README.Rmd

---
output: github_document
---

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```{r, include = FALSE}
knitr::opts_chunk$set(
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# aedseo <a href="https://ssi-dk.github.io/aedseo/"><img src="man/figures/logo.png" align="right" height="139" alt="aedseo website" /></a>


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## Description

The Automated and Early Detection of Seasonal Epidemic Onset (`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 and calculate the Sum of Cases (SoC) within those intervals. This package is particularly useful for 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 vestion

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 (`aedseo_tsd`) from your data using the `tsd()` function.
4. Apply the `aedseo()` function to estimate growth rates and detect seasonal epidemic onsets.

```r
# Load the package
library(aedseo)

# Create a aedseo_tsd object from your data
tsd_data <- tsd(
  observation = c(100, 120, 150, 180, 220, 270),
  time = as.Date(c(
    "2023-01-01",
    "2023-01-02",
    "2023-01-03",
    "2023-01-04",
    "2023-01-05",
    "2023-01-06")
    ),
    time_interval = "day"
  )

# Detect seasonal epidemic onsets
aedseo_results <- aedseo(tsd = tsd_data, k = 3, level = 0.95, family = "poisson")
```

## Vignette

For a more detailed introduction to the workflow of this package, see the introductory vignette.

``` r
# After installing the package
vignette("aedseo_introduction", package = "aedseo")
```

## Contributing

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