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Soybean-BioCro model definition

soybean.Rd

Initial values, parameters, direct modules, differential modules, and a differential equation solver that can be used to run soybean growth simulations in Champaign, Illinois and other locations. Along with the soybean circadian clock specifications (soybean_clock), these values define the soybean growth model of Matthews et al. (2022) [doi:10.1093/insilicoplants/diab032 ], which is commonly referred to as Soybean-BioCro.

To represent soybean growth in Champaign, IL, these values must be paired with the Champaign weather data (cmi_soybean_weather_data). This weather data includes the output from the soybean circadian clock model (soybean_clock), so the clock components do not need to be included when running a soybean growth simulation using this weather data. The parameters already include the clay_loam values from the soil_parameters dataset, which is the appropriate soil type for Champaign.

Some specifications, such as the values of photosynthetic parameters, would remain the same in any location; others, such as the latitude or longitude, would need to change when simulating crop growth in different locations. Care must be taken to understand each input quantity before attempting to run simulations in other places or for other cultivars.

Usage

soybean

Format

A list of 5 named elements that are suitable for passing to run_biocro, as described in the help page for crop_model_definitions.

Details

As improvements are made to the BioCro modules, their behavior changes, and the soybean model parameters must be updated. Following significant module updates, reparameterization is performed using a script that is included with the BioCro package; its location can be found by typing system.file('extdata', 'parameterize_soybean.R', package = 'BioCro') in an R session. The parameterization script generally uses the same method and data as used in Matthews et al. (2022), with a few differences, such as the separation of pod mass into separate seed and shell components.

The following is a summary of reparameterizations that have occurred since the original publication of the Soybean-BioCro model:

  • 2023-06-18: Several modules have been updated, and the value of the atmospheric transmittance has been changed from 0.85 to 0.6 based on Campbell and Norman, An Introduction to Environmental Biophysics, 2nd Edition, Pg 173. Due to these changes, reparameterization of the following was required: alphaLeaf, alphaRoot, alphaStem, alphaShell, betaLeaf, betaRoot, betaStem, betaShell, rateSeneLeaf, rateSeneStem, alphaSeneLeaf, betaSeneLeaf, alphaSeneStem, and betaSeneStem.

  • 2023-03-15: Several modules have been updated. The most significant changes are that (1) the BioCro:no_leaf_resp_neg_assim_partitioning_growth_calculator now reduces the leaf growth rate in response to water stress and (2) the partitioning modules now include a new tissue type (shell). The new component allows us to distinguish between components of the soybean pod, where shell represents the pericarp and grain represents the seed. This distinction has been found to be important for accurately predicting seed biomass, which is more important in agricultural settings than the entire pod mass, since the pericarp is not included in typical yield measurements. Due to these changes, reparameterization of the following was required: alphaLeaf, alphaRoot, alphaStem, alphaShell, betaLeaf, betaRoot, betaStem, betaShell, rateSeneLeaf, rateSeneStem, alphaSeneLeaf, betaSeneLeaf, alphaSeneStem, and betaSeneStem. It was also necessary to add a new direct module to the model definition: BioCro:leaf_water_stress_exponential. This module calculates the fractional reduction in leaf growth rate due to water stress.

  • 2024-09-12: Several changes have been made: (1) The mrc1 and mrc2 were renamed to grc_stem and grc_root, respectively. These two parameters are used to scale the assimilate rate, which is commonly called growth respiration coefficient (grc). (2) A new module, BioCro:maintenance_respiration, has been added to account for maintenance respiration during the biomass partitioning. This module removes a fraction from each organ by a constant parameter called mrc_* (e.g., mrc_leaf) and also by a temperature-dependent Q10 scaling factor. Among these mrc_* parameters, mrc_leaf and mrc_stem are set equal to represent maintenance respiration for the shoot, while mrc_grain is assigned a negligible value to prevent grain biomass reduction at the season end. No decreasing trends have been seen in the observed data. (3) Parameter optimizations against the 2002-2006 biomass datasets were performed to accommodate these changes.

