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README.md

Incidence Estimation Tools (inctools)

Tools for estimating HIV incidence from biomarker data, and calibrating recent infection tests.

This package is a more robust implementation of the deprecated spreadsheet tools released as ABIE and also contains the functionality previously available in the deprecated package ritcalib.

inctools is available on the Comprehensive R Archive Network. You can also find the latest stable release under Releases. Releases on this repository may be slightly ahead of the version available through CRAN, but we recommend installing from CRAN.

Older spreadsheet-based tools for inferring incidence using biomarkers for 'recent infection' can be found here. These tools are largely superceded by inctools.

About

These tools are released as an R package by the DST/NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA) in collaboration with the Consortium for the Evaluation and Performance of HIV Incidence Assays (CEPHIA) and other partners. The package maintainer can be contacted at eduardgrebe@sun.ac.za.

Installation

Install directly from CRAN as follows:

install.packages("inctools")

Current development version

To build and install the current development version, you will need to clone the repository and ensure that you have the required build tools installed on your system.

Install dependencies manually:

install.packages(c("cubature","ggplot2","glm2","MASS","plyr","dplyr","magrittr","pracma","foreach",
                   "parallel","doParallel","devtools","knitr","roxygen2","rmarkdown"))

Then use "build and reload" in RStudio or set your working directory to <repo location>/inctools/ and then execute:

devtools::install()

Usage terms

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

Contributors

Several people contributed to this package. We encourage contributions from the community of users.

Developers include Alex Welte, Eduard Grebe, Avery McIntosh, Petra Bäumler, Simon Daniel and Yuruo Li, with contributions by Cari van Schalkwyk, Reshma Kassanjee, Hilmarie Brand, Stefano Ongarello and Yusuke Asai.

Contact

For usage support and bug reports, please contact the package maintainer, Eduard Grebe, or submit issues on this repository.

References

For more information on incidence inference based on cross-sectionally obtained biomarkers for 'recent infection', see this page, and this timeline with links to references, as well as a brief review with references. The key reference for biomarker-based incidence estimation is Kassanjee, McWalter, Bärnighausen & Welte (2012).