Files in ebimodeling/biocro

Modular Crop Growth Simulations

.Rbuildignore

.clang-format

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.gitattributes

.github/actions/build_pkgdown_site/README.md

.github/actions/build_pkgdown_site/action.yml

.github/actions/doxygen-action/Dockerfile

.github/actions/doxygen-action/LICENSE

.github/actions/doxygen-action/README.md

.github/actions/doxygen-action/action.yml

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.github/actions/render_bookdown_book/action.yml

.github/actions/run_doxygen/README.md

.github/actions/run_doxygen/action.yml

.github/workflows/R-CMD-check-backend.yaml

.github/workflows/R-CMD-check.yaml

.github/workflows/README.md

.github/workflows/automatically-call-document.yml

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.github/workflows/document_quantities.yml

.github/workflows/strategy_matrix.json

.gitignore

.gitmodules

DESCRIPTION

LICENSE

LICENSE.md

LICENSE.note

NAMESPACE

NEWS.md R/add_time_to_weather_data.R R/framework_version.R R/function_from_package.R R/get_all.R R/get_all_modules_internal.R R/get_all_quantities_internal.R R/get_growing_season_climate.r R/input_checking_functions.R R/module_creators.R R/module_paste.R R/module_testing.R R/modules.R R/run_biocro.R R/system_derivatives.R R/validate_dynamical_system_inputs.R README.md

bookdown/.gitignore

bookdown/README

bookdown/README.md

bookdown/_bookdown.yml

bookdown/_output.yml

bookdown/book_source/README

bookdown/book_source/generating_documentation.md bookdown/index.Rmd bookdown/version_info.Rmd cran-comments.md

data/annualDB.rdata

data/annualDB2.rdata

data/catm_data.rdata

data/cmi_weather_data.rdata

data/default_ode_solvers.R data/miscanthus_x_giganteus.R

data/obsBea.rdata

data/obsBeaC.rdata

data/obsNaid.rdata

data/soil_parameters.R data/soybean.R data/soybean_clock.R

data/soybean_weather.rdata

data/willow.R developer_documentation/contribution_guidelines.Rmd developer_documentation/formatting_tools.Rmd documentation/README.md documentation/script/run_bookdown.R

documentation/script/run_bookdown.sh

documentation/script/run_pkgdown.R

documentation/script/run_pkgdown.sh

doxygen/.gitignore

doxygen/Doxyfile

doxygen/Makefile

doxygen/customizations/.gitignore

doxygen/customizations/Doxyfile_customization_sample

doxygen/customizations/dummy_fallback_file/Doxyfile

doxygen/generating_the_c++_documentation.Rmd doxygen/markdown/about.md

inst/CITATION

man/add_time_to_weather_data.Rd man/annualDB.Rd man/catm_data.Rd man/cmi_soybean_weather_data.Rd man/cmi_weather_data.Rd man/crop_model_definitions.Rd man/default_ode_solvers.Rd man/dynamical_system.Rd man/get_all.Rd man/get_growing_season_climate.Rd man/miscanthus_x_giganteus.Rd man/module_case_files.Rd man/module_creators.Rd man/module_paste.Rd man/module_testing.Rd man/modules.Rd man/obsBea.Rd man/obsBeaC.Rd man/obsNaid.Rd man/partial_application.Rd man/run_biocro.Rd man/soil_parameters.Rd man/soybean.Rd man/soybean_clock.Rd man/system_derivatives.Rd man/test_module.Rd man/test_module_library.Rd man/willow.Rd

