BioCro - BioCro 3.3.0

Changes in BioCro version 3.3.0

Minor User-Facing Changes

• Increased the minimum supported R version to 4.1.0.

  • This was necessary because the C++ standard was switched from C++11 to C++17, as required by CRAN.

  • The version of boost bundled with BioCro (1.71.0) was also not compatible with C++17, requiring an update to a new version (1.89.0).

• New multidimensional and 1D root finders written in C++ have been added to src/math/roots/. These are intended to support models requiring numerical solutions to sets of simultaneous equations, and they will eventually be moved to the biocro/framework repository.

  • For multidimensional root finders, see src/math/roots/multidim/zeros.h for example usage. Currently, only one method is available: Broyden's method.

  • For 1D root finders, see src/math/roots/onedim/roots.h for example usage and a list of available methods.

  • These new finders are now used in several places:

    • For Ci calculations, replaced the original fixed-point iteration method with the new 1D Dekker root finder. Fixed-point iteration is known to be unstable in these calculations; see Sun et al. (2012) "A numerical issue in calculating the coupled carbon and water fluxes in a climate model." Journal of Geophysical Research https://dx.doi.org/10.1029/2012JD018059.

    • For leaf temperature calculations, replaced the original fixed-point iteration method with the new 1D Dekker root finder.

    • For the Nikolov leaf boundary layer conductance model, replaced the original fixed-point iteration method with the new 1D Dekker root finder.

• Added a new module which computes day length from solar position: BioCro:daylength_calculator.

• Added a new model for leaf boundary layer conductance (from Campbell & Norman 1998). This model is now used in place of the Nikolov model for energy balance calculations, since it can be solved more easily, and does not have multiple solutions.

• Changed how growth respiration is calculated (so the rate of growth respiration is zero whenever the base rate of carbon available for growth is negative) and made sure it is calculated consistently across different modules.

• Renamed several quantities to make their meanings more clear:

  • mrc1 has been replaced by grc_leaf and grc_stem to better indicate that this is a growth respiration coefficient that was applied to two different tissues.

  • mrc2 has been replaced by grc_root and grc_rhizome for similar reasons.

  • mrc_root has been split into mrc_root and mrc_rhizome instead of using one coefficient for both.

  • mrc_grain has been split into mrc_grain and mrc_shell instead of using one coefficient for both.

  • Molar fluxes (with units of micromol / m^2 / s) are now distinguished from mass fluxes (with units of Mg / ha / hr) when necessary by replacing _rate with _molar_flux in the quantity name. For example, canopy_assimilation_molar_flux is a molar flux and canopy_assimilation_rate is a mass flux. Previously the molar fluxes had a suffix of _CO2, so this necessitated renaming two quantities: canopy_assimilation_rate_CO2 and canopy_photorespiration_rate_CO2.

  • GrossAssim_CO2 was renamed to canopy_gross_assimilation_molar_flux for consistency with other canopy-level molar flux outputs such as canopy_assimilation_molar_flux.

  • Rd was renamed to RL and its definition was updated to "the rate of non-photorespiratory CO2 release in the light" when necessary, following https://doi.org/10.1093/plphys/kiab076 and https://doi.org/10.1111/pce.14153. This avoid the ambiguity of using a subscript d (which can refer to "day" or "dark" in different contexts) and it reflects an updated understanding of the metabolic origin of this term (it is not exclusively, or even primarily, due to mitochondrial respiration).

  • Several quantities representing a value at 25 degrees C were renamed to better reflect this: jmax -> Jmax_at_25, Rd -> RL_at_25, tpu_rate_max -> Tp_at_25, vmax1 -> Vcmax_at_25, vmax -> Vcmax_at_25.

• The BioCro:parameter_calculator module no longer recalculates Vcmax_at_25.

• The rate of non-photorespiratory CO2 release in the light (RL or canopy_non_photorespiratory_CO2_release) is now included in the outputs of photosynthesis modules, including at the canopy level.

• The rate of whole-plant growth respiration is now included in the outputs of the canopy photosynthesis modules, including the C4 canopy, where whole-plant growth respiration had not been previously calculated.

