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Type: Package
Title: Deterministic Verbal Autopsy Coding with Expert Algorithm Verbal Autopsy
Version: 1.0.0
Maintainer: Emily Wilson <wilsonem@gmail.com>
Description: Expert Algorithm Verbal Autopsy assigns causes of death to 2016 WHO Verbal Autopsy Questionnaire data. odk2EAVA() converts data to a standard input format for cause of death determination building on the work of Thomas (2021) https://cran.r-project.org/src/contrib/Archive/CrossVA/. codEAVA() uses the presence and absence of signs and symptoms reported in the Verbal Autopsy interview to diagnose common causes of death. A deterministic algorithm assigns a single cause of death to each Verbal Autopsy interview record using a hierarchy of all common causes for neonates or children 1 to 59 months of age.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: stringi, stringr
RoxygenNote: 7.3.2
BugReports: https://github.com/emilybrownwilson/EAVA/issues
Depends: R (≥ 2.10)
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2025-05-02 20:16:49 UTC; EWilson
Author: Emily Wilson [aut, cre], Henry Kalter [aut], Abhi Datta [aut], Sandipan Pramanik [aut], Robert Black [aut], Gates Foundation [fnd]
Repository: CRAN
Date/Publication: 2025-05-06 08:50:08 UTC

codEAVA

Description

Assigns cause of death by Verbal Autopsy Expert Algorithm

Usage

codEAVA(df, age_group)

Arguments

df

A data frame with 2016 WHO VA responses in openVA input format

age_group

Age group input, either "neonate" or "child"

Value

A two-column data frame with unique identifier and cause of death

Examples

{
# load embedded example data or data from WHO 2016 Verbal Autopsy Questionnaire
data <- as.data.frame(data_public)
# first run odk2EAVA()
output <- odk2EAVA(data, id_col  = "comsa_id")
# run codEAVA() for neonates and children 1-to-59 months of age
EAVA_neonate <- codEAVA(output, "neonate")
EAVA_child <- codEAVA(output, "child")
head(EAVA_neonate)
head(EAVA_child)
}

Example Data

Description

A subset of mortaility surveilance data from the Countrywide Mortality Surveillance for Action project

Usage

data_public

Format

'data_public' is example data frame with 10 rows and 511 columns

Source

<https://comsamozambique.org/data-access>


odk2EAVA

Description

Converts 2016 WHO verbal autopsy (VA) data to an input file for Expert Algorithm Verbal Autopsy cause of death assignment by the codEAVA() function

Usage

odk2EAVA(odk, id_col)

Arguments

odk

A data frame which used open data kit (odk) to obtain 2016 WHO VA questionnaire responses

id_col

A unique identifier for each record within the odk data frame

Value

A data frame that contains variable names and values which have been converted to openVA convention

References

Thomas J, Choi E, Li Z, Maire N, McCormick T, Byass P, Clark S (2021). CrossVA: Verbal Autopsy Data Transformation for InSilicoVA and InterVA5 Algorithms_. R package version 1.0.0, <https://CRAN.R-project.org/package=CrossVA>.

Examples

{
# load embedded example data or data from WHO 2016 Verbal Autopsy Questionnaire
data <- as.data.frame(data_public)
# run odk2EAVA()
output <- odk2EAVA(data, id_col  = "comsa_id")
# view data converted for use in codEAVA()
head(output)
}

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