High-Performance Open-Source Archive
Addressed a compiler warning (changes-meaning) that
prevented BioCro compilation for some versions of linux/gcc. Also added
new checks to the GitHub actions used to check the package to catch this
if it occurs again in the future.
Addressed an issue with error message formatting in vignettes that prevented some articles from being built.
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mrc1 has been replaced by grc_leaf and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
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()).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).
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 micromol 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.org, 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.org/BioCro-documentation/latest/pkgdown/ to
https://biocro.org/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.
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