• The BioCro:maintenance_respiration module was split into two modules (a differential module called BioCro:maintenance_respiration and a direct module called BioCro:maintenance_respiration_calculator) to make maintenance respiration rates available as outputs.

• Several changes were made to the partitioning growth calculator modules:

  • Now there are only two such modules: BioCro:partitioning_growth_calculator and BioCro:partitioning_growth_calculator_leaf_costs.

  • The partitioning growth calculator modules now include growth respiration rates in their outputs.

  • They have also been standardized so they apply growth respiration to all tissues, and they both incorporate reductions in leaf growth rate due to water stress.

• The BioCro:partitioning_coefficient_logistic module can now calculate the rhizome partitioning coefficient using the logistic model.

• Two new modules were added for calculating cumulative flows of CO2 and water: BioCro:cumulative_carbon_dynamics and BioCro:cumulative_water_dynamics.

• A new module was added for calculating the total amounts of carbon used for growth and maintenance respiration: BioCro:total_growth_and_maintenance_respiration.

• Simplified the radiation use efficiency (RUE) model such that net CO2 assimilation is directly proportional to the incident quantum flux of photons.

• Altered test_module (and hence test_module_library) so that new module outputs produce a warning but don't cause an error on their own.

• Altered evaluate_module, partial_evaluate_module, and module_response_curve so that by default, module errors do not prevent response curve calculations from completing. The original behavior of these functions can be reproduced by setting stop_on_exception to TRUE when calling them.

• Following changes to the behavior of some modules, the soybean model was re-parameterized. The parameterization script is now included in the BioCro repository and package. See the help file for soybean for complete details.

• catm_data was updated to include the global average atmospheric CO2 concentration in 2024.

• Added a new workshop vignette, and removed an outdated vignette about the FvCB model.

• Links to the main BioCro documentation web site were changed from https://biocro.github.io to https://biocro.org

Internal changes

• Renamed the resp() function to growth_resp_Q10() to better indicate its purpose, and moved it to a respiration header file. The new header file (respiration.h) also includes a new maintenance respiration function (maintenance_respiration_Q10()) and a simpler growth respiration function that does not apply a Q10 response (growth_resp()).

Bug fixes

• Fixed a an issue where setting adaptive_max_steps to NA in R would cause run_biocro to fail at the first time point.

• Fixed a typo in the calculation of relative humidity just above the canopy (RH_canopy).

Biosphere - Plants and Vegetation - C++
Published by eloch216 22 days ago

BioCro - BioCro 3.2.0

Minor User-Facing Changes

• Added maintenance respiration for each organ in a new module called BioCro:maintenance_respiration. Maintenance respiration is modelled by removing a fraction of dry biomass. The fraction removed is determined by an organ-specific "maintenance respiration coefficient" (such as mrc_leaf) and follows a Q10 temperature response. This differs from the existing growth respiration that is applied to the stem and root, and from a separate canopy growth respiration that can be used to rescale the canopy assimilation rate.

• Separated the specific leaf area (SLA) calculations from the BioCro:parameter_calculator module to enable alternate approaches to SLA. The original method is now available as the BioCro:sla_linear module, and a new logistic method has been added: BioCro:sla_logistic. The stored crop model definitions were updated to use the linear SLA module.

• Provided a new direct module for determining development index from thermal time: BioCro:development_index_from_thermal_time. This module is an alternative to the BioCro:thermal_time_development_rate_calculator differential module.

• C3 temperature response parameters are no longer hard-coded into c3photoC():

  • There are now specialized structs for the temperature response parameters (c3_temperature_response_parameters) and the temperature-dependent values of key photosynthetic parameters (c3_param_at_tleaf).

  • There is also a dedicated function for calculating temperature-dependent parameter values: c3_temperature_response().

  • The temperature response parameters are now inputs to several modules: BioCro:c3_assimilation, BioCro:c3_canopy, BioCro:c3_leaf_photosynthesis.

  • There is also a dedicated module for calculating values of C3 parameters at leaf temperature: BioCro:c3_parameters.

  • The theta parameter was renamed to theta_0 for better consistency with the polynomial_response() function input argument names.

