# Estimate epidemiological delay distributions with `brms`

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license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epinowcast/epidist/blob/main/LICENSE.md)
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contributors](https://img.shields.io/github/contributors/epinowcast/epidist)](https://github.com/epinowcast/epidist/graphs/contributors)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14213017.svg)](https://doi.org/10.5281/zenodo.14213017)

## Summary

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, following Park et al. (2024)
[doi:10.1101/2024.01.12.24301247](https://doi.org/10.1101/2024.01.12.24301247)
and Charniga et al. (2024)
[doi:10.1371/journal.pcbi.1012520](https://doi.org/10.1371/journal.pcbi.1012520).
These issues are frequently overlooked, resulting in biased conclusions.
Built on top of ‘brms’, it allows for flexible modelling including
time-varying and spatial effects and partially pooled estimates of
demographic characteristics.

## Quickstart

To learn more about `epidist` we recommend reading the vignettes in this
order:

- To get started, [fitting a delay distribution to individual level
  data](https://epidist.epinowcast.org/articles/epidist.html).
- For the models we support and the biases each one corrects, the [model
  guide](https://epidist.epinowcast.org/articles/model.html).
- For a worked example on real data, [delays from symptom onset to
  positive test in an Ebola
  outbreak](https://epidist.epinowcast.org/articles/ebola.html).
- For fitting to published estimates, and adjusting them for how each
  study was estimated, the [meta
  model](https://epidist.epinowcast.org/articles/meta.html).
- For faster fits on larger data, [approximate Bayesian
  inference](https://epidist.epinowcast.org/articles/approx-inference.html).
- For questions that come up in use, the
  [FAQ](https://epidist.epinowcast.org/articles/faq.html).

## Installation

Installing the package

You can install the latest released version from CRAN using the standard
`install.packages` function:

``` r

install.packages("epidist")
```

Alternatively, you can install the latest release from our r-universe
repository:

``` r

install.packages("epidist", repos = "https://epinowcast.r-universe.dev")
```

To install the development version from GitHub (warning! this version
may contain breaking changes and/or bugs), use the [`pak`
package](https://pak.r-lib.org/):

``` r

pak::pak("epinowcast/epidist")
```

Similarly, you can install historical versions by specifying the release
tag (e.g.,
[`v0.4.0`](https://github.com/epinowcast/epidist/releases/tag/v0.4.0)):

``` r

pak::pak("epinowcast/epidist@v0.4.0")
```

*Note: You can also use the above approach to install a specific commit
if needed, for example, if you want to try out a specific unreleased
feature, but not the absolute latest developmental version.*

Installing CmdStan (optional)

By default `epidist` uses the `rstan` package for fitting models. If you
wish to use the `cmdstanr` package instead, you will need to install
[CmdStan](https://mc-stan.org/users/interfaces/cmdstan), which also
entails having a suitable C++ toolchain setup. We recommend using the
[`cmdstanr` package](https://mc-stan.org/cmdstanr/) to manage CmdStan.
The Stan team provides instructions in the [*Getting started with
`cmdstanr`*](https://mc-stan.org/cmdstanr/articles/cmdstanr.html)
vignette, with other details and support at the [package
site](https://mc-stan.org/cmdstanr/), but the brief version is:

``` r

# `cmdstanr` is not a dependency of `epidist`, so install it yourself
install.packages(
  "cmdstanr",
  repos = c("https://stan-dev.r-universe.dev", getOption("repos"))
)

# once `cmdstanr` is installed
cmdstanr::install_cmdstan()
```

*Note: You can speed up CmdStan installation using the `cores` argument.
If you are installing a particular version of `epidist`, you may also
need to install a past version of CmdStan, which you can do with the
`version` argument.*

## Resources

Organisation Website

Our [organisation website](https://www.epinowcast.org/) includes links
to other resources, [guest posts](https://www.epinowcast.org/blog.html),
and [seminar schedule](https://www.epinowcast.org/seminars.html) for
both upcoming and past recordings.

Community Forum

Our [community forum](https://community.epinowcast.org/) has areas for
[question and answer](https://community.epinowcast.org/c/interface/15)
and [considering new methods and
tools](https://community.epinowcast.org/c/projects/11), among others. If
you are generally interested in real-time analysis of infectious
disease, you may find this useful even if do not use `epidist`.

## Contributing

We welcome contributions and new contributors! We particularly
appreciate help on [identifying and identified
issues](https://github.com/epinowcast/epidist/issues). Please check and
add to the issues, and/or add a [pull
request](https://github.com/epinowcast/epidist/pulls) and see our
[contributing
guide](https://github.com/epinowcast/.github/blob/main/CONTRIBUTING.md)
for more information.

