web tool for estimating under-five deaths caused by poor-quality antimalarials in sub-Saharan Africa

This package allows users to calculate the number of under-five child deaths caused by consumption of poor quality antimalarials across 39 sub-Saharan nations. The package supports one function, that starts an interactive web tool created using the shiny R package. The web tool runs locally on the user's machine. The web tool allows users to set input parameters (prevalence of poor quality antimalarials, case fatality rate of children who take poor quality antimalarials, and sample size) which are then used to perform an uncertainty analysis following the Latin hypercube sampling scheme. Users can download the output figures as PDFs, and the output data as CSVs. Users can also download their input parameters for reference. This package was designed to accompany the analysis presented in: J. Patrick Renschler, Kelsey Walters, Paul Newton, Ramanan Laxminarayan "Estimated under-five deaths associated with poor-quality antimalarials in sub-Saharan Africa", 2014. Paper submitted.


About

pqantimalarials is a R package that runs an interactive web tool which allows users to reproduce and modify the estimates of under-five deaths caused by poor-quality antimalarials in sub-Saharan Africa presented in:

."Estimated under-five deaths associated with poor-quality antimalarials in sub-Saharan Africa". 2014. Paper submitted.

The pqantimalarials package only has one function, and this function starts the interactive web tool:

webtool()

To close the web tool:

  • Interrupt R, usually by hitting Esc or Ctrl + C

Users set input parameters using interactive sliders:

  • the number of simulations for an uncertainty and sensitivity analysis
  • the case fatality rate of under-five malaria positive children who consume poor-quality antimalarials
  • the prevalence of poor-quality antimalarials

Users are able to download:

  • input settings (CSV)
  • output plots (PDF)
  • output data (CSV)

For a given set of input settings, the downloaded files are tagged with a randomly generated ID number - so that users can download results generated using different input settings, and later be able to reference which settings were used for what outputs.

You can track development of this package at: http://github.com/renschler/pqantimalarials

Set Up

This web tool has been made available as an R package. To install and run enter the following lines into your R console.

install.packages("pqantimalarials")

library(pqantimalarials)

webtool()

FAQ

Q: When I download the CSV files and PDFs, what do the numbers at the beginnings of the filenames mean?

A: For every set of inputs, a random number is generated to "tag" your downloads.That way if you are iterating over different input settings you will know which downloads belong to which input settings. Be sure to download the input CSV if you want to be able to look up exactly what input settings you used to generate your results.

Package Citations

  • Erich Neuwirth (2011). RColorBrewer: ColorBrewer palettes. R package version 1.0-5. RColorBrewer
  • Hadley Wickham (2007). Reshaping Data with the reshape Package. Journal of Statistical Software, 21(12), 1-20. reshape2
  • Frank E Harrell Jr (2013). rms: Regression Modeling Strategies. R package version 4.0-0. rms
  • Hadley Wickham (2011). The Split-Apply-Combine Strategy for Data Analysis. Journal of Statistical Software, 40(1), 1-29. plyr
  • RStudio and Inc. (2013). shiny: Web Application Framework for R. R package version 0.8.0.99. shiny

News

pqantimalarials 0.2

  • changes to manuscript methods are reflected in this version
  • improvements to graphs
  • sensitivity analysis removed
  • additional UI changes (refresh buttons and input settings)

pqantimalarials 0.1

  • first stable release

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("pqantimalarials")

0.2 by J. Patrick Renschler, 5 years ago


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


Authors: J. Patrick Renschler <[email protected]>


Documentation:   PDF Manual  


GPL-3 license


Imports reshape2, RColorBrewer, plyr, shiny


See at CRAN