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.
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)To use tbSTATIS in your R scripts or projects, load the package using:
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.
vignette(package="tbSTATIS")Comprehensive documentation for tbSTATIS functions is available within R. You can access documentation using the ? operator followed by the function name. For example:
?plot_statestbSTATIS is distributed under the MIT License.
For questions, please contact:
Samantha Malatesta (samalate@bu.edu)