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.
CrossVA is an R package for transforming verbal autopsy records collected using the WHO VA 2016 instrument (Revision 1.4.1 or 1.5.1) 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.
Output A CSV file intended for processing by a coding algorithm.
For testing purposes, install via
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: (version 1.5.1)[https://github.com/verbal-autopsy-software/CrossVA/blob/master/CrossVA/inst/sample/who151_va_output.csv] and (version 1.4.1)[https://github.com/verbal-autopsy-software/CrossVA/blob/master/CrossVA/inst/sample/who_va_output.csv].
library(CrossVA) library(openVA) # InterVA4 & InSilicoVA(data.type = "WHO2012") 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 = ",") InterVA(output_data, HIV = "l", Malaria = "l") ## 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") # InterVA5 & InSilicoVA(data.type = "WHO2012") whoData2016_151 <- odk2openVA(records, version = "1.5.1") whoData2016_141 <- odk2openVA(records, version = "1.4.1") InterVA5(whoData2016_151, HIV = "l", Malaria = "l", directory = getwd()) insilico(whoData2016_141, data.type = "WHO2016")