### How to make a bug report or feature request

Please briefly describe your problem and what output you expect in an
[issue](https://github.com/epinowcast/epidist/issues).

If you have a question, please don’t open an issue. Instead, ask on our
[forum](https://community.epinowcast.org/).

See our [contributing
guide](https://github.com/epinowcast/.github/blob/main/CONTRIBUTING.md)
for more information.

### Code of Conduct

Please note that the `epidist` project is released with a [Contributor
Code of
Conduct](https://github.com/epinowcast/.github/blob/main/CODE_OF_CONDUCT.md).
By contributing to this project, you agree to abide by its terms.

## Citation

If you use `epidist` in your work, please consider citing it using
`citation("epidist")`.

Package citation information

``` r
citation("epidist")
To cite package 'epidist' in publications use:

  Howes A, Park S, Abbott S (2026). _epidist: Estimate Epidemiological
  Delay Distributions with 'brms'_. doi:10.5281/zenodo.14213017
  <https://doi.org/10.5281/zenodo.14213017>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {epidist: Estimate Epidemiological Delay Distributions with 'brms'},
    author = {Adam Howes and Sang Woo Park and Sam Abbott},
    year = {2026},
    doi = {10.5281/zenodo.14213017},
  }
```

If using our methodology, or the methodology on which ours is based,
please cite the relevant papers. This may include:

- [Estimating epidemiological delay distributions for infectious
  diseases](https://doi.org/10.1101/2024.01.12.24301247) by Park *et
  al.* (2024) – if using the latent model
- [Best practices for estimating and reporting epidemiological delay
  distributions of infectious diseases using public health surveillance
  and healthcare
  data](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012520)
  by Charniga *et al.* (2024)

If using the marginal model, please also cite the
[`primarycensored`](https://primarycensored.epinowcast.org/) package
using `citation("primarycensored")`.

## Contributors

All contributions to this project are gratefully acknowledged using the
[`allcontributors` package](https://github.com/ropensci/allcontributors)
following the [allcontributors](https://allcontributors.org)
specification. Contributions of any kind are welcome!

### Code

[seabbs](https://github.com/epinowcast/epidist/commits?author=seabbs),
[athowes](https://github.com/epinowcast/epidist/commits?author=athowes),
[parksw3](https://github.com/epinowcast/epidist/commits?author=parksw3),
[claude](https://github.com/epinowcast/epidist/commits?author=claude),
[sbfnk](https://github.com/epinowcast/epidist/commits?author=sbfnk),
[cherz4](https://github.com/epinowcast/epidist/commits?author=cherz4),
[damonbayer](https://github.com/epinowcast/epidist/commits?author=damonbayer),
[medewitt](https://github.com/epinowcast/epidist/commits?author=medewitt),
[kcharniga](https://github.com/epinowcast/epidist/commits?author=kcharniga)

### Issue Authors

[kgostic](https://github.com/epinowcast/epidist/issues?q=is%3Aissue+author%3Akgostic),
[TimTaylor](https://github.com/epinowcast/epidist/issues?q=is%3Aissue+author%3ATimTaylor),
[jamesmbaazam](https://github.com/epinowcast/epidist/issues?q=is%3Aissue+author%3Ajamesmbaazam),
[jonathonmellor](https://github.com/epinowcast/epidist/issues?q=is%3Aissue+author%3Ajonathonmellor),
[RodrigoZepeda](https://github.com/epinowcast/epidist/issues?q=is%3Aissue+author%3ARodrigoZepeda)

### Issue Contributors

[pearsonca](https://github.com/epinowcast/epidist/issues?q=is%3Aissue+commenter%3Apearsonca),
[SamuelBrand1](https://github.com/epinowcast/epidist/issues?q=is%3Aissue+commenter%3ASamuelBrand1),
[zsusswein](https://github.com/epinowcast/epidist/issues?q=is%3Aissue+commenter%3Azsusswein),
[oswaldogressani](https://github.com/epinowcast/epidist/issues?q=is%3Aissue+commenter%3Aoswaldogressani),
[DrAuxetic](https://github.com/epinowcast/epidist/issues?q=is%3Aissue+commenter%3ADrAuxetic),
[mark-burdon](https://github.com/epinowcast/epidist/issues?q=is%3Aissue+commenter%3Amark-burdon)

# Package index

## Data preparation

### Linelist data

Functions for preparing linelist data

- [`as_epidist_linelist_data()`](https://epidist.epinowcast.org/reference/as_epidist_linelist_data.md)
  : Create an epidist_linelist_data object

- [`as_epidist_linelist_data(`*`<data.frame>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_linelist_data.data.frame.md)
  : Create an epidist_linelist_data object from a data frame with event
  dates