pkgdown/_pkgdown.yml

script/.gitignore

script/create_quantity_table.R

script/generate_tags.sh

script/modules.xsl

script/quantities.xsl

src/Makevars

src/Makevars.win

src/R_dynamical_system.cpp

src/R_dynamical_system.h

src/R_framework_version.cpp

src/R_framework_version.h

src/R_get_all_ode_solvers.cpp

src/R_get_all_ode_solvers.h

src/R_module_library.cpp

src/R_module_library.h

src/R_modules.cpp

src/R_modules.h

src/R_run_biocro.cpp

src/R_run_biocro.h

src/R_system_derivatives.cpp

src/R_system_derivatives.h

src/init.cpp

src/module_library/AuxBioCro.cpp

src/module_library/AuxBioCro.h

src/module_library/BioCro.h

src/module_library/CanAC.cpp

src/module_library/CanAC.h

src/module_library/FvCB.h

src/module_library/FvCB_assim.cpp

src/module_library/FvCB_assim.h

src/module_library/aba_decay.h

src/module_library/ball_berry.h

src/module_library/ball_berry_gs.cpp

src/module_library/ball_berry_gs.h

src/module_library/biomass_leaf_n_limitation.h

src/module_library/buck_swvp.h

src/module_library/bucket_soil_drainage.h

src/module_library/c3CanAC.cpp

src/module_library/c3CanAC.h

src/module_library/c3EvapoTrans.cpp

src/module_library/c3_assimilation.h

src/module_library/c3_canopy.cpp

src/module_library/c3_canopy.h

src/module_library/c3_leaf_photosynthesis.cpp

src/module_library/c3_leaf_photosynthesis.h

src/module_library/c3photo.cpp

src/module_library/c3photo.h

src/module_library/c4_assimilation.h

src/module_library/c4_canopy.h

src/module_library/c4_leaf_photosynthesis.cpp

src/module_library/c4_leaf_photosynthesis.h

src/module_library/c4photo.cpp

src/module_library/c4photo.h

src/module_library/canopy_photosynthesis_outputs.h

src/module_library/collatz_photo.cpp

src/module_library/collatz_photo.h

src/module_library/conductance_limited_assim.h

src/module_library/development_index.h

src/module_library/eC4photo.cpp

src/module_library/eC4photo.h

src/module_library/example_model_mass_gain.h

src/module_library/example_model_partitioning.h

src/module_library/fake_solar.h

src/module_library/grimm_soybean_flowering.h

src/module_library/grimm_soybean_flowering_calculator.h

src/module_library/harmonic_oscillator.h

src/module_library/hyperbolas.h

src/module_library/incident_shortwave_from_ground_par.h

src/module_library/leaf_gbw_nikolov.h

src/module_library/leaf_gbw_thornley.h

src/module_library/leaf_shape_factor.h

src/module_library/leaf_water_stress_exponential.h

src/module_library/lightME.cpp

src/module_library/lightME.h

src/module_library/light_from_solar.h

src/module_library/linear_vmax_from_leaf_n.h

src/module_library/litter_cover.h

src/module_library/magic_clock.h

src/module_library/module_graph_test.h

src/module_library/module_library.cpp

src/module_library/module_library.h

src/module_library/multilayer_c3_canopy.cpp

src/module_library/multilayer_c3_canopy.h

src/module_library/multilayer_c4_canopy.cpp

src/module_library/multilayer_c4_canopy.h

src/module_library/multilayer_canopy_integrator.h

src/module_library/multilayer_canopy_photosynthesis.h

src/module_library/multilayer_canopy_properties.cpp

src/module_library/multilayer_canopy_properties.h

src/module_library/multilayer_rue_canopy.cpp

src/module_library/multilayer_rue_canopy.h

src/module_library/night_and_day_trackers.h

src/module_library/no_leaf_resp_neg_assim_partitioning_growth_calculator.h

src/module_library/no_leaf_resp_partitioning_growth_calculator.h

src/module_library/nr_ex.h

src/module_library/one_layer_soil_profile.h

src/module_library/one_layer_soil_profile_derivatives.h

src/module_library/oscillator_clock_calculator.h

src/module_library/parameter_calculator.h

src/module_library/partitioning_coefficient_logistic.h

src/module_library/partitioning_coefficient_selector.h

src/module_library/partitioning_growth.h

src/module_library/partitioning_growth_calculator.h