  • 2025-04-23: Several changes have been made since the previous update. Regarding modules, several new modules have been added: BioCro:format_time, BioCro:sla_linear, BioCro:carbon_assimilation_to_biomass, and BioCro:maintenance_respiration_calculator. These modules do not change the model's overall behavior; rather, they make some new quantities available in the outputs, such as maintenance respiration rates. The BioCro:format_time module is related to a change in how BioCro defines time; previously it was defined in units of days, but now it is given in hours. The partitioning growth calculator module was also changed to BioCro:partitioning_growth_calculator, since the previous module was removed from the library; this module has identical behavior to the old one (BioCro:no_leaf_resp_neg_assim_partitioning_growth_calculator). Regarding parameters, several modules now require new input parameters whose values were previously hard-coded: dry_biomass_per_carbon, grc_leaf, grc_rhizome, grc_grain, grc_shell, mrc_rhizome, mrc_shell, alphaRhizome, betaRhizome, kRhizome_emr_DVI, and several parameters related to the temperature dependence of FvCB model parameters (e.g. Gstar_c and Gstar_Ea). A few parameters have also been renamed to better indicate their meaning, such as Rd becoming RL_at_25. Finally, due to changes in the calculation of growth respiration rates, the model needed to be re-parameterized against the 2002-2006 biomass data sets. This resulted in changes to the values of alphaLeaf, alphaStem, betaLeaf, betaStem, alphaShell, betaShell, grc_root, grc_stem, mrc_leaf, mrc_root, mrc_stem, rateSeneLeaf, rateSeneStem, alphaSeneLeaf, alphaSeneStem, betaSeneLeaf, and betaSeneStem.

  • 2025-08-25: The leaf boundary layer conductance model has been changed to a model described in Campbell & Norman (1998), causing small differences in the simulated soybean biomass and requiring a reparameterization. This update alters the values of the same parameters that were changed in the previous update on 2025-04-23.

Whenever a reparameterization is made, this list should be updated, and any vignettes using the soybean model should be checked to see if any axis limits, etc., need to change.

Source

This model is described in detail in Matthews et al. (2022) [doi:10.1093/insilicoplants/diab032 ]. Here we make a few notes about some of its components.

General Comments

  • For historical reasons, the seed tissue in this model is called Grain. The entire pod biomass can be calculated by adding the Grain and Shell biomass.

  • For historical reasons, this model includes a Rhizome tissue. Soybean does not have a rhizome, so the rhizome-related values in the model are chosen such that the rhizome begins with zero mass and does not grow or senesce. These values include the initial Rhizome and RhizomeLitter, and the following parameters: alphaRhizome, betaRhizome, kRhizome_emr, kRhizome_emr_DVI, grc_rhizome, mrc_rhizome, rateSeneRhizome, alphaSeneRhizome, betaSeneRhizome, and retrans_rhizome.

  • Some parameter values are specific to Champaign, Illinois (2002-2006) and may need to change for other years and locations: the soil type, Catm, maturity_group, windspeed_height, lat, and longitude.

ode_solver

  • type: For this model, the ODE solver type should not be boost_rosenbrock or auto (which defaults to boost_rosenbrock when a fixed step size Euler ODE solver is not required, as in this case) since the integration will fail unless the tolerances are stringent (e.g., output_step_size = 0.01, adaptive_rel_error_tol = 1e-9, adaptive_abs_error_tol = 1e-9).

initial_values

  • Leaf: The initial leaf biomass is set to 80% of the mass per land area of seeds sown at the start of the season. For the initial total seed mass per land area, we use the following equation: Number of seeds per meter * weight per seed / row spacing. The number of seeds per meter is 20 and the row spacing is 0.38 m, as reported in Morgan et al. (2004) [doi:10.1104/pp.104.043968 ]. The weight per seed is based on the average of .12 to .18 grams, as reported by Feedipedia. Thus, we have an initial biomass of (20 seeds / m) * (0.15 g / seed) / (0.38 m) = 7.89 g / m^2, equivalent to 0.0789 Mg / ha in the typical BioCro units.