- [`as_epidist_linelist_data(`*`<default>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_linelist_data.default.md)
  : Create an epidist_linelist_data object from vectors of event times

- [`as_epidist_linelist_data(`*`<epidist_aggregate_data>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_linelist_data.epidist_aggregate_data.md)
  : Convert aggregate data to linelist format

- [`assert_epidist(`*`<epidist_linelist_data>`*`)`](https://epidist.epinowcast.org/reference/assert_epidist.epidist_linelist_data.md)
  :

  Assert validity of `epidist_linelist_data` objects

- [`is_epidist_linelist_data()`](https://epidist.epinowcast.org/reference/is_epidist_linelist_data.md)
  :

  Check if data has the `epidist_linelist_data` class

- [`new_epidist_linelist_data()`](https://epidist.epinowcast.org/reference/new_epidist_linelist_data.md)
  :

  Class constructor for `epidist_linelist_data` objects

### Aggregate data

Functions for preparing aggregate data

- [`as_epidist_aggregate_data()`](https://epidist.epinowcast.org/reference/as_epidist_aggregate_data.md)
  : Create an epidist_aggregate_data object

- [`as_epidist_aggregate_data(`*`<data.frame>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_aggregate_data.data.frame.md)
  : Create an epidist_aggregate_data object from a data.frame

- [`as_epidist_aggregate_data(`*`<default>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_aggregate_data.default.md)
  : Create an epidist_aggregate_data object from vectors of event times

- [`as_epidist_aggregate_data(`*`<epidist_linelist_data>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_aggregate_data.epidist_linelist_data.md)
  : Convert linelist data to aggregate format

- [`assert_epidist(`*`<epidist_aggregate_data>`*`)`](https://epidist.epinowcast.org/reference/assert_epidist.epidist_aggregate_data.md)
  :

  Assert validity of `epidist_aggregate_data` objects

- [`is_epidist_aggregate_data()`](https://epidist.epinowcast.org/reference/is_epidist_aggregate_data.md)
  :

  Check if data has the `epidist_aggregate_data` class

- [`new_epidist_aggregate_data()`](https://epidist.epinowcast.org/reference/new_epidist_aggregate_data.md)
  :

  Class constructor for `epidist_aggregate_data` objects

### Class methods

Methods that keep modified objects in their `epidist` class

- [`` `[`( ``*`<epidist_data>`*`)`](https://epidist.epinowcast.org/reference/epidist_data.md)
  [`` `[<-`( ``*`<epidist_data>`*`)`](https://epidist.epinowcast.org/reference/epidist_data.md)
  [`` `[[<-`( ``*`<epidist_data>`*`)`](https://epidist.epinowcast.org/reference/epidist_data.md)
  [`` `$<-`( ``*`<epidist_data>`*`)`](https://epidist.epinowcast.org/reference/epidist_data.md)
  [`` `names<-`( ``*`<epidist_data>`*`)`](https://epidist.epinowcast.org/reference/epidist_data.md)
  [`rbind(`*`<epidist_data>`*`)`](https://epidist.epinowcast.org/reference/epidist_data.md)
  [`dplyr_reconstruct(`*`<epidist_data>`*`)`](https://epidist.epinowcast.org/reference/epidist_data.md)
  [`dplyr_row_slice(`*`<epidist_data>`*`)`](https://epidist.epinowcast.org/reference/epidist_data.md)
  [`dplyr_col_modify(`*`<epidist_data>`*`)`](https://epidist.epinowcast.org/reference/epidist_data.md)
  [`group_by(`*`<epidist_data>`*`)`](https://epidist.epinowcast.org/reference/epidist_data.md)
  [`ungroup(`*`<epidist_data>`*`)`](https://epidist.epinowcast.org/reference/epidist_data.md)
  :

  Keep `epidist` objects in their class

- [`is_epidist_data()`](https://epidist.epinowcast.org/reference/is_epidist_data.md)
  :

  Check if data has the `epidist_data` class

### Estimates data

Functions for preparing published summary estimates

- [`as_epidist_estimates_data()`](https://epidist.epinowcast.org/reference/as_epidist_estimates_data.md)
  :

  Create an `epidist_estimates_data` object

- [`as_epidist_estimates_data(`*`<data.frame>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_estimates_data.data.frame.md)
  :

  Create an `epidist_estimates_data` object from a data frame

- [`as_epidist_estimates_data(`*`<epidist_estimates_data>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_estimates_data.epidist_estimates_data.md)
  :

  Return an `epidist_estimates_data` object unchanged

- [`as_epidist_estimates_data(`*`<epidist_multivariate>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_estimates_data.epidist_multivariate.md)
  :

  Create an `epidist_estimates_data` object from a multivariate
  representation

- [`as_epidist_estimates_data(`*`<list>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_estimates_data.list.md)
  :

