| 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)
}