Verbal Autopsy Data Transformation for InSilicoVA and InterVA5 Algorithms

Enables transformation of Verbal Autopsy data collected with the WHO 2016 questionnaire (versions 1.4.1 & 1.5.1) or the WHO 2014 questionnaire for automated coding of Cause of Death using the InSilicoVA (data.type = "WHO2016") and InterVA5 algorithms. Previous versions of this package supported user-supplied mappings (via the map_records function), but this functionality has been removed. This package is made available by WHO and the Bloomberg Data for Health Initiative.

Description

CrossVA is an R package for transforming verbal autopsy records into a format accepted by the InSilicoVA and InterVA5 R packages. Verbal autopsy records are expected to be collected using the WHO VA 2016 instrument (Revision 1.4.1 or 1.5.1) or the WHO VA 2014 instrument. This package is made available by WHO and the Bloomberg Data for Health Initiative.

Input

• CSV file containing submissions of the 2016 WHO VA questionnaire (Revision 1.4.1 or 1.5.1), exported from ODK Aggregate
• CSV file containing submissions of the 2014 WHO VA questionnaire (2-15-10 with form id: va-who_2014_final10), exported from ODK Aggregate

Output A CSV file intended for processing by a coding algorithm (i.e., InSilicoVA or InterVA)

Status

• odk2openVA is actively supported
• Future support for the WHO VA 2012 questionnaire and the PHMRC questionnaire will be available in a future release.

Testing

For testing purposes, install via

install.packages("devtools")
devtools::install_github("verbal-autopsy-software/CrossVA/CrossVA")

or download and install from here https://github.com/verbal-autopsy-software/CrossVA/

Use your own VA records, or one of the sythetic sample data sets included in the package for testing: (WHO VA 2016, version 1.5.1)[https://github.com/verbal-autopsy-software/CrossVA/blob/master/CrossVA/inst/sample/who151_odk_export.csv], (WHO VA 2016, version 1.4.1)[https://github.com/verbal-autopsy-software/CrossVA/blob/master/CrossVA/inst/sample/who141_odk_export.csv], or (WHO VA 2014)[https://github.com/verbal-autopsy-software/CrossVA/blob/master/CrossVA/inst/sample/who2014_odk_export.csv], or

Examples

library(CrossVA)
library(openVA)

# WHO VA Questionnaire 2016
## version 151
datafile_2016_151 <- system.file("sample", "who151_odk_export.csv", package = "CrossVA")
records_2016_151 <- read.csv(datafile_2016_151)
whoData2016_151 <- odk2openVA(records_2016_151, version = "1.5.1")

out1 <- insilico(whoData2016_151, data.type = "WHO2016")
summary(out1)
out2 <- InterVA5(whoData2016_151, HIV = "l", Malaria = "l", directory = getwd())
summary(out2)

## version 141
datafile_2016_141 <- system.file("sample", "who141_odk_export.csv", package = "CrossVA")
records_2016_141 <- read.csv(datafile_2016_141)
whoData2016_141 <- odk2openVA(records, version = "1.4.1")

out3 <- insilico(whoData2016_141, data.type = "WHO2016")
summary(out3)
out4 <- InterVA5(whoData2016_141, HIV = "l", Malaria = "l", directory = getwd())
summary(out4)

## WHO VA Questionnaire 2014
datafile_2014 <- system.file("sample", "who2014_odk_export.csv", package = "CrossVA")
records_2014 <- read.csv(datafile_2014)
whoData2014 <- odk2openVA(records, version = "2014")

out5 <- insilico(whoData2014, data.type = "WHO2016")
summary(out5)
out6 <- InterVA5(whoData2014, HIV = "l", Malaria = "l", directory = getwd())
summary(out6)