  Combine `epidist_estimates_data` objects from several studies

- [`assert_epidist(`*`<epidist_estimates_data>`*`)`](https://epidist.epinowcast.org/reference/assert_epidist.epidist_estimates_data.md)
  :

  Assert validity of `epidist_estimates_data` objects

- [`epidist_estimates_epireview()`](https://epidist.epinowcast.org/reference/epidist_estimates_epireview.md)
  :

  Report studies from an `epireview` parameter table

- [`epidist_estimates_parameters()`](https://epidist.epinowcast.org/reference/epidist_estimates_parameters.md)
  : Report a study that published the parameters of a distribution it
  fitted

- [`epidist_estimates_summaries()`](https://epidist.epinowcast.org/reference/epidist_estimates_summaries.md)
  : Report a study that published summaries of its delays

- [`is_epidist_estimates_data()`](https://epidist.epinowcast.org/reference/is_epidist_estimates_data.md)
  :

  Check if data has the `epidist_estimates_data` class

- [`new_epidist_estimates_data()`](https://epidist.epinowcast.org/reference/new_epidist_estimates_data.md)
  :

  Class constructor for `epidist_estimates_data` objects

### Multivariate representation

Functions for representing draws of a set of parameters

- [`as_epidist_multivariate()`](https://epidist.epinowcast.org/reference/as_epidist_multivariate.md)
  :

  Create an `epidist_multivariate` object

- [`as_epidist_multivariate(`*`<data.frame>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_multivariate.data.frame.md)
  :

  Create an `epidist_multivariate` object from a data frame of draws

- [`as_epidist_multivariate(`*`<matrix>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_multivariate.matrix.md)
  :

  Create an `epidist_multivariate` object from a matrix of draws

- [`assert_epidist(`*`<epidist_multivariate>`*`)`](https://epidist.epinowcast.org/reference/assert_epidist.epidist_multivariate.md)
  :

  Assert validity of `epidist_multivariate` objects

- [`is_epidist_multivariate()`](https://epidist.epinowcast.org/reference/is_epidist_multivariate.md)
  :

  Check if an object has the `epidist_multivariate` class

- [`new_epidist_multivariate()`](https://epidist.epinowcast.org/reference/new_epidist_multivariate.md)
  :

  Class constructor for `epidist_multivariate` objects

- [`print(`*`<epidist_multivariate>`*`)`](https://epidist.epinowcast.org/reference/print.epidist_multivariate.md)
  :

  Print an `epidist_multivariate` object

- [`vcov(`*`<epidist_multivariate>`*`)`](https://epidist.epinowcast.org/reference/vcov.epidist_multivariate.md)
  :

  The covariance matrix of an `epidist_multivariate` object

## Models

### Naive model

Specific methods for the naive model

- [`as_epidist_naive_model()`](https://epidist.epinowcast.org/reference/as_epidist_naive_model.md)
  :

  Convert an object to an `epidist_naive_model` object

- [`as_epidist_naive_model(`*`<epidist_aggregate_data>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_naive_model.epidist_aggregate_data.md)
  :

  The naive model method for `epidist_aggregate_data` objects

- [`as_epidist_naive_model(`*`<epidist_linelist_data>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_naive_model.epidist_linelist_data.md)
  :

  The naive model method for `epidist_linelist_data` objects

- [`epidist_formula_model(`*`<epidist_naive_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_formula_model.epidist_naive_model.md)
  :

  Define the model-specific component of an `epidist` custom formula for
  the naive model

- [`epidist_newdata(`*`<epidist_naive_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_newdata.epidist_naive_model.md)
  :

  Build `newdata` for the naive model

- [`epidist_stancode(`*`<epidist_naive_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_stancode.epidist_naive_model.md)
  : Define the Stan code of the naive model

- [`epidist_transform_data_model(`*`<epidist_naive_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_transform_data_model.epidist_naive_model.md)
  : Transform data for the naive model

- [`is_epidist_naive_model()`](https://epidist.epinowcast.org/reference/is_epidist_naive_model.md)
  :

  Check if data has the `epidist_naive_model` class

- [`new_epidist_naive_model()`](https://epidist.epinowcast.org/reference/new_epidist_naive_model.md)
  :

  Class constructor for `epidist_naive_model` objects

### Latent model

Specific methods for the latent model

- [`as_epidist_latent_model()`](https://epidist.epinowcast.org/reference/as_epidist_latent_model.md)
  :

  Convert an object to an `epidist_latent_model` object

- [`as_epidist_latent_model(`*`<epidist_aggregate_data>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_latent_model.epidist_aggregate_data.md)
  :

  The latent model method for `epidist_aggregate_data` objects

- [`as_epidist_latent_model(`*`<epidist_linelist_data>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_latent_model.epidist_linelist_data.md)
  :

