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.
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.
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.
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 or fewer 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. The submodule repository was also renamed from biocro/boost to
biocro/inc.
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.
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.
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.
biocro/BioCro-documentation repository, and it changes the
triggers of the workflow so that automatic publication happens when
a new release is published. Additionally, a symlink is created to
link the URL
https://biocro.github.io/BioCro-documentation/latest/pkgdown/ to
https://biocro.github.io/BioCro-documentation/This version introduces the concept of distinct module libraries, allowing
users to develop modules in private and to create collections of related
modules. There is an associated syntax change, where modules must now be
specified using fully-qualified names that include a module library name and
the local name of a module within that library; for example, the module that
was previously known as thermal_time_linear must now be referred to as
BioCro:thermal_time_linear.
Any R package representing a BioCro module library must now have four
non-exported functions related to accessing its modules: get_all_modules,
get_all_quantities, module_creators, and framework_version. When a
fully-qualified module name such as library_name:local_module_name is passed
to a function such as module_info, an internal call to
library_name:::module_creators(module_name) will be made to retrieve a
pointer to a module. Hence, library_name must be the same as the module
library package name. This is a required part of a method for passing C
objects from a module library to the core BioCro framework via R; the full
details are not discussed here.
The code in the src directory has been reorganized to reflect the division
between framework code, module code, and "R-to-C" code discussed in the
manuscript; now, src/framework contains the core C++ code,
src/module_library contains the module code, and the "R-to-C" code can be
found directly in src.
The C++ framework code in src/framework has been moved to a separate
repository and licensed under the GNU LGPL; it is included in the BioCro R
package repository as a Git submodule. This allows us to use a permissive
license for the BioCro R package while still protecting the code that
assembles and solves models. Associated with this change, the BioCro R package
is now licensed under the MIT license. See LICENSE.note for details.
The soil_type_selector module has been removed and replaced with a data
object called soil_parameters. For crop models that previously set the
soil_type_indicator to 6 to choose the soil parameter values, this
parameter has been replaced with the values from soil_parameters$clay_loam.
Crop model definitions are now stored as single lists rather than as multiple
objects; for example, soybean_parameters and soybean_initial_values are
now stored as two elements of the soybean list: soybean$parameters and
soybean$initial_values.
The function returned by partial_run_biocro can now properly respond to
vectors and lists of named elements.
Module testing functions have been added to the package namespace.
Many small improvements have been made to the documentation and the module
code in src/module_library; these changes are too numerous to list here.
The elements of the arg_names input to partial_run_biocro can now be in
any order; previously, they were required to be supplied in the same order as
the appear in the other inputs to partial_run_biocro, for example, the names
of any initial values were required to come before the names of any
parameters. If the arguments were supplied in the wrong order, then the inputs
to the function returned by partial_run_biocro would be interpreted in the
wrong order.
A bug that sometimes caused the last time point of a simulation to contain NaN
for all quantities has been fixed; this was related to an out-of-bounds error
when accessing vector elements in the C++ function
dynamical_system::update_drivers.
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.
Make it easier to swap related modules for comparison, for example, comparing the Farquhar-von-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 Lochocki et al., 2022 and in the vignettes included with the package:
A Practical Guide to BioCro
Quantitative Comparison Between Two Photosynthesis Models
An Introduction to BioCro for Those Who Want to Add Models
PDF versions of these vignettes corresponding to the latest version of BioCro can be obtained online from the Articles menu at the BioCro documentation website.