  • Stem: The initial stem biomass is set to 10% of the initial seed biomass; see Leaf for more info.

  • Root: The initial root biomass is set to 10% of the initial seed biomass; see Leaf for more info.

  • Grain: In principle, the initial seed mass should be zero, but here it is instead set to a very small value (1e-5) for compatibility with some models where key tissue masses cannot be zero.

  • Seed: Initialized to a small value for the same reasons as the Grain.

parameters

  • Optimized parameters: The following parameter values are determined using an optimization procedure: alphaLeaf, alphaStem, betaLeaf, betaStem, alphaShell, betaShell, grc_root, grc_stem, mrc_leaf, mrc_root, mrc_stem, rateSeneLeaf, rateSeneStem, alphaSeneLeaf, alphaSeneStem, betaSeneLeaf, and betaSeneStem.

  • Basic soil info: Soil parameter values corresponding to clay_loam from the soil_parameters dataset are used here, which is the appropriate soil type for Champaign, Illinois. These parameters are: soil_air_entry, soil_b_coefficient, soil_bulk_density, soil_clay_content, soil_field_capacity, soil_sand_content, soil_saturated_conductivity, soil_saturation_capacity, soil_silt_content, and soil_wilting_point.

  • iSp: Specific leaf area; determined using 2002 values of average_LAI / average_leaf_biomass as reported in Dermody et al. 2006 [doi:10.1111/j.1469-8137.2005.01565.x ] and Morgan et al. 2005 [doi:10.1111/j.1365-2486.2005.001017.x ].

  • Sp_thermal_time_decay: Set to 0 to ensure specific leaf area is constant with time.

  • maturity_group: Typical maturity group grown in Champaign, IL.

  • Soybean development (R0 - R1): The "emr - V0" values from Table 2 of Setiyono et al., 2007 [doi:10.1016/j.fcr.2006.07.011 ] were used for Tmin_R0R1, Topt_R0R1, and Tmax_R0R1.

  • Soybean development (emr - V0, R1 - R7): Values from Table 2 of Setiyono et al., 2007 [doi:10.1016/j.fcr.2006.07.011 ] were used for Rmax_emrV0, Tmin_emrV0, Topt_emrV0, Tmax_emrV0, Tmin_R1R7, Topt_R1R7, and Tmax_R1R7.

  • sowing_fractional_doy: Set to 0 because Soybean-BioCro uses the weather data to set the sowing time. In other words, the weather data is truncated so it begins at the beginning of the simulation.

  • atmospheric_transmittance: Campbell and Norman, An Introduction to Environmental Biophysics, 2nd Edition, Pg 173.

  • par_energy_content: Set to 1 / 4.57, as in Plant Growth Chamber Handbook. CHAPTER 1 - RADIATION - John C. Sager and J. Craig McFarlane. Table 2, Pg 3 online PDF

  • heightf: Estimated using a typical soybean LAI of 6 when canopy is 1 m tall.

  • chil: Campbell and Norman, An Introduction to Environmental Biophysics, 2nd Edition, Table 15.1, pg 253.

  • k_diffuse: Estimated from Campbell and Norman, An Introduction to Environmental Biophysics, 2nd Edition, Figure 15.4, pg 254

  • lnfun: Set to 0 to use the same value of Vcmax_at_25 for all canopy layers.