  The latent model method for `epidist_linelist_data` objects

- [`epidist_family_model(`*`<epidist_latent_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_family_model.epidist_latent_model.md)
  :

  Create the model-specific component of an `epidist` custom family

- [`epidist_formula_model(`*`<epidist_latent_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_formula_model.epidist_latent_model.md)
  :

  Define the model-specific component of an `epidist` custom formula for
  the latent model

- [`epidist_model_prior(`*`<epidist_latent_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_model_prior.epidist_latent_model.md)
  : Model specific prior distributions for latent models

- [`epidist_newdata(`*`<epidist_latent_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_newdata.epidist_latent_model.md)
  :

  Build `newdata` for the latent model

- [`is_epidist_latent_model()`](https://epidist.epinowcast.org/reference/is_epidist_latent_model.md)
  :

  Check if data has the `epidist_latent_model` class

- [`new_epidist_latent_model()`](https://epidist.epinowcast.org/reference/new_epidist_latent_model.md)
  :

  Class constructor for `epidist_latent_model` objects

### Marginal model

Specific methods for the marginal model

- [`as_epidist_marginal_model()`](https://epidist.epinowcast.org/reference/as_epidist_marginal_model.md)
  :

  Convert an object to an `epidist_marginal_model` object

- [`as_epidist_marginal_model(`*`<epidist_aggregate_data>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_marginal_model.epidist_aggregate_data.md)
  :

  The marginal model method for `epidist_aggregate_data` objects

- [`as_epidist_marginal_model(`*`<epidist_linelist_data>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_marginal_model.epidist_linelist_data.md)
  :

  The marginal model method for `epidist_linelist_data` objects

- [`epidist_family_model(`*`<epidist_marginal_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_family_model.epidist_marginal_model.md)
  :

  Create the model-specific component of an `epidist` custom family

- [`epidist_formula_model(`*`<epidist_marginal_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_formula_model.epidist_marginal_model.md)
  :

  Define the model-specific component of an `epidist` custom formula for
  the marginal model

- [`epidist_newdata(`*`<epidist_marginal_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_newdata.epidist_marginal_model.md)
  :

  Build `newdata` for the marginal model

- [`epidist_transform_data_model(`*`<epidist_marginal_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_transform_data_model.epidist_marginal_model.md)
  : Transform data for the marginal model

- [`is_epidist_marginal_model()`](https://epidist.epinowcast.org/reference/is_epidist_marginal_model.md)
  :

  Check if data has the `epidist_marginal_model` class

- [`new_epidist_marginal_model()`](https://epidist.epinowcast.org/reference/new_epidist_marginal_model.md)
  :

  Class constructor for `epidist_marginal_model` objects

### Meta model

Specific methods for the meta model

- [`as_epidist_meta_model(`*`<NULL>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_meta_model.NULL.md)
  : The meta model method for summary estimates only

- [`as_epidist_meta_model()`](https://epidist.epinowcast.org/reference/as_epidist_meta_model.md)
  :

  Convert an object to an `epidist_meta_model` object

- [`as_epidist_meta_model(`*`<epidist_aggregate_data>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_meta_model.epidist_aggregate_data.md)
  :

  The meta model method for `epidist_aggregate_data` objects

- [`as_epidist_meta_model(`*`<epidist_estimates_data>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_meta_model.epidist_estimates_data.md)
  :

  The meta model method for `epidist_estimates_data` objects

- [`as_epidist_meta_model(`*`<epidist_linelist_data>`*`)`](https://epidist.epinowcast.org/reference/as_epidist_meta_model.epidist_linelist_data.md)
  :

  The meta model method for `epidist_linelist_data` objects

- [`assert_epidist(`*`<epidist_meta_model>`*`)`](https://epidist.epinowcast.org/reference/assert_epidist.epidist_meta_model.md)
  :

  Assert validity of `epidist_meta_model` objects

- [`epidist_family_model(`*`<epidist_meta_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_family_model.epidist_meta_model.md)
  :

  Create the model-specific component of an `epidist` custom family

- [`epidist_formula_model(`*`<epidist_meta_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_formula_model.epidist_meta_model.md)
  :

  Define the model-specific component of an `epidist` custom formula for
  the meta model

- [`epidist_meta_leave_one_out()`](https://epidist.epinowcast.org/reference/epidist_meta_leave_one_out.md)
  : Refit a meta model leaving each study out in turn

- [`epidist_model_prior(`*`<epidist_meta_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_model_prior.epidist_meta_model.md)
  : Model specific prior distributions for the meta model

- [`epidist_newdata(`*`<epidist_meta_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_newdata.epidist_meta_model.md)
  :

