update namespace and docs

NAMESPACE

@@ -19,7 +19,6 @@ export(filter_obs_by_obs_time)
 export(filter_obs_by_ptime)
 export(filtered_censoring_adjusted_delay)
 export(filtered_naive_delay)
-export(get_targets_archive)
 export(latent_censoring_adjusted_delay)
 export(latent_truncation_censoring_adjusted_delay)
 export(linelist_to_cases)
@@ -39,9 +38,6 @@ export(primary_censoring_bias_correction)
 export(reverse_obs_at)
 export(sample_epinowcast_model)
 export(sample_model)
-export(save_csv)
-export(save_dataset)
-export(save_rds)
 export(simulate_double_censored_pmf)
 export(simulate_exponential_cases)
 export(simulate_gillespie)
@@ -51,9 +47,7 @@ export(summarise_draws)
 export(summarise_variable)
 export(truncation_adjusted_delay)
 export(truncation_censoring_adjusted_delay)
-export(upload_targets_archive)
 import(brms)
 import(cmdstanr)
 import(data.table)
 import(ggplot2)
-importFrom(ggplot2,ggsave)

README.md

@@ -0,0 +1,218 @@
+
+# Estimate epidemiological delay distributions for infectious diseases<a href='https://epidist.epinowcast.org'><img src='man/figures/logo.png' align="right" height="139" /></a>
+
+<!-- badges: start -->
+
+[![Lifecycle:
+experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
+[![R-CMD-check](https://github.com/epinowcast/epidist/workflows/R-CMD-check/badge.svg)](https://github.com/epinowcast/epidist/actions/workflows/R-CMD-check.yaml)
+[![Codecov test
+coverage](https://codecov.io/gh/epinowcast/epidist/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epinowcast/epidist)
+</br>
+[![Universe](https://epinowcast.r-universe.dev/badges/epidist)](https://epinowcast.r-universe.dev/epidist)
+[![MIT
+license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epinowcast/epidist/blob/master/LICENSE.md/)
+[![GitHub
+contributors](https://img.shields.io/github/contributors/epinowcast/epidist)](https://github.com/epinowcast/epidist/graphs/contributors)
+</br>
+[![DOI](https://zenodo.org/badge/422611952.svg)](https://zenodo.org/badge/latestdoi/422611952)
+<!-- badges: end -->
+
+*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
+
+<details>
+
+<summary>Installing the package</summary>
+
+You can install the latest released version using the normal `R`
+function, though you need to point to `r-universe` instead of CRAN:
+
+``` r
+install.packages(
+  "epidist", repos = "https://epinowcast.r-universe.dev"
+)
+```
+
+Alternatively, 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(
+  "epinowcast/epidist", dependencies = TRUE
+)
+```
+
+Similarly, you can install historical versions by specifying the release
+tag (e.g. this installs
+[`0.1.0`](https://github.com/epinowcast/epidist/releases/tag/v0.1.0)):
+
+``` r
+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.*
+
+</details>
+
+<details>
+
+<summary>Installing CmdStan</summary>
+
+If you wish to do model fitting and nowcasting, 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/). 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 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.*
+
+</details>
+
+<details>
+
+<summary>Alternative: Docker</summary>
+
+We also provide a [Docker](https://www.docker.com/get-started/) image
+with [`epinowcast` and all dependencies
+installed](https://github.com/orgs/epinowcast/packages/container/package/epidist).
+You can use this image to run `epidist` without installing dependencies.
+
+</details>
+
+## 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:
+
+<details>
+
+<summary>Package Website</summary>
+
+The [`epinowcast` website](https://package.epinowcast.org/) 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](https://package.epinowcast.org/dev/).
+
+</details>
+
+<details>
+
+<summary>R Vignettes</summary>
+
+We have created [package
+vignettes](https://package.epinowcast.org/articles) to help you [get
+started
+nowcasting](https://package.epinowcast.org/articles/epinowcast.html) and
+to [highlight other features with case
+studies](https://package.epinowcast.org/articles/germany-age-stratified-nowcasting.html).
+
+</details>
+
+<details>
+
+<summary>Organisation Website</summary>
+
+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.
+
+</details>
+
+<details>
+
+<summary>Community Forum</summary>
+
+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 `epinowcast`.
+
+</details>
+
+<details>
+
+<summary>Package Analysis Scripts</summary>
+
+In addition to the vignettes, the package also comes with [example
+analyses](https://github.com/epinowcast/epinowcast/tree/main/inst/examples).
+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:
+
+``` r
+list.files(
+  system.file("examples", package = "epinowcast"), full.names = TRUE
+)
+```
+
+</details>
+
+## 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](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 [Q and A
+page](https://github.com/epinowcast/dist/discussions/categories/q-a).
+See our [contributing guide](CONTRIBUTING.md) for more information.
+
+### Code of Conduct
+
+Please note that the `epidist` project is released with a [Contributor
+Code of Conduct](CODE_OF_CONDUCT.md). 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](https://epidist.epinowcast.org/articles/model.html). If you use
+`epidist` in your work, please consider citing it with
+`citation("epidist")`.