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:
openVA_1.1.2.tar.gz
openVA_1.1.2.zip(r-4.5)openVA_1.1.2.zip(r-4.4)openVA_1.1.2.zip(r-4.3)
openVA_1.1.2.tgz(r-4.4-any)openVA_1.1.2.tgz(r-4.3-any)
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://verbal-autopsy-software.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/verbal-autopsy-software/openva/issues
Last updated 8 months agofrom:4b2ebf87bf. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 27 2024 |
| R-4.5-win | OK | Aug 27 2024 |
| R-4.5-linux | OK | Aug 27 2024 |
| R-4.4-win | OK | Aug 27 2024 |
| R-4.4-mac | OK | Aug 27 2024 |
| R-4.3-win | OK | Aug 27 2024 |
| R-4.3-mac | OK | Aug 27 2024 |
Exports:codeVAConvertDataConvertData.phmrcCSMFCSMF5getCCCgetCSMFgetCSMF_accuracygetIndivProbgetPHMRC_urlgetTopCODinsilicoInterVAinterVA_trainInterVA5openVA_statusopenVA_updateplotVAstackplotVAtariff
Dependencies:cellrangerclicodacolorspacecpp11crayoncurlfansifarverggplot2gluegtablehmsInSilicoVAInterVA4InterVA5isobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigprettyunitsprogressR6RColorBrewerreadxlrematchrJavarlangscalesTarifftibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Running automated method on VA data | codeVA |
| Converting Input data with different coding scheme to standard format | ConvertData |
| Convert standard PHMRC data into binary indicator format | ConvertData.phmrc |
| Calculate Overall chance-corrected concordance (CCC) | getCCC |
| Obtain CSMF from fitted model | getCSMF |
| Calculate CSMF accuracy | getCSMF_accuracy |
| Extract individual distribution of cause of death | getIndivProb |
| Get the URL to the PHMRC dataset | getPHMRC_url |
| Extract the most likely cause(s) of death | getTopCOD |
| Extended InterVA method for non-standard input | interVA_train |
| Check openVA packages status | openVA_status |
| Update openVA packages | openVA_update |
| Plot top CSMF for a fitted model | plotVA |
| plot grouped CSMF from a "insilico" object | stackplotVA |
