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Soybean-BioCro model definition

soybean_sw.Rd

Alternate version of the soybean model, where the main difference is that soybean_sw uses a new set of soil water modules.

Usage

soybean_sw

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 this version of the soybean model was created:

  • 2026-08-07: Changes were made to the leaf-level photosynthesis calculations that reduce the frequency of convergence failures. The model was re-parameterized since these changes make a larger region of parameter space accessible to the optimizers.

  • 2026-06-22: The model was changed to use the new stomata_water_stress_bilinear module instead of the stomata_water_stress_linear, and the behavior of the partitioning_growth_calculator module when canopy assimilation is negative was altered. These changes produce more reasonable simulation results when there is severe water stress, especially late in the season during grain filling. A reparameterization was required after making these changes.

  • 2026-05-13: The soil water modules were updated by migrating the soil water modules from DSSAT into BioCro. This process required many changes to make the modules work with an hourly time step. Also, the StomataWS function was changed based on a calibration on stomatal conductance data from Gray et al. (2016). These changes caused large differences in the calculated biomass, therefore the partitioning coefficients were reparameterized.

Source

parameters

  • Basal crop coefficient: Values of kcbmax, kcbmin, and skc for maize and cotton are reported in Table 3 of DeJonge & Thorp (2017) [doi:10.13031/trans.12321 ]. The two crops have the same values of kcbmax and kcbmin (1.15 and 0) and nearly indentical values of skc (0.5 and 0.6, respectively), indicating that these parameters do not change much for different crops. Here we use 1.15, 0, and 0.55 for soybean, where the skc value is the mean of the maize and cotton values.

  • Stomatal water stress parameters: Values of StomataWS_gradient and StomataWS_intercept were determined by matching predicted and values of stomatal conductance with observed ones as reported in Gray et al. 2016. A script for determining the values is included with the BioCro package; its location can be found by typing system.file('extdata', 'optimize_StomataWS_linear.R', package = 'BioCro') in an R session.

  • Regarding soil types in Champaign County: according to the Web Soil Survey, soils in this region are predominantly silty clay loam, loam, and silt loam, with variation across soil depth. In BioCro, soil types 4–7 correspond to loamy soils. Although this classification does not provide the most accurate representation of soil hydraulic properties, it is reasonable to constrain our parameterization within this range for consistency. In our current setup, we assign type 7 (silty clay loam) to layers 3–6 and type 6 (clay loam) to layers 1–2. This configuration produces reasonably good agreement with observed soil water dynamics at SoyFACE.

See also