Estimate epidemiological delay distributions for infectious diseases
Warning: This package is a prototype and is under active development. Breaking changes are likely.
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.
Installation
Installing the package
You can install the latest released version using the normal R
function, though you need to point to r-universe
instead of CRAN:
install.packages(
"epidist", repos = "https://epinowcast.r-universe.dev"
)
Alternatively, you can use the remotes
package to install the development version
from Github (warning! this version may contain breaking changes and/or
bugs):
remotes::install_github(
"epinowcast/epidist", dependencies = TRUE
)
Similarly, you can install historical versions by specifying the release
tag (e.g. this installs
0.1.0
):
remotes::install_github(
"epinowcast/epidist", dependencies = TRUE, ref = "v0.2.0"
)
Note: You can also use that last approach to install a specific commit if needed, e.g. if you want to try out a specific unreleased feature, but not the absolute latest developmental version.
Installing CmdStan
If you wish to do model fitting and nowcasting, you will need to install
CmdStan, which also
entails having a suitable C++ toolchain setup. We recommend using the
cmdstanr
package. The Stan team
provides instructions in the Getting started with
cmdstanr
vignette, with other details and support at the package
site, but the brief version is:
# if you not yet installed `epinowcast`, 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 epinowcast
, you may also
need to install a past version of CmdStan, which you can do with the
version
argument.
Alternative: Docker
We also provide a Docker image
with epinowcast
and all dependencies
installed.
You can use this image to run epidist
without installing dependencies.
Resources
As you use the package, the documentation available via ?enw_
should
be your first stop for troubleshooting. We also provide a range of other
documentation, case studies, and community spaces to ask (and answer!)
questions:
Package Website
The epinowcast
website includes a
function reference, model outline, and case studies using the package.
The site mainly concerns the release version, but you can also find
documentation for the latest development
version.
R Vignettes
We have created package vignettes to help you get started nowcasting and to highlight other features with case studies.
Organisation Website
Our organisation website includes links to other resources, guest posts, and seminar schedule for both upcoming and past recordings.
Community Forum
Our community forum has areas for
question and answer
and considering new methods and
tools, among others. If
you are generally interested in real-time analysis of infectious
disease, you may find this useful even if do not use epinowcast
.
Package Analysis Scripts
In addition to the vignettes, the package also comes with example
analyses.
These are not as polished as the vignettes, but we typically explore new
features with these and they may help you if you are using a development
version. After installing epinowcast
, you can find them via:
list.files(
system.file("examples", package = "epinowcast"), full.names = TRUE
)
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 and see our contributing guide 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. If you have a question, please don’t open an issue. Instead, ask on our Q and A page. See our contributing guide for more information.
Code of Conduct
Please note that the epidist
project is released with a Contributor
Code of Conduct. By contributing to this project,
you agree to abide by its terms.
Citation
If making use of our methodology or the methodology on which ours is
based, please cite the relevant papers from our model
outline. If you use
epidist
in your work, please consider citing it with
citation("epidist")
.