  Build `newdata` for the meta model

- [`epidist_transform_data_model(`*`<epidist_meta_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_transform_data_model.epidist_meta_model.md)
  : Transform data for the meta model

- [`is_epidist_meta_model()`](https://epidist.epinowcast.org/reference/is_epidist_meta_model.md)
  :

  Check if data has the `epidist_meta_model` class

- [`new_epidist_meta_model()`](https://epidist.epinowcast.org/reference/new_epidist_meta_model.md)
  :

  Class constructor for `epidist_meta_model` objects

## Model fitting

### Model fitting

Functions for fitting delay distribution models using `brms`

- [`epidist()`](https://epidist.epinowcast.org/reference/epidist.md) :

  Fit epidemiological delay distributions using a `brms` interface

### Prediction data

Functions for building `newdata` to predict from

- [`epidist_newdata()`](https://epidist.epinowcast.org/reference/epidist_newdata.md)
  :

  Build `newdata` for prediction from an `epidist` data object

- [`epidist_newdata(`*`<default>`*`)`](https://epidist.epinowcast.org/reference/epidist_newdata.default.md)
  :

  Default method for building `newdata`

- [`epidist_newdata(`*`<epidist_latent_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_newdata.epidist_latent_model.md)
  :

  Build `newdata` for the latent model

- [`epidist_newdata(`*`<epidist_marginal_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_newdata.epidist_marginal_model.md)
  :

  Build `newdata` for the marginal model

- [`epidist_newdata(`*`<epidist_meta_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_newdata.epidist_meta_model.md)
  :

  Build `newdata` for the meta model

- [`epidist_newdata(`*`<epidist_naive_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_newdata.epidist_naive_model.md)
  :

  Build `newdata` for the naive model

### Postprocess

Functions for postprocessing model output

- [`add_summaries()`](https://epidist.epinowcast.org/reference/add_summaries.md)
  : Add natural scale summaries of the delay distribution

- [`as_dist_spec(`*`<epidist_fit>`*`)`](https://epidist.epinowcast.org/reference/as_dist_spec.epidist_fit.md)
  :

  Export a fitted delay distribution as a `distspec` distribution

- [`delay_parameter_draws()`](https://epidist.epinowcast.org/reference/delay_parameter_draws.md)
  [`add_delay_parameter_draws()`](https://epidist.epinowcast.org/reference/delay_parameter_draws.md)
  : Posterior draws of the delay distribution parameters

- [`delay_summary_draws()`](https://epidist.epinowcast.org/reference/delay_summary_draws.md)
  : Posterior draws of the delay distribution, summarised

- [`` `[`( ``*`<epidist_delay_draws>`*`)`](https://epidist.epinowcast.org/reference/epidist_delay_draws.md)
  [`` `names<-`( ``*`<epidist_delay_draws>`*`)`](https://epidist.epinowcast.org/reference/epidist_delay_draws.md)
  [`dplyr_reconstruct(`*`<epidist_delay_draws>`*`)`](https://epidist.epinowcast.org/reference/epidist_delay_draws.md)
  [`dplyr_row_slice(`*`<epidist_delay_draws>`*`)`](https://epidist.epinowcast.org/reference/epidist_delay_draws.md)
  [`dplyr_col_modify(`*`<epidist_delay_draws>`*`)`](https://epidist.epinowcast.org/reference/epidist_delay_draws.md)
  [`group_by(`*`<epidist_delay_draws>`*`)`](https://epidist.epinowcast.org/reference/epidist_delay_draws.md)
  [`ungroup(`*`<epidist_delay_draws>`*`)`](https://epidist.epinowcast.org/reference/epidist_delay_draws.md)
  :

  Keep the `epidist_delay_draws` class through `dplyr` verbs

- [`epidist_strata()`](https://epidist.epinowcast.org/reference/epidist_strata.md)
  : Unique combinations of the predictors in a model

- [`epidist_meta_leave_one_out()`](https://epidist.epinowcast.org/reference/epidist_meta_leave_one_out.md)
  : Refit a meta model leaving each study out in turn

### Diagnostic functions

- [`epidist_diagnostics()`](https://epidist.epinowcast.org/reference/epidist_diagnostics.md)
  :

