Files in ahgroup/modelbuilder

Building Compartmental Simulation Models Without Coding

NEWS.md R/add_model_flow.R R/add_model_par.R R/add_model_var.R R/analyze_model.R R/check_model.R R/generate_buildUI.R R/generate_discrete.R R/generate_equations.R R/generate_function_documentation.R R/generate_function_inputs.R R/generate_ggplot.R R/generate_model.R R/generate_model_file.R R/generate_ode.R R/generate_plotly.R R/generate_shinyinput.R R/generate_stochastic.R R/generate_stratified_model.R R/generate_stratifier_list.R R/generate_tables.R R/generate_text.R R/get_math.R R/get_vars_pars.R R/load_model.R R/modelbuilder.R R/remove_model_flow.R R/remove_model_par.R R/remove_model_var.R R/remove_model_variableModal.R README.Rmd README.md auxiliary/docsfordevelopers/WEST-Additions-Information.md auxiliary/docsfordevelopers/documentation.md auxiliary/docsfordevelopers/ideas-and-to-do.md auxiliary/helperfunctions/processing_script.R auxiliary/modelfiles/DSAIDE/Characteristics_of_ID_file.R auxiliary/modelfiles/DSAIDE/Complex_ID_Control_file.R auxiliary/modelfiles/DSAIDE/Drug_Resistance_Evolution_file.R auxiliary/modelfiles/DSAIDE/Environmental_Transmission_model_file.R auxiliary/modelfiles/DSAIDE/Host_Heterogeneity_Model_file.R auxiliary/modelfiles/DSAIDE/SEIRSd_model_file.R auxiliary/modelfiles/DSAIDE/SIRSd_model_file.R auxiliary/modelfiles/DSAIDE/SIR_model_file.R auxiliary/modelfiles/DSAIDE/Vector_transmission_model_file.R auxiliary/modelfiles/DSAIDE/simulators/simulate_Characteristics_of_ID_discrete.R auxiliary/modelfiles/DSAIDE/simulators/simulate_Characteristics_of_ID_stochastic.R auxiliary/modelfiles/DSAIDE/simulators/simulate_Complex_ID_Control_discrete.R auxiliary/modelfiles/DSAIDE/simulators/simulate_Complex_ID_Control_stochastic.R auxiliary/modelfiles/DSAIDE/simulators/simulate_Drug_Resistance_Evolution_discrete.R auxiliary/modelfiles/DSAIDE/simulators/simulate_Drug_Resistance_Evolution_ode.R auxiliary/modelfiles/DSAIDE/simulators/simulate_Environmental_Transmission_model_discrete.R auxiliary/modelfiles/DSAIDE/simulators/simulate_Environmental_Transmission_model_stochastic.R auxiliary/modelfiles/DSAIDE/simulators/simulate_Host_Heterogeneity_Model_discrete.R auxiliary/modelfiles/DSAIDE/simulators/simulate_Host_Heterogeneity_Model_stochastic.R auxiliary/modelfiles/DSAIDE/simulators/simulate_SEIRSd_model_discrete.R auxiliary/modelfiles/DSAIDE/simulators/simulate_SEIRSd_model_ode.R auxiliary/modelfiles/DSAIDE/simulators/simulate_SIRSd_model_discrete.R auxiliary/modelfiles/DSAIDE/simulators/simulate_SIR_model_stochastic.R auxiliary/modelfiles/DSAIDE/simulators/simulate_Vector_transmission_model_discrete.R auxiliary/modelfiles/DSAIDE/simulators/simulate_Vector_transmission_model_stochastic.R auxiliary/modelfiles/DSAIRM/Acute_Virus_IR_model_file.R auxiliary/modelfiles/DSAIRM/Acute_Virus_Infection_and_IR_Model_file.R auxiliary/modelfiles/DSAIRM/Basic_Bacteria_model_file.R auxiliary/modelfiles/DSAIRM/Basic_Virus_model_file.R auxiliary/modelfiles/DSAIRM/Chronic_Virus_IR_model_file.R auxiliary/modelfiles/DSAIRM/Chronic_Virus_Infection_and_IR_Model_file.R auxiliary/modelfiles/DSAIRM/simulators/simulate_Acute_Virus_Infection_and_IR_Model_discrete.R auxiliary/modelfiles/DSAIRM/simulators/simulate_Acute_Virus_Infection_and_IR_Model_ode.R auxiliary/modelfiles/DSAIRM/simulators/simulate_Acute_Virus_Infection_and_IR_Model_stochastic.R auxiliary/modelfiles/DSAIRM/simulators/simulate_Basic_Bacteria_Model_discrete.R auxiliary/modelfiles/DSAIRM/simulators/simulate_Basic_Bacteria_Model_ode.R auxiliary/modelfiles/DSAIRM/simulators/simulate_Basic_Bacteria_Model_stochastic.R