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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. If you use the Anaconda python distribution, the package r-inctools can also installed from the conda-forge channel.

Status

CRAN status CRAN downloads Build Status codecov

Installation

Install released version from CRAN as follows:

install.packages("inctools")

Install the released version from the conda-forge channel for the Anaconda scientific python distribution, by executing the following from your shell:

conda install r-inctools -c conda-forge

Current development version

To build and install the current development version, make sure you have devtools installed and execute the following line:

devtools::install_github("SACEMA/inctools/inctools")

Note: pay attention to whether the current build is passing or failing before installing the development version.

At times the bleeding edge version can be installed from Eduard Grebe's fork of the repository (not recommended!) with the following line:

devtools::install_github("eduardgrebe/inctools/inctools")

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 at Eduard.Grebe@ucsf.edu, 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).

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