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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# tbSTATIS
<!-- badges: start -->
<!-- badges: end -->
The `tbSTATIS` package implements the tuberculosis SeveriTy Assessment Tool for Informed Stratification (TB-STATIS) to classify TB disease severity for individuals using data collected at time of diagnosis. We include functions to estimate the model, quantify model uncertainty, and visualize results. We provide a detailed vignette that walks through an example analysis using `tbSTATIS`.
For a more formal discussion of the theory behind and usage of this method, see the following paper:
Malatesta S, Jacobson KR, Horsburgh CR, Farhat MR, Gile KJ, Kolaczyk ED, White LF. Data-driven classification of tuberculosis disease severity.
Code to replicate all simulation results from this paper is available [here](https://github.com/samalatesta/tbSTATISpaper).
## Installation
You can install the development version of `tbSTATIS` from [GitHub](https://github.com/). We recommend setting the option `build_vignettes=T` when installing so the package vignette can be accessed in your local R environment (note: this may take a while). The `devtools` package must be installed prior to installing `tbSTATIS`.
``` r
# install.packages("devtools")
devtools::install_github("samalatesta/tbSTATIS", build.vignette = T)
```
## Usage
To use `tbSTATIS` in your R scripts or projects, load the package using:
```R
library(tbSTATIS)
```
For detailed information on how to use each function, please refer to the package documentation and vignette. The vignette can be viewed locally after package installation or the knitted html is also included in the `\vignettes` directory.
```R
vignette(package="tbSTATIS")
```
## Documentation
Comprehensive documentation for tbSTATIS functions is available within R. You can access documentation using the ? operator followed by the function name. For example:
```R
?plot_states
```
## License
tbSTATIS is distributed under the MIT License.
## Contact
For questions, please contact:
Samantha Malatesta (samalate@bu.edu)