• Added a new vignette explaining key features of BioCro's multilayer canopy model, and made several changes to sunML() and related functions to ensure that the code matches the model description in the vignette:

  • Stopped calculating and using the "average" incident PPFD and absorbed shortwave radiation for leaves in the canopy.

  • Stopped using the "thick layer absorption" equation for determining the absorbed shortwave radiation within the canopy, replacing it with the thin layer absorption equation.

  • Used a simpler equation for calculating the fraction of sunlit leaves.

  • Used the same absorptivity value for direct and diffuse light.

  • Used separate leaf transmittance and reflectance values for PAR and NIR radiation within the canopy, rather than always assuming that light in the two bands are absorbed and scattered equally; in general, this caused a reduction in the absorbed shortwave energy for all leaves.

  • Started calculating absorptivity as 1 - R - T, where R and T are the leaf reflectance and transmittance coefficients, respectively. This ensures that the constraint A + R + T = 1 is always satisfied.

• Made several changes to BioCro's time handling:

  • The time variable is now required to be sequential and evenly spaced, where the time interval must be equal to timestep. A consequence is that time and timestep must have the same units.

  • With this change, it was necessary to change the definition of time used with the crop models. Now it is expected to be expressed as the (fractional) number of hours since midnight on January 1, rather than a fractional day of year.

  • There is a new module for calculating doy and hour from time, called BioCro:format_time. This module ensures that doy always takes integer values in the output from run_biocro.

  • In most cases, old scripts calling run_biocro will continue to function following these changes because time will be correctly computed from doy and hour, and BioCro:format_time will be automatically added to module lists.

  • The redefinition of time from days to hours may require changes to plotting commands or other operations using time. In most cases, instances of time in old scripts can be replaced by fractional_doy, which is equivalent to the definition of time used in previous versions of BioCro.

• Added a new function for generating C++ header files for new module classes: module_write.

• Added several functions to help with model regression tests: compare_model_output, model_test_case, run_model_test_cases, and update_stored_model_results. Previously, these were part of tests/testthat/crop_model_testing_helper_functions.R.

• The conversion of CO2 assimilation to biomass is no longer hard coded into the photosynthesis functions and modules, such as c3CanAC(), CanAC(), and BioCro:ten_layer_multilayer_canopy_integrator.

  • These functions and modules now produce canopy assimilation rates as molecular fluxes (with units of micromol CO2 / m^2 / s).

  • A new module called BioCro:carbon_assimilation_to_biomass now performs the conversion to rates of dry biomass acculumation (with units of Mg / ha / hr). A new parameter dry_biomass_per_carbon controls the conversion.

  • All affected models have the same behavior as before if the new module is used with dry_biomass_per_carbon set to 30.026 g / mol.

• The soybean model was re-parameterized following changes to module behavior.

Other Changes

• Consolidated all temperature response functions into a single header file (src/module_library/temperature_response_functions.h) that now includes arrhenius_exponential(), Q10_temperature_response(), johnson_eyring_williams_response(), and polynomial_response().

• The developer documentation was updated to include a section about pull requests.

Bug fixes

• Fixed incorrect year column values in the weather data.

• Fixed a mistake where the CMI weather data for 2023 was a copy of the 2022 data.

• The ode_solver input argument of run_biocro is now checked to ensure the essential list elements are provided.

Biosphere - Plants and Vegetation - C++
Published by eloch216 10 months ago

BioCro - BioCro 3.1.3

• This is the first version of BioCro to be accepted by CRAN! Most of the changes since version 3.1.0 were needed to comply with CRAN policies and requirements.

• Several changes have been made to reduce the package size from over 20 MB to less than 5 MB:

  • Crop model regression tests only store 1 of every 24 rows (one time point from each day)
  • The stored weather data has been rounded to 3 significant digits
    • The solar values have been rounded to the nearest integer
    • The rh values have been rounded to 2 significant digits
  • The stored crop model regression test data has been rounded to 5 significant digits
  • All previously-existing vignettes were converted to "web only," meaning they will be available through the pkgdown website but not included with the package itself
  • A new vignette has been added (BioCro.Rmd) that simply redirects readers to the documentation website

• Moved the included boost libraries from inc to src/inc since CRAN will not allow a nonstandard top-level directory. Some paths were shortened during this move.