auxiliary/modelfiles/DSAIRM/simulators/simulate_Basic_Virus_Model_discrete.R auxiliary/modelfiles/DSAIRM/simulators/simulate_Basic_Virus_Model_ode.R auxiliary/modelfiles/DSAIRM/simulators/simulate_Basic_Virus_Model_stochastic.R auxiliary/modelfiles/DSAIRM/simulators/simulate_Chronic_Virus_Infection_and_IR_Model_discrete.R auxiliary/modelfiles/DSAIRM/simulators/simulate_Chronic_Virus_Infection_and_IR_Model_ode.R auxiliary/modelfiles/DSAIRM/simulators/simulate_Chronic_Virus_Infection_and_IR_Model_stochastic.R auxiliary/modelfiles/alexis_models/ID_Surveillance_file.R auxiliary/modelfiles/incomplete/Coronavirus_vaccine_model_file.R auxiliary/modelfiles/incomplete/Coronavirus_vaccine_model_v2_file.R auxiliary/modelfiles/other/Basic_Inoculum_Model_file.R auxiliary/modelfiles/other/Cholera_model_file.R auxiliary/modelfiles/other/Complex_ID_Control_Scenarios_file.R auxiliary/modelfiles/other/Control_of_different_populations_file.R auxiliary/modelfiles/other/Influenza_Antibody_Model_file.R auxiliary/modelfiles/other/Influenza_OAS_Model_file.R auxiliary/modelfiles/other/Influenza_OAS_simpleModel_file.R auxiliary/modelfiles/other/SIR_seasonal_model_file.R auxiliary/modelfiles/other/Stratified_Inoculum_Model_file.R auxiliary/modelfiles/other/Time_dependent_SIR_model_file.R auxiliary/modelfiles/other/simulators/simulate_Cholera_model_discrete.R auxiliary/modelfiles/other/simulators/simulate_Cholera_model_ode.R auxiliary/modelfiles/other/simulators/simulate_Cholera_model_stochastic.R auxiliary/modelfiles/other/simulators/simulate_Complex_ID_Control_Scenarios_discrete.R auxiliary/modelfiles/other/simulators/simulate_Complex_ID_Control_Scenarios_ode.R auxiliary/modelfiles/other/simulators/simulate_Complex_ID_Control_Scenarios_stochastic.R auxiliary/modelfiles/other/simulators/simulate_Control_of_different_populations_discrete.R auxiliary/modelfiles/other/simulators/simulate_Control_of_different_populations_ode.R auxiliary/modelfiles/other/simulators/simulate_Control_of_different_populations_stochastic.R auxiliary/modelfiles/other/simulators/simulate_Influenza_Antibody_Model_discrete.R auxiliary/modelfiles/other/simulators/simulate_Influenza_Antibody_Model_ode.R auxiliary/modelfiles/other/simulators/simulate_Influenza_Antibody_Model_stochastic.R auxiliary/modelfiles/other/simulators/simulate_Influenza_OAS_Model_discrete.R auxiliary/modelfiles/other/simulators/simulate_Influenza_OAS_Model_ode.R auxiliary/modelfiles/other/simulators/simulate_Influenza_OAS_Model_stochastic.R auxiliary/modelfiles/other/simulators/simulate_Influenza_OAS_simpleModel_discrete.R auxiliary/modelfiles/other/simulators/simulate_Influenza_OAS_simpleModel_ode.R auxiliary/modelfiles/other/simulators/simulate_Influenza_OAS_simpleModel_stochastic.R auxiliary/modelfiles/other/simulators/simulate_SIR_seasonal_model_discrete.R auxiliary/modelfiles/other/simulators/simulate_SIR_seasonal_model_ode.R auxiliary/modelfiles/other/simulators/simulate_SIR_seasonal_model_stochastic.R auxiliary/modelfiles/other/simulators/simulate_Stratified_Inoculum_Model_discrete.R auxiliary/modelfiles/other/simulators/simulate_Stratified_Inoculum_Model_ode.R auxiliary/modelfiles/other/simulators/simulate_Stratified_Inoculum_Model_stochastic.R auxiliary/modelfiles/other/simulators/simulate_Time_dependent_SIR_model_discrete.R auxiliary/modelfiles/other/simulators/simulate_Time_dependent_SIR_model_ode.R auxiliary/modelfiles/other/simulators/simulate_Time_dependent_SIR_model_stochastic.R auxiliary/old code/analyze_model_nested.R auxiliary/old code/app.R auxiliary/old code/app_20210107.R