Package: openVA 1.2.0

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 [aut, cre], Jason Thomas [aut], Tyler H. McCormick [aut], Samuel J. Clark [aut]

openVA_1.2.0.tar.gz
openVA_1.2.0.zip(r-4.7-any)openVA_1.2.0.zip(r-4.6-any)openVA_1.2.0.zip(r-4.5-any)
openVA_1.2.0.tgz(r-4.6-any)openVA_1.2.0.tgz(r-4.5-any)
openVA_1.2.0.tar.gz(r-4.7-any)openVA_1.2.0.tar.gz(r-4.6-any)
openVA_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
openVA/json (API)

# 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

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

On CRAN:

Conda:

pipelineopenjdk

6.56 score 1 stars 1 packages 68 scripts 403 downloads 4 mentions 21 exports 37 dependencies

Last updated from:22abc68420. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK252
source / vignettesOK239
linux-releaseOK265
macos-releaseOK232
macos-oldrelOK215
windows-develOK165
windows-releaseOK172
windows-oldrelOK166
wasm-releaseOK162

Exports:codeVAConvertDataConvertData.phmrcCSMFCSMF5getCCCgetCSMFgetCSMF_accuracygetIndivProbgetPHMRC_urlgetTopCODinsilicoInterVAinterVA_trainInterVA5openVA_statusopenVA_updateplotVAprepCalibrationstackplotVAtariff

Dependencies:cellrangerclicodacpp11crayoncurlfarverggplot2gluegtablehmsInSilicoVAInterVA4InterVA5isobandlabelinglatticelifecyclemagrittrpillarpkgconfigprettyunitsprogressR6RColorBrewerreadxlrematchrJavarlangS7scalesTarifftibbleutf8vctrsviridisLitewithr

Expert Algorithms for Neonatal and Child Causes of Death
Expert Algorithms for Neonatal and Child Causes of Death | Introduction | Getting Started | Data | Assigning Causes of Death | EAVA | InSilicoVA | Summarizing EAVA Results | Comparing CoD Assignments: EAVA & InSilicoVA | CSMFs | Individual Cause Assignment | Conclusion
Rendered fromeava-vignette.html.asisusingR.rsp::asis

Last update: 2025-09-22
Started: 2025-09-22

VA Calibration
Introduction | Getting Started | Cause Assignment (uncalibrated) | Results | tabular summaries | plots | Conclusion | References
Rendered fromvacalibration-vignette.html.asisusingR.rsp::asis

Last update: 2025-09-22
Started: 2025-09-22

Getting started with openVA
Introduction | Overview of openVA | Data preparation | The WHO standard format | The PHMRC format | Customized format | Modeling data collected with WHO 2012 questionnaire | Modeling the PHMRC data | Summarizing results | CSMF Accuracy | Individual COD summary | Visualization | Incorporating additional information in the InSilicoVA algorithm | Sub-population specific CSMFs | Physician coding | Removal of physically impossible causes | Acknowledgement | References
Rendered fromopenVA-vignette.html.asisusingR.rsp::asis

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

Readme and manuals

Help Manual

Help pageTopics
Running automated method on VA datacodeVA
Converting Input data with different coding scheme to standard formatConvertData
Convert standard PHMRC data into binary indicator formatConvertData.phmrc
Calculate CSMF from EAVA::codEAVA outputcsmf_eava
1,736 records of Sample InputDataEAVA
Calculate Overall chance-corrected concordance (CCC)getCCC
Obtain CSMF from fitted modelgetCSMF
Calculate CSMF accuracygetCSMF_accuracy
Extract individual distribution of cause of deathgetIndivProb
Get the URL to the PHMRC datasetgetPHMRC_url
Extract the most likely cause(s) of deathgetTopCOD
Mapping for child causes of death to the list used by the EAVA algorithm.grouping_eava_child
Mapping for neonate causes of death to the list used by the EAVA algorithm.grouping_eava_neonate
Extended InterVA method for non-standard inputinterVA_train
200 records of Sample InputNeonatesVA5
Check openVA packages statusopenVA_status
Update openVA packagesopenVA_update
Create CSMF plot for EAVA::codEAVA outputplot.eava
Plot CSMF from a vacalibration objectplot.vacalibration
Plot top CSMF for a fitted modelplotVA
Convert the assigned causes to the format expected by vacalibration::vacalibration().prepCalibration
Print method for "eava" class.print.eava
Print method for summarizing results from EAVA algorithm.print.eava_summary
Print method for vacalibration model fitsprint.vacalibration
Print method for summarizing vacalibration resultsprint.vacalibration_summary
1,736 records of Sample InputRandomVA6
plot grouped CSMF from a "insilico" objectstackplotVA
Summary of results obtained by fitting the EAVA algorithm.summary.eava
Summary of results obtained by vacalibrationsummary.vacalibration