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:
solar values have been rounded to the nearest integerrh values have been rounded to 2 significant digitsBioCro.Rmd) that simply redirects readers
to the documentation websiteMoved 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
deSolve package cannot be built on Mac for R versions below 4.2.0Another 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:
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:
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.