src/module_library/penman_monteith_leaf_temperature.cpp

src/module_library/penman_monteith_leaf_temperature.h

src/module_library/penman_monteith_transpiration.h

src/module_library/phase_clock.h

src/module_library/photosynthesis_outputs.h

src/module_library/poincare_clock.h

src/module_library/priestley_transpiration.h

src/module_library/rasmussen_specific_heat.cpp

src/module_library/rasmussen_specific_heat.h

src/module_library/rh_to_mole_fraction.h

src/module_library/rue_leaf_photosynthesis.cpp

src/module_library/rue_leaf_photosynthesis.h

src/module_library/senescence_coefficient_logistic.h

src/module_library/senescence_logistic.h

src/module_library/shortwave_atmospheric_scattering.h

src/module_library/soil_evaporation.h

src/module_library/soil_sunlight.h

src/module_library/solar_position_michalsky.h

src/module_library/song_flowering.h

src/module_library/soybean_development_rate_calculator.h

src/module_library/stomata_outputs.h

src/module_library/stomata_water_stress_exponential.h

src/module_library/stomata_water_stress_linear.h

src/module_library/stomata_water_stress_linear_aba_response.h

src/module_library/stomata_water_stress_sigmoid.h

src/module_library/sunML.cpp

src/module_library/sunML.h

src/module_library/thermal_time_and_frost_senescence.h

src/module_library/thermal_time_beta.h

src/module_library/thermal_time_bilinear.h

src/module_library/thermal_time_development_rate_calculator.h

src/module_library/thermal_time_linear.h

src/module_library/thermal_time_linear_extended.h

src/module_library/thermal_time_senescence.h

src/module_library/thermal_time_trilinear.h

src/module_library/total_biomass.h

src/module_library/two_layer_soil_profile.h

src/module_library/varying_Jmax25.h

src/module_library/water_and_air_properties.h

src/module_library/water_vapor_properties_from_air_temperature.h

src/parameters.h

tests/README.md

tests/module_test_cases/BioCro_FvCB.csv

tests/module_test_cases/BioCro_Module_1.csv

tests/module_test_cases/BioCro_Module_2.csv

tests/module_test_cases/BioCro_Module_3.csv

tests/module_test_cases/BioCro_aba_decay.csv

tests/module_test_cases/BioCro_ball_berry.csv

tests/module_test_cases/BioCro_biomass_leaf_n_limitation.csv

tests/module_test_cases/BioCro_buck_swvp.csv

tests/module_test_cases/BioCro_bucket_soil_drainage.csv

tests/module_test_cases/BioCro_c3_assimilation.csv

tests/module_test_cases/BioCro_c3_canopy.csv

tests/module_test_cases/BioCro_c3_leaf_photosynthesis.csv

tests/module_test_cases/BioCro_c4_assimilation.csv

tests/module_test_cases/BioCro_c4_canopy.csv

tests/module_test_cases/BioCro_c4_leaf_photosynthesis.csv

tests/module_test_cases/BioCro_development_index.csv

tests/module_test_cases/BioCro_example_model_mass_gain.csv

tests/module_test_cases/BioCro_example_model_partitioning.csv

tests/module_test_cases/BioCro_fake_solar.csv

tests/module_test_cases/BioCro_golden_ratio_hyperbola.csv

tests/module_test_cases/BioCro_grimm_soybean_flowering.csv

tests/module_test_cases/BioCro_grimm_soybean_flowering_calculator.csv

tests/module_test_cases/BioCro_harmonic_energy.csv

tests/module_test_cases/BioCro_harmonic_oscillator.csv

tests/module_test_cases/BioCro_hyperbola_2d.csv

tests/module_test_cases/BioCro_incident_shortwave_from_ground_par.csv

tests/module_test_cases/BioCro_leaf_gbw_nikolov.csv

tests/module_test_cases/BioCro_leaf_gbw_thornley.csv

tests/module_test_cases/BioCro_leaf_shape_factor.csv

tests/module_test_cases/BioCro_leaf_water_stress_exponential.csv

tests/module_test_cases/BioCro_light_from_solar.csv

tests/module_test_cases/BioCro_linear_vmax_from_leaf_n.csv

tests/module_test_cases/BioCro_litter_cover.csv

tests/module_test_cases/BioCro_magic_clock.csv

tests/module_test_cases/BioCro_night_and_day_trackers.csv

tests/module_test_cases/BioCro_no_leaf_resp_neg_assim_partitioning_growth_calculator.csv

