BioCro

• Several new temperature response functions, including peaked_arrhenius_response, were also added to temperature_response_functions.h
• The Dekker method is now used to check for consistent values of stomatal conductance when solving the combined assimilation + energy balance models in the BioCro:c3_leaf_photosynthesis, BioCro:c3_canopy, BioCro:c4_leaf_photosynthesis, and BioCro:c4_canopy modules.
• Added two new years of weather data (2023 and 2025) to the weather data set and one year of globally-averaged atmospheric CO2 concentration (2025) to the catm_data data set.
• Added several new modules for simulating soil water dynamics, which are generally based on DSSAT and its original sources:
• BioCro:atmospheric_pressure_from_elevation
• BioCro:multi_layer_soil_profile
• BioCro:multilayer_soil_profile_avg
• BioCro:soil_evaporation_ritchie
• BioCro:soil_surface_runoff
• BioCro:soil_type_selector
• BioCro:soil_water_downflow
• BioCro:soil_water_dynamic_rooting
• BioCro:soil_water_tiledrain
• BioCro:soil_water_upflow
• BioCro:soil_water_uptake

These modules are now used in the soybean_sw model. Eventually, soybean_sw

will replace the original soybean model, but it will take some time to

ensure that all examples that currently use soybean will be able to to work

with soybean_sw.

• The BioCro:stomata_water_stress_linear module was updated to be more flexible, and a related module was added (BioCro:stomata_water_stress_bilinear). The soybean model now uses the bilinear version since it produces more realistic results when the soil is dry.
• The new stomata water stress modules use input parameters called StomataWS_gradient and StomataWS_intercept. A script for calibrating the values of these parameters for soybean has been added to the package: inst/extdata/optimize_StomataWS_linear.R.
• The C3 photosynthesis calculations now include mesophyll conductance, and they determine Cc along with Ci. Setting gm_at_25 to infinity will ensure that Cc = Ci, reproducing the behavior of previous BioCro versions.
• The inst/extdata/parameterize_soybean.R script has been updated to use a better approach, where the evolutionary optimizer is followed by a Nelder-Mead optimizer.
• The upper bound for the grc_ parameters in the parmaterization script was changed to a safer value.
• The behavior of the BioCro:partitioning_growth_calculator module was changed so that respiratory losses are subtracted from each tissue proportional to its biomass, rather than proportional to its partitioning factor.

Internal changes

• Refactored code organization:
• Renamed sunML struct/function to canopy_light and Light_model to atmosphere_light_scattering for improved clarity.
• Moved canopy light distribution functions to canopy_light_helpers.h.
• Moved atmospheric light scattering calculations to atmosphere_light_scattering.h.
• Added photosynthesis utilities including the new leaf_assim vector-space type and canopy_integrand functor to photosynthesis.h.
• New tests were added to test.cumulative_modules.R to ensure that all carbon and water mass is conserved.

Bug Fixes

• Changed the minimum version of macOS checked by the R-CMD-check from 4.2.0 to 4.3.0.
• CRAN now only provides R versions 4.2.3 and above for Mac.
• Somehow the vignette builder cannot find the knitr package when using the the online testing setup for R version 4.2.0 or 4.2.3 even when knitr is installed, causing a spurious test failure. This problem does not occur for R version 4.3.0.
• A small typo was fixed in the BioCro:solar_position_michalsky module; this typo had no influence on the model outputs.