R version of the 'InterVA5' software (http://www.byass.uk/interva) for coding cause of death from verbal autopsies. It also provides simple graphical representation of individual and population level statistics.
This is an R package replicating InterVA-5 software. For stable version of the package please visit http://cran.r-project.org/web/packages/InterVA5/index.html. R can be downloaded and installed from https://cran.r-project.org/.
If you have any questions regarding this package, or have concerns/find bugs/have new ideas in better implementations to share, please contact Richard Li at [email protected].
To install the package from CRAN, run the script:
install.packages("InterVA5")Here is an example session of how to use the InterVA5 with the example data set:
> library(InterVA5)
> data(RandomVA5)
> ## assign caueses
> sample_output <- InterVA5(Input = RandomVA5, HIV = "h", Malaria = "v", write=TRUE,
directory = tempdir(), filename = "VA5_result")
Using Probbase version: probbase v19 20210720
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> ## CSMF of top 10 causes
> summary(sample_output, top=10)
InterVA5 fitted on 200 deaths
CSMF calculated using reported causes by InterVA5 only
The remaining probabilities are assigned to 'Undetermined'
Top 10 CSMFs:
cause likelihood
Undetermined 0.1398
HIV/AIDS related death 0.1391
Digestive neoplasms 0.0981
Other and unspecified infect dis 0.0685
Renal failure 0.0620
Reproductive neoplasms MF 0.0541
Other and unspecified cardiac dis 0.0536
Pulmonary tuberculosis 0.0496
Stroke 0.0477
Acute abdomen 0.0412
Top 6 Circumstance of Mortality Category:
cause likelihood
Culture 0.570
Knowledge 0.160
Inevitable 0.110
Multiple 0.110
Emergency 0.030
Resources 0.015
## Get CSMF with plot
CSMF5(sample_output)