  • Leaf optical properties: Leaf reflectance and transmittance in the PAR band (leaf_reflectance_par and leaf_transmittance_par) are estimated from [doi:10.2134/agronmonogr31.c7 ], [doi:10.2134/agronj1971.00021962006300010038x ], and [doi:10.2134/agronj1991.00021962008300030026x ]. Reflectance and transmittance in the NIR band (leaf_reflectance_nir and leaf_transmittance_nir) are from [doi:10.2134/agronmonogr31.c7 ].

  • FvCB model (temperature response of Rubisco kinetic properties): The following values are from Table 1 of Bernacchi et al. 2001 [doi:10.1111/j.1365-3040.2001.00668.x ]: Gstar_c, Gstar_Ea, Kc_c, Kc_Ea, Ko_c, Ko_Ea, Vcmax_c, Vcmax_Ea.

  • FvCB model (temperature response of non-photorespiratory CO2 release): RL_c and RL_Ea are from Table 1 of Bernacchi et al. 2001 [doi:10.1111/j.1365-3040.2001.00668.x ].

  • FvCB model (temperature response of electron transport): The following values are from Table 1 of Bernacchi et al. 2003 [doi:10.1046/j.0016-8025.2003.01050.x ]: Jmax_c and Jmax_Ea. The following are from Table 2: phi_PSII_0, phi_PSII_1, phi_PSII_2, theta_0, theta_1, theta_2.

  • FvCB model (temperature response of triose phosphate utilization): The following values are from the caption of Figure 7 of Yang et al. 2016 [doi:10.1007/s00425-015-2436-8 ]: Tp_Ha, Tp_Hd, and Tp_S. The value of Tp_c was chosen to ensure that Tp_norm = 1 at 25 degrees C.

  • FvCB model (light response): beta_PSII, electrons_per_carboxylation, and electrons_per_oxygenation are from Bernacchi et al. 2003 [doi:10.1046/j.0016-8025.2003.01050.x ].

  • FvCB model (rates at 25 degrees C): Vcmax_at_25 and Jmax_at_25 are seasonal averages across 2002 as reported in Bernacchi et. al. 2005 [doi:10.1007/s00425-004-1320-8 ]. RL_at_25 is from Davey et al. 2004 [doi:10.1104/pp.103.030569 ] (Table 3, cv Pana, co2 368 ppm). Tp_at_25 was estimated from unpublished data provided by A. Digrado (UIUC, August 2019).

  • Ball-Berry model: b0 and b1 are from Leakey et al. 2006 [doi:10.1111/j.1365-3040.2006.01556.x ].

  • Catm: Global average value for 2002.

  • leafwidth: Estimate based on large mature leaflets.

  • rateSeneRoot: Set to 0 to disable root senescence.

  • phi2: from Sugarcane-BioCro, Jaiswal et al. 2017 [doi:10.1038/nclimate3410 ].

The following parameters are not used by Soybean-BioCro, but are defined for compatability with current or historical modules:

  • alpha1: Needed for the BioCro:parameter_calculator module, but not used for C3 plants.

  • alphab1: Needed for the BioCro:parameter_calculator module, but not used for C3 plants.

  • LeafN: Needed for the BioCro:parameter_calculator module, but not used for C3 plants.

  • LeafN_0: Needed for the BioCro:parameter_calculator module, but not used for C3 plants.

  • kpLN: Has no influence on Soybean-BioCro because lnfun is set to to 0.

  • FvCB model (varying Jmax): For compatability with the BioCro:varying_Jmax25 module, Jmax_at_25_mature is set to the same value as Jmax_at_25. sf_jmax is also needed for this module.

  • alphaSeneRoot: Has no influence on Soybean-BioCro because rateSeneRoot is set to 0.

  • betaSeneRoot: Has no influence on Soybean-BioCro because rateSeneRoot is set to 0.

  • km_leaf_litter: Needed for compatability with the BioCro:litter_cover module. Estimated based on 2021-2022 Energy Farm measurements, where the final leaf litter mass was around 1.5 - 2.5 Mg / Ha and covered around half of the ground area near the plants.

See also