For documentation and a tutorial, checkout the website!
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. An Integrated Data-Driven Model for Clinical Phenotyping of Tuberculosis Disease Severity.
Code to replicate all simulation results from this paper is available here.
Installation
You can install the development version of tbSTATIS from GitHub. 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.
# 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:
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.
vignette(package="tbSTATIS")