auxiliary/old code/check_model_old.R auxiliary/old code/convert_from_desolve.R auxiliary/old code/export_flows.R auxiliary/old code/find_interaction_flows.R auxiliary/old code/find_modelsettings.R auxiliary/old code/generate_fctcall.R auxiliary/old code/generate_flowchart.R auxiliary/old code/generate_flowchart_diagram.R auxiliary/old code/generate_flowchart_ggplot.R auxiliary/old code/generate_function_documentation_nested.R auxiliary/old code/generate_model.R auxiliary/old code/generate_ode_nested.R auxiliary/old code/generate_plots.R auxiliary/old code/generate_rxode.R auxiliary/old code/generate_shinyinput.R auxiliary/old code/generate_text.R auxiliary/old code/global.R auxiliary/old code/launch_app.R auxiliary/old code/oldanalyzeapp.R auxiliary/references/2016_Book_SystemsMedicine.pdf auxiliary/references/fidler19cptpsp - Nonlinear Mixed‐Effects Model Development and Simulation Using nlmixr and Related R Open‐Source Packages.pdf auxiliary/references/getz18epidemics - Modeling epidemics - A primer and Numerus Model Builder implementation.pdf auxiliary/references/medley18pcb - Tellurium notebooks - An environment for reproducible dynamical modeling in systems biology.pdf auxiliary/references/smith17cptpsp - Model Description Language (MDL) - A Standard for Modeling and Simulation.pdf auxiliary/stratification_functionality_testing/base_models/COVAX1_file.R auxiliary/stratification_functionality_testing/base_models/Coronavirus_vaccine_model_v2_file.R auxiliary/stratification_functionality_testing/base_models/SIRSd2_file.R auxiliary/stratification_functionality_testing/base_models/SIRSd_model_file.R auxiliary/stratification_functionality_testing/base_models/simulate_COVAX1_ode.R auxiliary/stratification_functionality_testing/cache/stratification-testing.R auxiliary/stratification_functionality_testing/model_analysis_script.R auxiliary/stratification_functionality_testing/model_generation_script.R auxiliary/stratification_functionality_testing/stratification-antigen-model.R auxiliary/stratification_functionality_testing/stratification-testing.R auxiliary/stratification_functionality_testing/stratified_models/COVAX1_vaccine_file.R auxiliary/stratification_functionality_testing/stratified_models/simulate_COVAX1_vaccine_ode.R auxiliary/stratification_functionality_testing/stratified_models/simulate_Coronavirus_vaccine_model_v2_risk_age_ode.R auxiliary/stratification_functionality_testing/stratified_models/simulate_SIRSd2_risk_age_ode.R auxiliary/stratification_functionality_testing/stratified_models/simulate_SIRSd2_vaccine_age_ode.R cran-comments.md inst/modelbuilder/app.R man/add_model_flow.Rd man/add_model_par.Rd man/add_model_var.Rd man/analyze_model.Rd man/check_model.Rd man/generate_buildUI.Rd man/generate_discrete.Rd man/generate_equations.Rd man/generate_function_documentation.Rd man/generate_function_inputs.Rd man/generate_ggplot.Rd man/generate_model.Rd man/generate_model_file.Rd man/generate_ode.Rd man/generate_plotly.Rd man/generate_shinyinput.Rd man/generate_stochastic.Rd man/generate_stratified_model.Rd man/generate_stratifier_list.Rd man/generate_tables.Rd man/generate_text.Rd man/get_math.Rd man/get_vars_pars.Rd man/load_model.Rd man/modelbuilder.Rd man/remove_model_flow.Rd man/remove_model_par.Rd man/remove_model_var.Rd man/remove_model_variableModal.Rd tests/testthat.R tests/testthat/Rplots.pdf tests/testthat/test-analyze_model.R tests/testthat/test-generate_ggplot.R tests/testthat/test-generate_plotly.R tests/testthat/test-generate_plots.R tests/testthat/test-generate_text.R vignettes/modelbuilder.Rmd