tests/module_test_cases/BioCro_no_leaf_resp_partitioning_growth_calculator.csv

tests/module_test_cases/BioCro_nr_ex.csv

tests/module_test_cases/BioCro_one_layer_soil_profile.csv

tests/module_test_cases/BioCro_one_layer_soil_profile_derivatives.csv

tests/module_test_cases/BioCro_oscillator_clock_calculator.csv

tests/module_test_cases/BioCro_parameter_calculator.csv

tests/module_test_cases/BioCro_partitioning_coefficient_logistic.csv

tests/module_test_cases/BioCro_partitioning_coefficient_selector.csv

tests/module_test_cases/BioCro_partitioning_growth.csv

tests/module_test_cases/BioCro_partitioning_growth_calculator.csv

tests/module_test_cases/BioCro_penman_monteith_leaf_temperature.csv

tests/module_test_cases/BioCro_penman_monteith_transpiration.csv

tests/module_test_cases/BioCro_phase_clock.csv

tests/module_test_cases/BioCro_poincare_clock.csv

tests/module_test_cases/BioCro_priestley_transpiration.csv

tests/module_test_cases/BioCro_rasmussen_specific_heat.csv

tests/module_test_cases/BioCro_rh_to_mole_fraction.csv

tests/module_test_cases/BioCro_rue_leaf_photosynthesis.csv

tests/module_test_cases/BioCro_senescence_coefficient_logistic.csv

tests/module_test_cases/BioCro_senescence_logistic.csv

tests/module_test_cases/BioCro_shortwave_atmospheric_scattering.csv

tests/module_test_cases/BioCro_soil_evaporation.csv

tests/module_test_cases/BioCro_soil_sunlight.csv

tests/module_test_cases/BioCro_soil_type_selector.csv

tests/module_test_cases/BioCro_solar_position_michalsky.csv

tests/module_test_cases/BioCro_song_flowering.csv

tests/module_test_cases/BioCro_soybean_development_rate_calculator.csv

tests/module_test_cases/BioCro_stomata_water_stress_exponential.csv

tests/module_test_cases/BioCro_stomata_water_stress_linear.csv

tests/module_test_cases/BioCro_stomata_water_stress_linear_and_aba_response.csv

tests/module_test_cases/BioCro_stomata_water_stress_sigmoid.csv

tests/module_test_cases/BioCro_ten_layer_c3_canopy.csv

tests/module_test_cases/BioCro_ten_layer_c4_canopy.csv

tests/module_test_cases/BioCro_ten_layer_canopy_integrator.csv

tests/module_test_cases/BioCro_ten_layer_canopy_properties.csv

tests/module_test_cases/BioCro_ten_layer_rue_canopy.csv

tests/module_test_cases/BioCro_thermal_time_and_frost_senescence.csv

tests/module_test_cases/BioCro_thermal_time_beta.csv

tests/module_test_cases/BioCro_thermal_time_bilinear.csv

tests/module_test_cases/BioCro_thermal_time_development_rate_calculator.csv

tests/module_test_cases/BioCro_thermal_time_linear.csv

tests/module_test_cases/BioCro_thermal_time_linear_extended.csv

tests/module_test_cases/BioCro_thermal_time_senescence.csv

tests/module_test_cases/BioCro_thermal_time_trilinear.csv

tests/module_test_cases/BioCro_total_biomass.csv

tests/module_test_cases/BioCro_two_layer_soil_profile.csv

tests/module_test_cases/BioCro_varying_Jmax25.csv

tests/module_test_cases/BioCro_water_vapor_properties_from_air_temperature.csv

tests/test_data/miscanthus_x_giganteus_simulation.csv

tests/test_data/soybean_simulation.csv

tests/test_data/willow_simulation.csv

tests/testthat.R tests/testthat/crop_model_testing_helper_functions.R tests/testthat/test.CropModels.R tests/testthat/test.HarmonicOscillationModeling.R tests/testthat/test.ModuleReordering.R tests/testthat/test.Modules.R tests/testthat/test.NumericalIntegratorSettings.R tests/testthat/test.PartialApplication.R tests/testthat/test.SystemConstruction.R tests/testthat/test.c3photo.R tests/testthat/test.check_distinct_names.R tests/testthat/test.check_out_module.R tests/testthat/test.compare_framework_versions.R tests/testthat/test.function_from_package.R tests/testthat/test.parse_module_name.R vignettes/BioCro-II_Paper--Section-1.1-example.Rmd

vignettes/a_practical_guide_to_biocro.Rnw

vignettes/a_practical_guide_to_biocro/doxygen_comment.txt

vignettes/a_practical_guide_to_biocro/doxygen_screenshot.png

vignettes/a_practical_guide_to_biocro/leaf_units.txt

vignettes/a_practical_guide_to_biocro/soybean_vcmax_exercise.pdf vignettes/a_practical_guide_to_biocro/temperature_response_curve.pdf

vignettes/an_introduction_to_biocro.Rnw

vignettes/an_introduction_to_biocro/example_gro.png

vignettes/an_introduction_to_biocro/heating_degree_days.h

vignettes/an_introduction_to_biocro/solar_zenith_angle_in_degrees.h

vignettes/an_introduction_to_biocro/test-heating_degree_days.R vignettes/an_introduction_to_biocro/test-heating_degree_days_with_run_biocro.R vignettes/an_introduction_to_biocro/test-solar_zenith_angle_in_degrees.R vignettes/an_introduction_to_biocro/test-solar_zenith_angle_in_degrees_with_run_biocro.R vignettes/avoiding_pitfalls_fvcb.Rmd vignettes/ball_berry_model.Rmd vignettes/building_the_vignettes.md

vignettes/chicago-author-date.csl

vignettes/chicago-author-date.notes

vignettes/dynamical_systems.Rmd vignettes/pdf_vignette_index.Rmd

vignettes/quantitative_model_comparison.Rnw

vignettes/references/BioCro.bibtex

vignettes/references/ball_berry_references.bib

vignettes/references/dynamical_systems.bibtex

vignettes/references/fvcb_references.bib

vignettes/references/thick_layer_references.bib

vignettes/thick_layer_absorption.Rmd

ebimodeling/biocro documentation built on April 23, 2024, 7:06 p.m.