1 Introduction

The nbc4va package implements the Naive Bayes Classifier (NBC) algorithm for verbal autopsy data based on code and methods provided by Miasnikof et al (2015).

This package is intended to be used for experimenting with the NBC algorithm to predict causes of death using verbal autopsy data.

1.1 Acknowledgements

This package was developed at the Centre for Global Health Research (CGHR) in Toronto, Ontario, Canada. The original NBC algorithm code was developed by Pierre Miaskinof and Vasily Giannakeas. The original performance metrics code was provided by Dr. Mireille Gomes whom also offered guidance in metrics implementation and user testing. Special thanks to Richard Zehang Li for providing a standard structure for the package and Patrycja Kolpak for user testing of the GUI.

1.2 Quick Start

Run the nbc4va Graphical User Interface (GUI) and follow the instructions in your browser:

library(nbc4va)
nbc4vaGUI()

Exit the GUI by closing the browser window and pressing Esc in a R console to stop the GUI process.

1.3 Background Knowledge

Before using the nbc4va package, ensure that the training and testing data inputs are formatted correctly and that the terms used in this package are understood:

  1. It is strongly suggested to review the Methods section for an understanding of terms and metrics
  2. Please also review the input data specifications detailed in the Data section

1.4 Using the Package

The nbc4va package contains help sections with code samples and references for usage:

  • The Basic Usage section is suited for users of all levels
  • The Advanced Usage section is suited for users of the package that have some R programming experience
  • The Functions section provides an organized list of package functions with brief descriptions

1.5 Getting Help

By using the help() function (or ? shortform) in an R console, you can access details about particular functions and methods in the nbc4va package:

library(nbc4va)  # load the nbc4va package

# View this help page as a vignette
browseVignettes("nbc4va")

# Access details about certain functions
help("nbc4va") # access the nbc4va package docs
help("nbc4vaGUI") # access GUI details
help("nbc4vaIO") # access file in and out details
help("nbc") # access the nbc algorithm function
help("summary.nbc") # access the summary function
help("plot.nbc") # access the results plot function

# Access details about example data
help("nbc4vaData")
help("nbc4vaDataRaw")

# Alternative short forms
?nbc4va
?nbc4vaGUI
?nbc4vaIO
?nbc
?nbc4vaData
?nbc4vaDataRaw
?summary.nbc
?plot.nbc

1.6 Issues, Bugs, and Fixes

For help with bugs, issues, enhancements, and related inquiries, please submit a new issue at:

https://github.com/rrwen/nbc4va/issues

1.7 Citing this Package

  • Miasnikof P, Giannakeas V, Gomes M, Aleksandrowicz L, Shestopaloff AY, Alam D, Tollman S, Samarikhalaj, Jha P. Naive Bayes classifiers for verbal autopsies: comparison to physician-based classification for 21,000 child and adult deaths. BMC Medicine. 2015;13:286. 10.1186/s12916-015-0521-2.

To view citation information for the nbc4va package, use the code below in an R console:

library(nbc4va)
citation("nbc4va")