• Added the Boost organization to the authors as a copyright holder to comply with CRAN policies

• Addressed a missing-field-initializers warning from the compiler by explicitly setting iterations to 0 in the output from rue_leaf_photosynthesis

• Addressed a mistake in thermal_time_and_frost_senescence.h where the leaf death rate due to frost had been unintentionally set to 0 in all conditions. This mistake was caught by a compiler that reported a "ignoring return value of function declared with 'nodiscard' attribute" warning.

• Changed the minimum version of macOS checked by the R-CMD-check from 3.6.0 to 4.2.0

  • CRAN now only provides R versions 4.1.0 and above for Mac
  • The deSolve package cannot be built on Mac for R versions below 4.2.0

Biosphere - Plants and Vegetation - C++
Published by eloch216 over 1 year ago

BioCro - BioCro 3.1.1

The package date in its DESCRIPTION file was updated to meet CRAN submission requirements (must be less than one month old)

Biosphere - Plants and Vegetation - C++
Published by eloch216 over 1 year ago

BioCro - BioCro 3.1.0

MINOR USER-FACING CHANGES

• Another bug was corrected in src/module_library/c3photoC.cpp: The photorespiration value Rp is now calculated using the value of Ci from the current loop iteration (rather than the previous loop iteration).

• Modified some testing-related functions so that warnings due to mismatched framework versions do not trigger test failures: the tryCatch call in test_module now only catches errors (not warnings) when evaluating the module, and test_plant_model (in crop_model_testing_helper_functions.R) now uses expect_no_error instead of expect_silent.

• Changed the energy_par_content constant to 0.219. This is a conversion rate from photon flux density (in micromoles per square meter per second) to energy flux density (in joules per square meter per second or watts per square meter) for photosynthetically active radiation (PAR). It equals 1/4.57, 4.57 being a commonly used constant to convert PAR in W m^-2 to micromole m^-2 s^-1. Users should take care to ensure that if processing of radiation data is required to prepare it for use with BioCro, the same conversion factor is used. See more details in Plant Growth Chamber Handbook. CHAPTER 1 – RADIATION– John C. Sager and J. Craig McFarlane. Table 2, Pg 3 (https://www.controlledenvironments.org/wp-content/uploads/sites/6/2017/06/Ch01.pdf)

• The C++ framework has been updated to v1.1.3. Since the framework is included as a git submodule, it will be necessary to use the --recurse-submodule flag when using git pull, git checkout, or git switch to update a local copy of the BioCro repository, or to move to or from this branch.

• Replaced the inc/boost directory with a submodule pointing to the new biocro/boost repository.

• The (unexported) lightME function has been removed from the R package, since its functionality can be reproduced using the BioCro:solar_position_michalsky and BioCro:shortwave_atmospheric_scattering modules.

OTHER CHANGES

• All instances of fabs or unqualified abs have been replaced by std::abs. The use of unqualified abs in src/module_library/c3photoC.cpp had been causing test failures when running BioCro on Windows using R version 3.6.0.

• This version adds a description of the BioCro git branching model to contribution_guidelines.Rmd and clarifies the process of updating NEWS.md.

• The R-CMD-check workflow has been changed in the following ways:

  • When the check workflow is run manually, there are two new input options:

    • The user can now choose whether or not to run R CMD check with the --as-cran option. Formerly, this was always used.

    • The user can choose whether and when to throw an error on R CMD check failures. Formerly, an error was thrown whenever the R CMD check failure was either "warning" or "error".

  • Output that was formerly shown only on manual runs when the "debug" checkbox was selected is now always shown. The "debug" option has been changed to "dry-run", which results in the debug output being shown but the actual check, and those set-up steps needed only to carry out the check, are skipped.

  • The debug output steps are grouped together when possible, and the output is shown earlier on in the workflow.

  • The R-CMD-check workflow has been modified to work around a problem with testing R version 3.6.0 on Windows. And for all platforms, we now specify the tested minimum R version as 3.6.0 rather than simply 3.6 in order to ensure that we are actually testing the minimum required R version specified in the DESCRIPTION file, rather than some later 3.6.x version such as version 3.6.3.

