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)
[tools:::Rd_expr_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.
soybeanA list of 5 named elements that are suitable for passing to
run_biocro, as described in the help page for
crop_model_definitions.
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.
run_biocro
modules
crop_model_definitions
soybean_clock