Estimate epidemiological delay distributions with brms
Summary
Understanding and accurately estimating epidemiological delay distributions is important for public health policy. These estimates directly influence epidemic situational awareness, control strategies, and resource allocation. In this package, we provide methods to address the key challenges in estimating these distributions, including truncation, interval censoring, and dynamical biases. Despite their importance, these issues are frequently overlooked, often resulting in biased conclusions.
Quickstart
To learn more about epidist we recommend reading the vignettes in this
order:
- Getting started with
epidist - Using
epidistto estimate delay between symptom onset and positive test for an Ebola outbreak in Sierra Leone - Approximate Bayesian inference in
epidist
Installation
Installing the package
You can use the [`remotes` package](https://remotes.r-lib.org/) to install the development version from Github (warning! this version may contain breaking changes and/or bugs): ``` r remotes::install_github( file.path("epinowcast", "epidist"), dependencies = TRUE ) ```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 # if you have not yet installed `epidist`, or you installed it without # `Suggests` dependencies install.packages( "cmdstanr", repos = c("https://mc-stan.org/r-packages/", 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. Please check and add to the issues, and/or add a pull request.
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: Adam Howes, Park S, Sam Abbott (NULL). _epidist: Estimate Epidemiological Delay Distributions With brms_. doi:10.5281/zenodo.5637165If 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 by Park et al. (2024)
- Best practices for estimating and reporting epidemiological delay distributions of infectious diseases using public health surveillance and healthcare data by Charniga et al. (2024)
Contributors
All contributions to this project are gratefully acknowledged using the
allcontributors
package following the
all-contributors specification.
Contributions of any kind are welcome!
Code
seabbs, athowes, parksw3, damonbayer, medewitt
Issue Authors
kgostic, TimTaylor, jamesmbaazam