• Modified the R-CMD-check workflow so that the manual is not checked when the workflow runs automatically. This has also been made the default when the workflow is run manually.

• GitHub workflows and actions in the repository have been updated to use the latest versions of all GitHub and 3rd-party actions.

• Updates related to changing the GitHub hosting organization from "ebimodeling" to "biocro":

  Most references to the ebimodeling GitHub organization have been removed; references to ebimodeling/biocro have been updated to point to biocro/biocro instead. Most of these occurred in various places in the documentation. Most links to the online documentation have been replaced with links to https://biocro.github.io, with (in some cases) instructions on how to navigate to the particular section of the documentation of interest. This decreases dependence on the precise layout of the online documentation. Some other changes and clarifications to the documentation have been made as well.

• Addressed some format-security compiler warnings related to calling Rf_error and Rprintf without a format specifier; a format specifier of "%s" should always be used when printing the value of a string variable.

Biosphere - Plants and Vegetation - C++
Published by eloch216 almost 2 years ago

BioCro - BioCro 3.0.2

This version adds several missing references to the main README file.

Biosphere - Plants and Vegetation - C++
Published by eloch216 about 2 years ago

BioCro - BioCro 3.0.1

This is a patch release that changes the publication location for the documentation workflow. It also changes the workflow trigger so that publication of the latest documentation happens when a new release is published.

Biosphere - Plants and Vegetation - C++
Published by gsrohde about 2 years ago

BioCro - BioCro 3.0.0

This version is another major update of the design. In this version, modules can be written in separate packages that communicate with the BioCro package. The design allows authors to write modules in separate repositories, so that anyone can write a module without forking all of BioCro. It will make publishing updates to the framework and individual models easier since there will be less need to identify and separate parts that are not ready to be made public.

Writing a module package involves setting up a repository using a template, or skeleton, package. This only needs to be done once for a repository. Then development within that repository can continue in a similar manner as has been done in the BioCro repository. The skeleton package and instructions for setting it up are here: https://github.com/biocro/skelBML.

Biosphere - Plants and Vegetation - C++
Published by justinmcgrath about 2 years ago

BioCro - BioCro 2.0.0

This version is a major update to the design of BioCro. In this version, subsets of a model are called modules. The design attempts to meet the following goals.

Make it easier to reuse modules between species, such as the C3 photosynthesis modules for multiple species.
Swap related modules for comparison, for example comparing the Farquhar-vom Caemmerer-Berry model to a radiation use efficiency model.
Simplify parameter optimization and sensitivity analysis by providing an interface readily useable by common optimizers and similar functions.

More details can be found in the peer-reviewed publication in in silico Plants (https://doi.org/10.1093/insilicoplants/diac003) and in the "An introduction to BioCro" and "A practical guide to BioCro" vignettes included with the package.

Biosphere - Plants and Vegetation - C++
Published by justinmcgrath over 3 years ago

BioCro - minor fix

Removes radiation from 0.95 threshold https://github.com/ebimodeling/biocro/issues/16

Biosphere - Plants and Vegetation - C++
Published by dlebauer almost 5 years ago

BioCro - Last release of old framework.

Biosphere - Plants and Vegetation - C++
Published by justinmcgrath over 8 years ago

BioCro - BioCro v0.93 Short Rotation Coppice Willow

This version of BioCro adds the simulation of Willow

Described in: Wang, Jaiswal, LeBauer, Wertin, Bollero, Leakey, and Long 2015 A physiological and biophysical model of coppice willow (Salix spp.) production yields for the contiguous USA in current and future climate scenarios. Plant, Cell and Environment 38, 1850–1865 doi: 10.1111/pce.12556

Please also cite use of BioCro v 0.93 as

Fernando Miguez, Deepak Jaiswal, David LeBauer, Dan Wang, & Stephen Long (2015, March 5). BioCro: v 0.93 Short Rotation Coppice Willow. Zenodo. http://doi.org/10.5281/zenodo.15859

Biosphere - Plants and Vegetation - C++
Published by dlebauer almost 11 years ago