Package: BioCro 3.2.0

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_3.2.0.tar.gz
BioCro_3.2.0.zip(r-4.5)BioCro_3.2.0.zip(r-4.4)BioCro_3.2.0.zip(r-4.3)
BioCro_3.2.0.tgz(r-4.5-x86_64)BioCro_3.2.0.tgz(r-4.5-arm64)BioCro_3.2.0.tgz(r-4.4-x86_64)BioCro_3.2.0.tgz(r-4.4-arm64)BioCro_3.2.0.tgz(r-4.3-x86_64)BioCro_3.2.0.tgz(r-4.3-arm64)
BioCro_3.2.0.tar.gz(r-4.5-noble)BioCro_3.2.0.tar.gz(r-4.4-noble)
BioCro_3.2.0.tgz(r-4.4-emscripten)BioCro_3.2.0.tgz(r-4.3-emscripten)
BioCro.pdf |BioCro.html✨
BioCro/json (API)
NEWS

# 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:

On CRAN:

Conda:

cpp

8.09 score 45 stars 81 scripts 478 downloads 27 exports 0 dependencies

Last updated 25 days agofrom:b8ed26816d. Checks:1 OK, 11 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 07 2025
R-4.5-win-x86_64NOTEMar 07 2025
R-4.5-mac-x86_64NOTEMar 07 2025
R-4.5-mac-aarch64NOTEMar 07 2025
R-4.5-linux-x86_64NOTEMar 07 2025
R-4.4-win-x86_64NOTEMar 07 2025
R-4.4-mac-x86_64NOTEMar 07 2025
R-4.4-mac-aarch64NOTEMar 07 2025
R-4.4-linux-x86_64NOTEMar 07 2025
R-4.3-win-x86_64NOTEMar 07 2025
R-4.3-mac-x86_64NOTEMar 07 2025
R-4.3-mac-aarch64NOTEMar 07 2025

Exports:add_csv_rowadd_time_to_weather_datacasecases_from_csvcompare_model_outputevaluate_moduleget_all_modulesget_all_ode_solversget_all_quantitiesget_growing_season_climateinitialize_csvmodel_test_casemodule_infomodule_pastemodule_response_curvemodule_writepartial_evaluate_modulepartial_run_biocroquantity_list_from_namesrun_biocrorun_model_test_casessystem_derivativestest_moduletest_module_libraryupdate_csv_casesupdate_stored_model_resultsvalidate_dynamical_system_inputs

Dependencies:

BioCro

Rendered fromBioCro.Rmdusingknitr::rmarkdownon Mar 07 2025.

Last update: 2025-03-07
Started: 2024-04-30

Readme and manuals

Help Manual

Help pageTopics
Add a time component to inputadd_time_to_weather_data
Miscanthus dry biomass data.annualDB annualDB2
Global annual mean atmopspheric CO2 levelscatm_data
Champaign, IL weather data for Soybean-BioCrocmi_soybean_weather_data soybean_weather
Champaign, IL weather datacmi_weather_data weather
Compare new and stored results for a BioCro model test casecompare_model_output
Crop model definitionscrop_model_definitions
Default ODE solver settingsdefault_ode_solvers
Validating dynamical system inputsdynamical_system validate_dynamical_system_inputs
Get lists of modules, quantities, and solversget_all get_all_modules get_all_ode_solvers get_all_quantities
Truncate weather data to one growing seasonget_growing_season_climate
Miscanthus model definitionmiscanthus_x_giganteus
Define BioCro model test casesmodel_test_case
The BioCro model testing systemmodel_testing
Define and modify BioCro module test case filesadd_csv_row initialize_csv module_case_files update_csv_cases
Create instances of modulesmodule_creators
Prepend library name to module namesmodule_paste
The BioCro module testing systemmodule_testing
Generate a BioCro module header file.module_write
BioCro module functionsevaluate_module modules module_info module_response_curve quantity_list_from_names
Miscanthus assimilation field dataobsBea
Complete Miscanthus assimilation field dataobsBeaC
Miscanthus assimilation dataobsNaid
Convenience Functions for Partial Applicationpartial_application partial_evaluate_module partial_run_biocro
Simulate Crop Growth with BioCrorun_biocro
Run BioCro model test casesrun_model_test_cases
Soil propertiessoil_parameters
Soybean-BioCro model definitionsoybean
Soybean-BioCro circadian clock model definitionsoybean_clock
Calculate Derivatives for Differential Quantitiessystem_derivatives
Run BioCro module test casescase cases_from_csv test_module
Run module test cases for an entire BioCro module librarytest_module_library
The `time` variable in BioCrotime Time Variable
Updated stored result for a BioCro model test caseupdate_stored_model_results
Willow model definitionwillow