  Diagnostics for `epidist_fit` models

## Plotting

### Plotting

Functions for plotting data and posterior draws

- [`plot(`*`<epidist_delay_draws>`*`)`](https://epidist.epinowcast.org/reference/plot.epidist_delay_draws.md)
  [`autoplot(`*`<epidist_delay_draws>`*`)`](https://epidist.epinowcast.org/reference/plot.epidist_delay_draws.md)
  : Plot posterior draws of the delay distribution
- [`plot_delays()`](https://epidist.epinowcast.org/reference/plot_delays.md)
  : Plot the observed delay distribution
- [`plot_delays(`*`<default>`*`)`](https://epidist.epinowcast.org/reference/plot_delays.default.md)
  : Default method for plotting observed delays
- [`plot_delays(`*`<epidist_fit>`*`)`](https://epidist.epinowcast.org/reference/plot_delays.epidist_fit.md)
  : Plot the delays a fitted model predicts over the delays it was
  fitted to
- [`plot_delays(`*`<epidist_linelist_data>`*`)`](https://epidist.epinowcast.org/reference/plot_delays.epidist_linelist_data.md)
  : Plot the observed delays of a dataset
- [`plot_delays(`*`<list>`*`)`](https://epidist.epinowcast.org/reference/plot_delays.list.md)
  : Compare the observed delays of several datasets
- [`plot_events()`](https://epidist.epinowcast.org/reference/plot_events.md)
  : Plot the primary and secondary event windows of each case

## Model specification

### Family

Functions related to specifying custom `brms` families

- [`epidist_family()`](https://epidist.epinowcast.org/reference/epidist_family.md)
  :

  Define `epidist` family

- [`epidist_family_model()`](https://epidist.epinowcast.org/reference/epidist_family_model.md)
  :

  The model-specific parts of an
  [`epidist_family()`](https://epidist.epinowcast.org/reference/epidist_family.md)
  call

- [`epidist_family_model(`*`<default>`*`)`](https://epidist.epinowcast.org/reference/epidist_family_model.default.md)
  : Default method for defining a model specific family

- [`epidist_family_param(`*`<default>`*`)`](https://epidist.epinowcast.org/reference/epidist_family_param.default.md)
  : Default method for families which do not require a
  reparameterisation

- [`epidist_family_param(`*`<gengamma>`*`)`](https://epidist.epinowcast.org/reference/epidist_family_param.gengamma.md)
  :

  Method for the
  [`gengamma()`](https://epidist.epinowcast.org/reference/gengamma.md)
  family

- [`gengamma()`](https://epidist.epinowcast.org/reference/gengamma.md) :
  Generalised gamma delay distribution family

### Formula

Functions related to specifying custom `brms` formula

- [`epidist_formula()`](https://epidist.epinowcast.org/reference/epidist_formula.md)
  : Define a model specific formula

- [`epidist_formula_model()`](https://epidist.epinowcast.org/reference/epidist_formula_model.md)
  :

  The model-specific parts of an
  [`epidist_formula()`](https://epidist.epinowcast.org/reference/epidist_formula.md)
  call

- [`epidist_formula_model(`*`<default>`*`)`](https://epidist.epinowcast.org/reference/epidist_formula_model.default.md)
  : Default method for defining a model specific formula

### Prior distributions

Functions for specifying prior distributions

- [`epidist_family_prior()`](https://epidist.epinowcast.org/reference/epidist_family_prior.md)
  : Family specific prior distributions
- [`epidist_family_prior(`*`<default>`*`)`](https://epidist.epinowcast.org/reference/epidist_family_prior.default.md)
  : Default family specific prior distributions
- [`epidist_family_prior(`*`<gengamma>`*`)`](https://epidist.epinowcast.org/reference/epidist_family_prior.gengamma.md)
  : Family specific prior distributions for the generalised gamma family
- [`epidist_family_prior(`*`<lognormal>`*`)`](https://epidist.epinowcast.org/reference/epidist_family_prior.lognormal.md)
  : Family specific prior distributions for the lognormal family
- [`epidist_model_prior()`](https://epidist.epinowcast.org/reference/epidist_model_prior.md)
  : Model specific prior distributions
- [`epidist_model_prior(`*`<default>`*`)`](https://epidist.epinowcast.org/reference/epidist_model_prior.default.md)
  : Default model specific prior distributions
- [`epidist_model_prior(`*`<epidist_meta_model>`*`)`](https://epidist.epinowcast.org/reference/epidist_model_prior.epidist_meta_model.md)
  : Model specific prior distributions for the meta model
- [`epidist_prior()`](https://epidist.epinowcast.org/reference/epidist_prior.md)
  : Define custom prior distributions for epidist models

### Stan code

Functions for specifying custom Stan code to put into `brms`

- [`epidist_stancode()`](https://epidist.epinowcast.org/reference/epidist_stancode.md)
  : Define model specific Stan code
- [`epidist_stancode(`*`<default>`*`)`](https://epidist.epinowcast.org/reference/epidist_stancode.default.md)
  : Default method for defining model specific Stan code

## Package internals

### Transform data

Transform data using the formula and family information

- [`epidist_transform_data_model()`](https://epidist.epinowcast.org/reference/epidist_transform_data_model.md)
  :

  The model-specific parts of an
  [`epidist_transform_data()`](https://epidist.epinowcast.org/reference/epidist_transform_data.md)
  call

- [`epidist_transform_data_model(`*`<default>`*`)`](https://epidist.epinowcast.org/reference/epidist_transform_data_model.default.md)
  : Default method for transforming data for a model

### Generator model functions

Generator functions for creating family specific model utilities.

