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aedseo

Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels

https://github.com/ssi-dk/aedseo

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (20.1%) to scientific vocabulary

Keywords

burden-of-disease epidemic-model epidemic-modelling onset-detection surveillance-systems
Last synced: 9 months ago · JSON representation

Repository

Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels

Basic Info
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 0
  • Open Issues: 4
  • Releases: 4
Topics
burden-of-disease epidemic-model epidemic-modelling onset-detection surveillance-systems
Created over 2 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# aedseo aedseo website



[![R-CMD-check](https://github.com/ssi-dk/aedseo/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ssi-dk/aedseo/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/ssi-dk/aedseo/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ssi-dk/aedseo?branch=master)
[![CRAN status](https://www.r-pkg.org/badges/version/aedseo)](https://CRAN.R-project.org/package=aedseo)


## Description

The Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels (`aedseo`)
package provides a powerful tool for automating the early detection of seasonal epidemic
onsets in time series data. It offers the ability to estimate growth rates for consecutive
time intervals. With use of the average observations within those intervals and an estimated
disease-specific threshold it also offers the possibility to estimate seasonal onset of epidemics.
Additionally it offers the ability to estimate burden levels for seasons based on historical data.
It is aimed towards epidemiologists, public health professionals, and researchers seeking to
identify and respond to seasonal epidemics in a timely fashion.

## Installation

``` r
# Install aedseo from CRAN
install.packages("aedseo")
```

### Development version

You can install the development version of `aedseo` from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("ssi-dk/aedseo")
```

## Getting started

To quickly get started with `aedseo`, follow these steps:

1.  Install the package using the code provided above.
2.  Load the package with `library(aedseo)`.
3.  Create a time series data object (`tsd`) from your data using
    the `to_time_series()` function or `generate_seasonal_data()` functions.
4.  Apply the `combined_seasonal_output()` function to get a comprehensive
    seasonal analysis with seasonal onset and burden levels.

## Vignette

For a more detailed introduction to the workflow of this package, see
the `Get Started` vignette or run; `vignette("aedseo")`.

## Contributing

We welcome contributions to the `aedseo` package. Feel free to open issues, submit pull requests, or provide feedback to help us improve.

Owner

  • Name: Statens Serum Institut
  • Login: ssi-dk
  • Kind: organization
  • Location: Denmark

GitHub Events

Total
  • Issues event: 19
  • Watch event: 1
  • Delete event: 33
  • Issue comment event: 5
  • Push event: 241
  • Pull request review comment event: 148
  • Pull request event: 71
  • Pull request review event: 96
  • Create event: 39
Last Year
  • Issues event: 19
  • Watch event: 1
  • Delete event: 33
  • Issue comment event: 5
  • Push event: 241
  • Pull request review comment event: 148
  • Pull request event: 71
  • Pull request review event: 96
  • Create event: 39

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 27
  • Total pull requests: 86
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 3 days
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 0.26
  • Average comments per pull request: 0.06
  • Merged pull requests: 71
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 10
  • Pull requests: 73
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 days
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.05
  • Merged pull requests: 58
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • telkamp7 (14)
  • SofiaOtero (6)
  • LasseEngboChr (4)
Pull Request Authors
  • SofiaOtero (77)
  • telkamp7 (12)
  • LasseEngboChr (7)
Top Labels
Issue Labels
enhancement (13) documentation (4)
Pull Request Labels
enhancement (36) documentation (26) bug (17) refactor (14) good first issue (2)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 321 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
cran.r-project.org: aedseo

Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 321 Last month
Rankings
Forks count: 27.9%
Dependent packages count: 28.9%
Stargazers count: 34.6%
Dependent repos count: 36.9%
Average: 43.0%
Downloads: 86.6%
Maintainers (1)
lsec@ssi.dk
Last synced: 10 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/lint.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • base * imports
  • dplyr * imports
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  • lubridate * imports
  • magrittr * imports
  • purrr * imports
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  • stats * imports
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  • ISOweek * suggests
  • ggplot2 * suggests
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  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests
  • tidyr * suggests