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 supportedTesting
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)