- [`epidist_gen_log_lik()`](https://epidist.epinowcast.org/reference/epidist_gen_log_lik.md)
  : Create a function to calculate the marginalised log likelihood for
  double censored and truncated delay distributions
- [`epidist_gen_meta_log_lik()`](https://epidist.epinowcast.org/reference/epidist_gen_meta_log_lik.md)
  : Create a function to calculate the meta model log likelihood
- [`epidist_gen_meta_predict()`](https://epidist.epinowcast.org/reference/epidist_gen_meta_predict.md)
  : Create a function to draw from the meta model posterior predictive
  distribution
- [`epidist_gen_posterior_epred()`](https://epidist.epinowcast.org/reference/epidist_gen_posterior_epred.md)
  : Create a function to draw from the expected value of the posterior
  predictive distribution for a model
- [`epidist_gen_posterior_predict()`](https://epidist.epinowcast.org/reference/epidist_gen_posterior_predict.md)
  : Create a function to draw from the posterior predictive distribution
  for a double censored and truncated delay distribution

### Assert validity of objects

Functions used to assert the validity of package objects

- [`assert_epidist()`](https://epidist.epinowcast.org/reference/assert_epidist.md)
  : Validation for epidist objects

## Simulation and Data

### Simulation

Tools for simulating datasets

- [`simulate_dates()`](https://epidist.epinowcast.org/reference/simulate_dates.md)
  : Convert simulated event times to dates
- [`simulate_exponential_cases()`](https://epidist.epinowcast.org/reference/simulate_exponential_cases.md)
  : Simulate exponential cases
- [`simulate_gillespie()`](https://epidist.epinowcast.org/reference/simulate_gillespie.md)
  : Simulate cases from a stochastic SIR model
- [`simulate_secondary()`](https://epidist.epinowcast.org/reference/simulate_secondary.md)
  : Simulate secondary events based on a delay distribution
- [`simulate_study()`](https://epidist.epinowcast.org/reference/simulate_study.md)
  : Simulate the summaries a published study would have reported
- [`simulate_uniform_cases()`](https://epidist.epinowcast.org/reference/simulate_uniform_cases.md)
  : Simulate cases from a uniform distribution

### Data

Data included with the package

- [`sierra_leone_ebola_data`](https://epidist.epinowcast.org/reference/sierra_leone_ebola_data.md)
  : Ebola linelist data from Fang et al. (2016)

## Reexported functions

- [`reexports`](https://epidist.epinowcast.org/reference/reexports.md)
  [`lognormal`](https://epidist.epinowcast.org/reference/reexports.md)
  [`weibull`](https://epidist.epinowcast.org/reference/reexports.md)
  [`Gamma`](https://epidist.epinowcast.org/reference/reexports.md)
  [`bf`](https://epidist.epinowcast.org/reference/reexports.md) :
  Objects exported from other packages

# Articles

### All vignettes

- [Approximate Bayesian inference in
  epidist](https://epidist.epinowcast.org/articles/approx-inference.md):

  “A demonstration of how to fit models in epidist using approximate
  Bayesian inference methods such as the Laplace approximation, ADVI,
  and Pathfinder.”

- [Using epidist to estimate delay between symptom onset and positive
  test for an Ebola outbreak in Sierra
  Leone](https://epidist.epinowcast.org/articles/ebola.md):

  A more detailed guide to using the epidist R package

- [Getting started with
  epidist](https://epidist.epinowcast.org/articles/epidist.md):

  A quick start guide to using the epidist R package

- [Extending
  epidist](https://epidist.epinowcast.org/articles/extending-epidist.md):

  Building your own model type

- [Frequently asked questions and
  tips](https://epidist.epinowcast.org/articles/faq.md):

- [Left truncation with
  delay_min](https://epidist.epinowcast.org/articles/left-truncation.md):

  “How to use the delay_min argument to account for delays that are only
  observed above a minimum value.”

- [Fitting to published estimates with the meta
  model](https://epidist.epinowcast.org/articles/meta.md):

  Fitting to summarised, potentially biased, published estimates jointly
  with individual level data

- [Guide to the statistical models implemented in
  epidist](https://epidist.epinowcast.org/articles/model.md):

- [Primary event
  distributions](https://epidist.epinowcast.org/articles/primary-events.md):

  “How to set the distribution of the primary event within its censoring
  window, and when it matters.”