Working with posterior samples | Getting a data.frame of posterior samples | Using random variables (rvars) for uncertainty propagation | How can I assess whether sampling has converged? | How can I perform posterior predictive checks? | What is an observation in the meta model? | I'd like to run a simulation study | How are the default priors for epidist chosen? | How can I assess how sensitive the fitted posterior distribution is to the prior distribution used? | What do the parameters in my model output correspond to? | How can I generate predictions with my fitted epidist model? | How can I use the marginaleffects package with my fitted epidist model? | How can I use the cmdstanr backend? | References
Package: epidist 0.5.0
Sam Abbott
epidist: Estimate Epidemiological Delay Distributions with 'brms'
Understanding and accurately estimating epidemiological delay distributions is important for public health policy. These estimates influence epidemic situational awareness, control strategies, and resource allocation. This package provides methods to address the key challenges in estimating these distributions, including truncation, interval censoring, and dynamical biases. These issues are frequently overlooked, resulting in biased conclusions. Built on top of 'brms', it allows for flexible modelling including time-varying spatial components and partially pooled estimates of demographic characteristics.
Authors:
epidist_0.5.0.tar.gz
epidist_0.5.0.zip(r-4.7-any)epidist_0.5.0.zip(r-4.6-any)epidist_0.5.0.zip(r-4.5-any)
epidist_0.5.0.tgz(r-4.6-any)epidist_0.5.0.tgz(r-4.5-any)
epidist_0.5.0.tar.gz(r-4.7-any)epidist_0.5.0.tar.gz(r-4.6-any)
epidist_0.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
epidist/json (API)
| # Install 'epidist' in R: |
| install.packages('epidist', repos = c('https://epinowcast.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/epinowcast/epidist/issues
Pkgdown/docs site:https://epidist.epinowcast.org
Datasets:
- sierra_leone_ebola_data - Ebola linelist data from Fang et al.
Last updated from:51d8d33ad5 (on v0.5.0). Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 348 | ||
| source / vignettes | OK | 312 | ||
| linux-release | OK | 347 | ||
| macos-release | OK | 227 | ||
| macos-oldrel | OK | 321 | ||
| windows-devel | OK | 306 | ||
| windows-release | OK | 299 | ||
| windows-oldrel | OK | 299 | ||
| wasm-release | OK | 193 |
Exports:add_delay_parameter_drawsadd_summariesas_epidist_aggregate_dataas_epidist_estimates_dataas_epidist_latent_modelas_epidist_linelist_dataas_epidist_marginal_modelas_epidist_meta_modelas_epidist_multivariateas_epidist_naive_modelassert_epidistbfdelay_parameter_drawsdelay_summary_drawsepidistepidist_diagnosticsepidist_estimates_epireviewepidist_estimates_parametersepidist_estimates_summariesepidist_familyepidist_family_modelepidist_family_priorepidist_formulaepidist_formula_modelepidist_gen_log_likepidist_gen_meta_log_likepidist_gen_meta_predictepidist_gen_posterior_epredepidist_gen_posterior_predictepidist_meta_leave_one_outepidist_model_priorepidist_newdataepidist_priorepidist_stancodeepidist_strataepidist_transform_data_modelGammais_epidist_aggregate_datais_epidist_datais_epidist_estimates_datais_epidist_latent_modelis_epidist_linelist_datais_epidist_marginal_modelis_epidist_meta_modelis_epidist_multivariateis_epidist_naive_modellognormalnew_epidist_aggregate_datanew_epidist_estimates_datanew_epidist_latent_modelnew_epidist_linelist_datanew_epidist_marginal_modelnew_epidist_meta_modelnew_epidist_multivariatenew_epidist_naive_modelplot_delaysplot_eventssimulate_datessimulate_exponential_casessimulate_gillespiesimulate_secondarysimulate_studysimulate_uniform_casesweibull
Dependencies:abindbackportsbayesplotBHbridgesamplingbrmsBrobdingnagcallrcheckmateclicodacodetoolscpp11descdigestdistributionaldplyrfarverfuturefuture.applygenericsggdistggplot2ggridgesglobalsgluegridExtragtableinlineisobandlabelinglatticelifecyclelistenvloolubridatemagrittrMatrixmatrixStatsmgcvmvtnormnleqslvnlmenumDerivotelparallellypillarpkgbuildpkgconfigplyrposteriorprimarycensoredprocessxpspurrrquadprogQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreshape2rlangrstanrstantoolsS7scalesStanHeadersstringistringrtensorAtibbletidyrtidyselecttimechangeutf8vctrsviridisLitewithr
Frequently asked questions and tips
Last update: 2026-09-25
Started: 2024-07-22
Using epidist to estimate delay between symptom onset and positive test for an Ebola outbreak in Sierra Leone
Using the cmdstanr backend | Data preparation | Fitting sex-district stratified delay distributions | Model fitting | Intercept-only model | Sex-stratified model | Sex-district stratified model | Posterior expectations | Linear predictor posteriors | Delay posterior distributions | Discrete probability mass function | Continuous probability density function | Conclusion | References
Last update: 2026-09-25
Started: 2024-09-09
Guide to the statistical models implemented in epidist
Background | Forwards and backwards distributions | Right truncation | Interval censoring | The naive model | The latent model | Bounding the latent primary event time | A non-uniform primary event | The marginal model | The meta model | Sampling likelihoods | A reported mean | A reported standard deviation | A reported quantile | Summaries from the same study | A vector of summaries with a covariance | Reported distribution parameters | Individual level records | What we need from each study | The biased estimands | Censoring adjustment | An estimated growth rate | Left truncation | Quantiles of the estimands | References
Last update: 2026-09-25
Started: 2025-02-18
Approximate Bayesian inference in epidist
Background | Alternative approximate inference algorithms | Laplace method | Variational inference using ADVI | Pathfinder | Demonstration | Comparison of parameter posterior distributions | Comparison of resulting delay distributions | Comparison of time taken | Conclusion | References
Last update: 2026-09-22
Started: 2024-07-15
Fitting to published estimates with the meta model
What we need from a study | Setup | Simulating biased published estimates | Fitting and comparing models | A bias-adjusted fit to the summaries alone | Allowing studies to differ | What happens with the wrong metadata | A mixed fit: summaries plus individual records | Reference: the marginal model on the full line list | Comparing the fits | Real world estimates from epireview | Adjusting for the phase of the outbreak | The population level delay and the size of the phase bias | Comparing with a modern re-analysis of the same line list | Learning more | References
Last update: 2026-09-22
Started: 2026-09-04
Getting started with epidist
Key concepts in delay distribution estimation | Setup | Simulating data | Preprocessing the data | The observation process | Fitting models | Fit a model that doesn't account for censoring and truncation | Fit a model that accounts for biases and truncation | Compare the two models estimated delay parameters | Visualise posterior predictions of the true delay distribution | Learning more | References
Last update: 2026-09-22
Started: 2023-12-08
Primary event distributions
Background | Simulating from a growing epidemic | Uniform against exponential growth | A growth rate that varies | Identifying the growth rate | Summary | References
Last update: 2026-09-22
Started: 2026-09-02
Left truncation with delay_min
Setup | Simulate left truncated data | Fit models with and without the adjustment | Compare parameter estimates | Compare the estimated delay distributions | Summary
Last update: 2026-09-12
Started: 2026-08-26
Extending epidist
Why extend epidist? | Adding a data source | Adding a model type | Exploring how cfrnow extends epidist | Getting help
Last update: 2026-08-26
Started: 2026-08-26
