Package: daedalus 0.3.7

Pratik Gupte

daedalus: Model Health, Social, and Economic Costs of a Pandemic

Model the health, education, and economic costs of directly transmitted respiratory virus pandemics, under different scenarios of prior vaccine investment, policy interventions, and public behavioural change, using the 'DAEDALUS' integrated health-economics model adapted from Haw et al. (2022) <doi:10.1038/s43588-022-00233-0>.

Authors:Pratik Gupte [aut, cre], Patrick Doohan [aut], Robert Johnson [aut], Pablo Perez-Guzman [aut], Rich FitzJohn [aut], Emma Russell [aut], David Mears [aut], Katharina Hauck [aut], Abdul Latif Jameel Institute for Disease and Emergency Analytics [fnd], Imperial College of Science, Technology and Medicine [cph, fnd]

daedalus_0.3.7.tar.gz
daedalus_0.3.7.zip(r-4.7)daedalus_0.3.7.zip(r-4.6)daedalus_0.3.7.zip(r-4.5)
daedalus_0.3.7.tgz(r-4.6-x86_64)daedalus_0.3.7.tgz(r-4.6-arm64)daedalus_0.3.7.tgz(r-4.5-x86_64)daedalus_0.3.7.tgz(r-4.5-arm64)
daedalus_0.3.7.tar.gz(r-4.7-arm64)daedalus_0.3.7.tar.gz(r-4.7-x86_64)daedalus_0.3.7.tar.gz(r-4.6-arm64)daedalus_0.3.7.tar.gz(r-4.6-x86_64)
daedalus_0.3.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
daedalus/json (API)

# Install 'daedalus' in R:
install.packages('daedalus', repos = c('https://jameel-institute.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jameel-institute/daedalus/issues

Pkgdown/docs site:https://jameel-institute.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

decision-supportepidemiological-modelshealth-economicspandemic-preparednesspublic-healthrcppsdg-3cppopenmp

6.96 score 7 stars 1 packages 19 scripts 22 exports 13 dependencies

Last updated from:48a3ddd472. Checks:11 OK, 2 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK265
linux-devel-x86_64OK277
source / vignettesOK344
linux-release-arm64OK260
linux-release-x86_64OK274
macos-release-arm64OK163
macos-release-x86_64OK620
macos-oldrel-arm64OK249
macos-oldrel-x86_64OK401
windows-develWARNING291
windows-releaseWARNING298
windows-oldrelOK308
wasm-releaseOK254

Exports:daedalusdaedalus_countrydaedalus_infectiondaedalus_multi_infectiondaedalus_new_behaviourdaedalus_npidaedalus_old_behaviourdaedalus_timed_npidaedalus_vaccinationget_costsget_dataget_epidemic_summaryget_fiscal_costsget_incidenceget_life_years_lostget_new_vaccinationsis_daedalus_behaviouris_daedalus_countryis_daedalus_infectionis_daedalus_npiis_daedalus_vaccinationset_data

Dependencies:abindbackportsBHcheckmateclicpp11daedalus.datadata.tabledust2montyRcppRcppEigenrlang

Getting started with DAEDALUS
Representing countries and territories | Representing infection parameters | Representing vaccine investment for pandemic preparedness | Running the model | References
Rendered fromdaedalus.Rmdusingknitr::rmarkdown

Last update: 2026-04-30
Started: 2024-07-09

Modelling multiple contact settings
Default contact settings | Basic example using POLYMOD | Passing setting-specific contact scaling | Future developments | References
Rendered frommultiple_contact_settings.Rmdusingknitr::rmarkdown

Last update: 2026-04-30
Started: 2026-03-30

Modelling time-limited economic closures
Creating an NPI class object | Common rules for NPI triggers | Time-limiting a pre-canned response | Bespoke time-limited response | Repeated time-limited response
Rendered fromtimed_response.Rmdusingknitr::rmarkdown

Last update: 2026-04-30
Started: 2025-09-09

Modelling outcomes under uncertainty in infection parameters
Rendered frominfection_parameter_uncertainty.Rmdusingknitr::rmarkdown

Last update: 2026-02-05
Started: 2025-06-03

Modelling threshold-dependent economic closures
Rendered fromthresholded_response.Rmdusingknitr::rmarkdown

