Package index

Model functions

Run the DAEDALUS integrated economic-epidemiological model.

daedalus(): DAEDALUS model for health, social and economic costs of a pandemic
daedalus_multi_infection(): Run daedalus for multiple infection parameter sets

Class `<daedalus_country>`

Represent and access country or territory characteristics.

daedalus_country() is_daedalus_country() print(<daedalus_country>): Represent countries and territories for DAEDALUS

Class `<daedalus_infection>`

Represent and access infection characteristics.

daedalus_infection() is_daedalus_infection() print(<daedalus_infection>): Represent infection parameters for DAEDALUS

Class `<daedalus_vaccination>`

Represent and access vaccine investment scenarios.

daedalus_vaccination() is_daedalus_vaccination() print(<daedalus_vaccination>): Represent vaccine investment scenarios for DAEDALUS

Class `<daedalus_npi>`

Represent and access non-pharmaceutical intervention scenarios.

daedalus_npi() is_daedalus_npi() print(<daedalus_npi>) daedalus_timed_npi(): Represent non-pharmaceutical intervention strategies for DAEDALUS

Class `<daedalus_behaviour>`

Represent and access parameters for behavioural models.

daedalus_old_behaviour() daedalus_new_behaviour() is_daedalus_behaviour() print(<daedalus_behaviour>): Represent behaviour-change mechanisms in DAEDALUS

Class `<daedalus_output>`

Represent and store model output for further processing.

as_daedalus_output() validate_daedalus_output() is_daedalus_output() print(<daedalus_output>): Create and work with <daedalus_output> objects

Model output post-processing

Functions to process model output to calculate pandemic costs and other outcomes.

get_costs(): Get epidemic costs from a DAEDALUS model run
get_fiscal_costs(): Get pandemic fiscal costs from a model run
get_incidence() get_epidemic_summary() get_new_vaccinations(): Calculate daily incidences and summarise epidemic measures
get_life_years_lost(): Get life-years lost by demographic group.

Package generics

Generics with methods for package S3 classes.

get_data(): Get parameters from DAEDALUS classes
set_data(): Set parameters in DAEDALUS classes

Model constants

Useful constants used internally.

N_AGE_GROUPS i_AGE_GROUPS N_VACCINE_STRATA N_VACCINE_DATA_GROUPS AGE_GROUPS i_WORKING_AGE i_SCHOOL_AGE N_ECON_SECTORS i_ECON_SECTORS i_EDUCATION_SECTOR N_ECON_STRATA i_NOT_WORKING DIM_AGE_GROUPS DIM_EPI_COMPARTMENTS DIM_ECON_SECTORS DIM_VACCINE_STRATA i_UNVACCINATED_STRATUM i_VACCINATED_STRATUM i_NEW_VAX_STRATUM VACCINE_GROUPS N_OUTPUT_COLS N_FLAGS FLAG_NAMES: DAEDALUS model constants
COMPARTMENTS idx_COMPARTMENTS N_EPI_COMPARTMENTS i_EPI_COMPARTMENTS N_MODEL_COMPARTMENTS N_INFECTION_SUBSYSTEM: Epidemiological compartments and indices
SUMMARY_MEASURES SUMMARY_GROUPS: Model output measures and groups for summaries and derived time-series
edu_effectiveness_remote edu_annual_ror work_expected_years earnings_loss_discount: Economic constants used in DAEDALUS

Internal functions

Functions used internally.

new_daedalus_response() response_class_names is_daedalus_response() validate_daedalus_response(): Constructor for the <daedalus_response> super-class and sub-classes
country_name_from_arg(): Get country name from arg
daedalus-package: daedalus: Model Health, Social, and Economic Costs of a Pandemic
daedalus_internal(): Internal function for daedalus
dummy_npi(): Dummy NPI
dummy_vaccination(): Dummy vaccination
get_beta(): Calculate transmission parameter from infection and contact parameters
get_daedalus_multi_response_times(): Get response times from a dust2 system with multiple groups
get_daedalus_response_times(): Get model response times from dust2 output
get_state_indices(): Get a vector of state indices
get_value_lost_earnings(): Calculate the present value of lost earnings due to educational disruption
get_value_school_year(): Calculate the value of a school year
initial_flags(): Initial values for model flags
assert_class_fields(): Check that a class has expected names
make_initial_state(): Generate a default initial state for DAEDALUS
make_susc_matrix(): Prepare susceptibility matrix for a vaccine-country pair
new_daedalus_hosp_overflow(): Make a hospital overflow response
out_list_to_df(): Reshape output data
make_conmat_large() make_work_contacts() make_consumer_contacts() make_full_contacts(): Make large contact matrix for Cpp model.
prepare_output(): Prepare DAEDALUS data
prepare_parameters(): Prepare infection parameters for model
process_event_times(): Process event data
get_ngm(): Calculate the effective R
drop_null() first() last() weighted_rowsums() interest_accumulation() annual_rate_daily(): Helper functions
uptake_percent_to_number(): Convert an uptake limit from a percentage to a number
validate_behaviour_input(): Internal helper function to prepare parameters
validate_country_input(): Validate country input
validate_infection_input() validate_infection_list_input(): Validate and return infection input
validate_npi_input(): Validate npi inputs
validate_vaccination_input(): Validate vaccination inputs

Model functions

Class <daedalus_country>

Class <daedalus_infection>

Class <daedalus_vaccination>

Class <daedalus_npi>

Class <daedalus_behaviour>

Class <daedalus_output>