "jmax_mature" = 195,
#> "sf_jmax" = 0.2,
#> "electrons_per_carboxylation" = 4.5,
#> "electrons_per_oxygenation" = 5.25,
#> "tpu_rate_max" = 13,
#> "Rd" = 1.28,
#> "Catm" = 372.59,
#> "O2" = 210,
#> "b0" = 0.008,
#> "b1" = 10.6,
#> "Gs_min" = 0.001,
#> "windspeed_height" = 5,
#> "beta_PSII" = 0.5,
#> "leafwidth" = 0.1,
#> "growth_respiration_fraction" = 0,
#> "grc_stem" = 0.02828,
#> "grc_root" = 0.0027,
#> "mrc_leaf" = 0.00048836,
#> "mrc_stem" = 0.00048836,
#> "mrc_root" = 1e-05,
#> "mrc_grain" = 1e-05,
#> "retrans" = 0.9,
#> "retrans_rhizome" = 1,
#> "rateSeneLeaf" = 0.012198,
#> "rateSeneStem" = 0.000117,
#> "rateSeneRoot" = 0,
#> "rateSeneRhizome" = 0,
#> "alphaSeneLeaf" = 48.32,
#> "alphaSeneStem" = 4.1937,
#> "alphaSeneRoot" = 10,
#> "alphaSeneRhizome" = 10,
#> "betaSeneLeaf" = -29.5393,
#> "betaSeneStem" = -3.3124,
#> "betaSeneRoot" = -10,
#> "betaSeneRhizome" = -10,
#> "remobilization_fraction" = 0.6,
#> "soil_depth1" = 0,
#> "soil_depth2" = 2.5,
#> "soil_depth3" = 10,
#> "wsFun" = 2,
#> "hydrDist" = 0,
#> "rfl" = 0.2,
#> "rsdf" = 0.44,
#> "phi1" = 0.01,
#> "phi2" = 1.5,
#> "tbase" = 10,
#> "km_leaf_litter" = 2,
#> "timestep" = 1
#> )
#> )