Verbal Autopsy Data Transform for Use with Various Coding Algorithms

Enables transformation of Verbal Autopsy data collected with the WHO 2016 questionnaire (versions 1.4.1 & 1.5.1) for automated coding of Cause of Death using different computer algorithms. Currently supports user-supplied mappings, and provides unvalidated, experimental-stage mapping definitions to transform to InterVA4, InterVA5, Tariff 2, and InSilicoVA. This package is made available by WHO, in collaboration with the Swiss Tropical and Public Health Institute and the Bloomberg Data for Health Initiative.


Description

CrossVA is an R package for transforming verbal autopsy records collected using the WHO VA 2016 instrument (Revision 1.4.1) to be used as input for different coding algorithms. Currently supports user-supplied mappings, and provides unvalidated mapping definitions to transform to InterVA4, Tariff 2, and InSilicoVA. This package is made available by WHO, in collaboration with Swiss Tropical and Public Health Institute. Craig Hales from CDC reviewed and commented on earlier version of the mapping definitions.

Input

  • CSV file containing submissions of the 2016 WHO VA questionnaire (Revision 1.4.1, exported from ODKAggregate using ODKBriefcase)
  • A mapping files (tab-delimited text file). Minimal content: the first columns contains the names of all indicators needed by the coding algorithm (called "target indicators" here). The second column contains the mapping to each target indicators, as a valid R expression: expressions can be functions of zero or more variables of the WHO VA instrument, or any of the preceding target indicators. In addition to standard R functions, a small set of convenience functions which is provided in utils.R can be called to achieve the mapping. The release comes with currently two mapping files, one for interVA4, and one for tariff2).

Output A CSV file intended for processing by a coding algorithm.

Status

Initial, not intended for production use

Testing

For testing purposes, install via

install.packages("devtools")
devtools::install_github("SwissTPH/CrossVA")

or download and install from here https://github.com/SwissTPH/CrossVA/releases

Use your own VA records, or the sythetic sample data set included in the package for testing.

Examples

library(CrossVA)
record_f_name <- system.file('sample', 'who_va_output.csv', package = 'CrossVA')
records <- read.csv(record_f_name)
#map to interva4, use name of algorithm
output_data <- map_records(records, 'interva4')
output_f_name <- "output_for_interva4.csv"
write.table(output_data, output_f_name, row.names = FALSE, na = "", qmethod = "escape", sep = ",")

#map by providing a mapping file (here using the package-provided tariff2 mapping)
mapping_file <- system.file('mapping', 'tariff2_mapping.txt', package = 'CrossVA')
output_data <- map_records(records, mapping_file)
output_f_name <- "output_for_smartva.csv"
write.table(output_data, output_f_name, row.names = FALSE, na = "", qmethod = "escape", sep = ",")

#convenience wrapper (here using the package-provided InsilicoVA mapping)
output_data<-map_records_insilicova(records, "isoutput.csv")

News

Reference manual

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install.packages("CrossVA")

0.9.5 by Jason Thomas, a month ago


Browse source code at https://github.com/cran/CrossVA


Authors: Eungang Choi [aut] , Sam Clark [aut] , Zehang Li [aut] , Nicolas Maire [aut] , Jason Thomas [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Imports lubridate, stringi

Suggests knitr, rmarkdown, testthat, openVA


See at CRAN