Last update: 2026-02-05
Started: 2024-09-10

Value of life-years lost
Value of a life year | Life expectancy and years of life lost | Value of a statistical life | Value of lives lost | References
Rendered frominfo_life_value.Rmdusingknitr::rmarkdown

Last update: 2025-11-12
Started: 2024-11-25

General model description
Rationale | Epidemiological model | Model structure | Ordinary differential equations | Age-sector classes | Vaccination classes | Model transition parameters | Seed and force of infection | Disease transition rates | Vaccination | Modelling economic losses | Economic activity losses | References
Rendered frominfo_model_description.Rmdusingknitr::rmarkdown

Last update: 2025-11-12
Started: 2025-06-13

Value of educational time lost
Value of a school year | Valuation constants | Country GNI | Present value of future earnings | Value of education lost | Future developments
Rendered frominfo_edu_value.Rmdusingknitr::rmarkdown

Last update: 2024-11-25
Started: 2024-11-25

Evaluating the costs of pandemic scenarios
Rendered frompandemic_costs.Rmdusingknitr::rmarkdown

Last update: 2024-09-20
Started: 2024-09-20

Readme and manuals

Help Manual

Help pageTopics
Represent behaviour-change mechanisms in DAEDALUSclass_behaviour daedalus_new_behaviour daedalus_old_behaviour is_daedalus_behaviour print.daedalus_behaviour
Represent countries and territories for DAEDALUSclass_country daedalus_country is_daedalus_country print.daedalus_country
Create and work with <daedalus_output> objectsas_daedalus_output class_daedalus_output is_daedalus_output print.daedalus_output validate_daedalus_output
Represent infection parameters for DAEDALUSclass_infection daedalus_infection is_daedalus_infection print.daedalus_infection
Represent non-pharmaceutical intervention strategies for DAEDALUSclass_npi daedalus_npi daedalus_timed_npi is_daedalus_npi print.daedalus_npi
Represent vaccine investment scenarios for DAEDALUSclass_vaccination daedalus_vaccination is_daedalus_vaccination print.daedalus_vaccination
DAEDALUS model for health, social and economic costs of a pandemicdaedalus
Get epidemic losses from a DAEDALUS model rundaedalus_costs get_costs get_costs.daedalus_output get_costs.data.frame
Run daedalus for multiple infection parameter setsdaedalus_multi_infection
Economic constants used in DAEDALUSEARNINGS_LOSS_DISCOUNT econ_constants EDU_ANNUAL_ROR EDU_EFFECTIVENESS_REMOTE WORK_EXPECTED_YEARS
Epidemiological compartments and indicesCOMPARTMENTS epi_constants idx_COMPARTMENTS i_EPI_COMPARTMENTS N_EPI_COMPARTMENTS N_INFECTION_SUBSYSTEM N_MODEL_COMPARTMENTS
Calculate daily incidences and summarise epidemic measuresepi_output_helpers get_epidemic_summary get_incidence get_new_vaccinations
Get parameters from DAEDALUS classesget_data get_data.daedalus_country get_data.daedalus_infection get_data.daedalus_npi get_data.daedalus_output get_data.daedalus_vaccination
Get pandemic fiscal costs from a model runget_fiscal_costs
Get life-years lost by demographic group.get_life_years_lost
DAEDALUS model constantsAGE_GROUPS DIM_AGE_GROUPS DIM_ECON_SECTORS DIM_EPI_COMPARTMENTS DIM_VACCINE_STRATA FLAG_NAMES i_AGE_GROUPS i_ECON_SECTORS i_EDUCATION_SECTOR i_NEW_VAX_STRATUM i_NOT_WORKING i_SCHOOL_AGE i_UNVACCINATED_STRATUM i_VACCINATED_STRATUM i_WORKING_AGE MIN_DATA_COL_NAMES model_constants N_AGE_GROUPS N_ECON_SECTORS N_ECON_STRATA N_FLAGS N_OUTPUT_COLS N_VACCINE_DATA_GROUPS N_VACCINE_STRATA VACCINE_GROUPS
Set parameters in DAEDALUS classesset_data set_data.daedalus_infection set_data.daedalus_vaccination
Model output measures and groups for summaries and derived time-seriessummary_constants SUMMARY_GROUPS SUMMARY_MEASURES