# Evaluation Platform in Chronic Obstructive Pulmonary Disease

## Documentation for package ‘epicR’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

epicR-package | 'epicR' package
calc_event_stack_size | Calculate recommended event_stack_size for a given number of agents
calibrate_COPD_inc | Solves stochastically for COPD incidence rate equation.
calibrate_explicit_mortality | Calibrates explicit mortality
calibrate_explicit_mortality2 | Calibrates explicit mortality by Amin
calibrate_smoking | Calibrates smoking
config | epicR Configuration Management
configuration | epicR Configuration Management
copy_configs_to_user | Copy default configs to user directory
epicR | 'epicR' package
epicR-config | epicR Configuration Management
estimate_memory_required | Estimate memory required for simulation
export_figures | Runs the model and exports an excel file with all output data
express_matrix | Express matrix.
get_agent_events | Returns all events of an agent.
get_agent_size_bytes | Returns the size of agent struct in bytes
get_all_events | Returns all events.
get_all_events_matrix | Returns a matrix containing all events
get_available_memory | Get available system memory (platform-specific)
get_default_settings | Exports default settings
get_errors | Returns errors
get_event | Returns the events stack.
get_events_by_type | Returns all events of a certain type.
get_input | Returns a list of default model input values
get_inputs | Returns inputs
get_list_elements | Get list elements
get_n_events | Returns total number of events.
get_output | Main outputs of the current run.
get_output_ex | Extra outputs from the model
get_progress | Returns current simulation progress.
get_runtime_stats | Returns run time stats.
get_sample_output | Returns a sample output for a given year and gender.
get_settings | Returns current settings.
get_smith | Returns agent Smith.
get_user_config_dir | Get user config directory path
init_session | Initializes a model. Allocates memory to the C engine.
list_available_jurisdictions | List available config jurisdictions
mvrnormArma | Samples from a multivariate normal
report_COPD_by_ctime | Reports COPD related stats.
report_exacerbation_by_time | Reports exacerbation-related stats.
reset_model_input | Reset the cached model input
reset_user_configs | Reset user configs to package defaults
resume | Resumes running of model.
sanity_check | Basic tests of model functionality. Serious issues if the test does not pass.
sanity_COPD | Basic COPD test.
set_input_var | Sets input variables.
set_settings_var | Sets model settings.
simulate | Convenience function: run simulation and return results
terminate_session | Terminates a session and releases allocated memory.
test_case_detection | Returns results of Case Detection strategies
user_config_exists | Check if user config exists
validate_config | Validate a config file
validate_COPD | Returns results of validation tests for COPD
validate_diagnosis | Returns results of validation tests for diagnosis
validate_exacerbation | Returns results of validation tests for exacerbation rates
validate_gpvisits | Returns results of validation tests for GP visits
validate_lung_function | Returns results of validation tests for lung function
validate_medication | Returns results of validation tests for medication module.
validate_mortality | Returns results of validation tests for mortality rate
validate_overdiagnosis | Returns results of validation tests for overdiagnosis
validate_payoffs | Returns results of validation tests for payoffs, costs and QALYs
validate_population | Returns simulated vs. predicted population table and a plot
validate_smoking | Returns results of validation tests for smoking module.
validate_survival | Returns the Kaplan Meier curve comparing COPD and non-COPD
validate_symptoms | Returns results of validation tests for Symptoms
validate_treatment | Returns results of validation tests for Treatment