Package: openVA 1.1.2

Zehang Richard Li

openVA: Automated Method for Verbal Autopsy

Implements multiple existing open-source algorithms for coding cause of death from verbal autopsies. The methods implemented include 'InterVA4' by Byass et al (2012) <doi:10.3402/gha.v5i0.19281>, 'InterVA5' by Byass at al (2019) <doi:10.1186/s12916-019-1333-6>, 'InSilicoVA' by McCormick et al (2016) <doi:10.1080/01621459.2016.1152191>, 'NBC' by Miasnikof et al (2015) <doi:10.1186/s12916-015-0521-2>, and a replication of 'Tariff' method by James et al (2011) <doi:10.1186/1478-7954-9-31> and Serina, et al. (2015) <doi:10.1186/s12916-015-0527-9>. It also provides tools for data manipulation tasks commonly used in Verbal Autopsy analysis and implements easy graphical visualization of individual and population level statistics. The 'NBC' method is implemented by the 'nbc4va' package that can be installed from <https://github.com/rrwen/nbc4va>. Note that this package was not developed by authors affiliated with the Institute for Health Metrics and Evaluation and thus unintentional discrepancies may exist in the implementation of the 'Tariff' method.

Authors:Zehang Richard Li, Jason Thomas, Tyler H. McCormick, Samuel J. Clark

openVA_1.1.2.tar.gz
openVA_1.1.2.tar.gz(r-4.5-noble)openVA_1.1.2.tar.gz(r-4.4-noble)
openVA_1.1.2.tgz(r-4.4-emscripten)openVA_1.1.2.tgz(r-4.3-emscripten)
openVA.pdf |openVA.html
openVA/json (API)
NEWS

# Install 'openVA' in R:
install.packages('openVA', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/verbal-autopsy-software/openva/issues

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

3.97 score 47 scripts 451 downloads 4 mentions 20 exports 43 dependencies

Last updated 9 months agofrom:e841c23a4e. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-linuxOKOct 26 2024

Exports:codeVAConvertDataConvertData.phmrcCSMFCSMF5getCCCgetCSMFgetCSMF_accuracygetIndivProbgetPHMRC_urlgetTopCODinsilicoInterVAinterVA_trainInterVA5openVA_statusopenVA_updateplotVAstackplotVAtariff

Dependencies:cellrangerclicodacolorspacecpp11crayoncurlfansifarverggplot2gluegtablehmsInSilicoVAInterVA4InterVA5isobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigprettyunitsprogressR6RColorBrewerreadxlrematchrJavarlangscalesTarifftibbleutf8vctrsviridisLitewithr

Getting started with openVA

Rendered fromopenVA-vignette.html.asisusingR.rsp::asison Oct 26 2024.

Last update: 2022-10-01
Started: 2022-10-01