Package: BioCro 3.3.1

Justin M. McGrath

BioCro: Modular Crop Growth Simulations

A cross-platform representation of models as sets of equations that facilitates modularity in model building and allows users to harness modern techniques for numerical integration and data visualization. Documentation is provided by several vignettes included in this package; also see Lochocki et al. (2022) <doi:10.1093/insilicoplants/diac003>.

Authors:Justin M. McGrath [cre, aut], Edward B. Lochocki [aut], Yufeng He [aut], Scott W. Oswald [aut], Scott Rohde [aut], Deepak Jaiswal [aut], Megan L. Matthews [aut], Fernando E. Miguez [aut], Stephen P. Long [aut], Dan Wang [ctb], David LeBauer [ctb], BioCro authors [cph], Boost Organization [cph]

BioCro_3.3.1.tar.gz
BioCro_3.3.1.zip(r-4.7)BioCro_3.3.1.zip(r-4.6)BioCro_3.3.1.zip(r-4.5)
BioCro_3.3.1.tgz(r-4.6-x86_64)BioCro_3.3.1.tgz(r-4.6-arm64)BioCro_3.3.1.tgz(r-4.5-x86_64)BioCro_3.3.1.tgz(r-4.5-arm64)
BioCro_3.3.1.tar.gz(r-4.7-arm64)BioCro_3.3.1.tar.gz(r-4.7-x86_64)BioCro_3.3.1.tar.gz(r-4.6-arm64)BioCro_3.3.1.tar.gz(r-4.6-x86_64)
BioCro_3.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BioCro/json (API)

# Install 'BioCro' in R:

install.packages('BioCro', repos = c('https://biocro.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/biocro/biocro/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

annualDB - Miscanthus dry biomass data.
annualDB2 - Miscanthus dry biomass data.
catm_data - Global annual mean atmopspheric CO2 levels
default_ode_solvers - Default ODE solver settings
miscanthus_x_giganteus - Miscanthus model definition
obsBea - Miscanthus assimilation field data
obsBeaC - Complete Miscanthus assimilation field data
obsNaid - Miscanthus assimilation data
soil_parameters - Soil properties
soybean - Soybean-BioCro model definition
soybean_clock - Soybean-BioCro circadian clock model definition
soybean_weather - Champaign, IL weather data for Soybean-BioCro
weather - Champaign, IL weather data
willow - Willow model definition

On CRAN:

cpp

7.98 score 48 stars 125 scripts 371 downloads 27 exports 0 dependencies

Last updated from:f66ccf7419. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	205
linux-devel-x86_64	OK	230
source / vignettes	OK	325
linux-release-arm64	OK	247
linux-release-x86_64	OK	194
macos-release-arm64	OK	226
macos-release-x86_64	OK	413
macos-oldrel-arm64	OK	297
macos-oldrel-x86_64	OK	580
windows-devel	OK	258
windows-release	OK	292
windows-oldrel	OK	338
wasm-release	OK	167

Exports:add_csv_row add_time_to_weather_data case cases_from_csv compare_model_output evaluate_module get_all_modules get_all_ode_solvers get_all_quantities get_growing_season_climate initialize_csv model_test_case module_info module_paste module_response_curve module_write partial_evaluate_module partial_run_biocro quantity_list_from_names run_biocro run_model_test_cases system_derivatives test_module test_module_library update_csv_cases update_stored_model_results validate_dynamical_system_inputs

Dependencies:

BioCro

Overview | An example | Getting Started | License

Rendered fromBioCro.Rmdusingknitr::rmarkdown

Last update: 2026-02-09
Started: 2024-04-30

Help page	Topics
Add a time component to input	add_time_to_weather_data
Miscanthus dry biomass data.	annualDB annualDB2
Global annual mean atmopspheric CO2 levels	catm_data
Champaign, IL weather data for Soybean-BioCro	cmi_soybean_weather_data soybean_weather
Champaign, IL weather data	cmi_weather_data weather
Compare new and stored results for a BioCro model test case	compare_model_output
Crop model definitions	crop_model_definitions
Default ODE solver settings	default_ode_solvers
Validating dynamical system inputs	dynamical_system validate_dynamical_system_inputs
Get lists of modules, quantities, and solvers	get_all get_all_modules get_all_ode_solvers get_all_quantities
Truncate weather data to one growing season	get_growing_season_climate
Miscanthus model definition	miscanthus_x_giganteus
Define BioCro model test cases	model_test_case
The BioCro model testing system	model_testing
Define and modify BioCro module test case files	add_csv_row initialize_csv module_case_files update_csv_cases
Create instances of modules	module_creators
Prepend library name to module names	module_paste
The BioCro module testing system	module_testing
Generate a BioCro module header file.	module_write
BioCro module functions	evaluate_module modules module_info module_response_curve quantity_list_from_names
Miscanthus assimilation field data	obsBea
Complete Miscanthus assimilation field data	obsBeaC
Miscanthus assimilation data	obsNaid
Convenience Functions for Partial Application	partial_application partial_evaluate_module partial_run_biocro
Simulate Crop Growth with BioCro	run_biocro
Run BioCro model test cases	run_model_test_cases
Soil properties	soil_parameters
Soybean-BioCro model definition	soybean
Soybean-BioCro circadian clock model definition	soybean_clock
Calculate Derivatives for Differential Quantities	system_derivatives
Run BioCro module test cases	case cases_from_csv test_module
Run module test cases for an entire BioCro module library	test_module_library
The `time` variable in BioCro	time Time Variable
Updated stored result for a BioCro model test case	update_stored_model_results
Willow model definition	willow

Package: BioCro 3.3.1

BioCro: Modular Crop Growth Simulations

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