inst/extdata/README.md

In denvax: Simple Dengue Test and Vaccinate Cost Thresholds

Project Template

The denvax::build.project(...) function creates a skeleton project your analysis.

The Makefile provides the relationships between the various single step scripts, and a way to run them as a workflow. Alternatively, they can be run manually from the command line or in an application like Rstudio.

The simple.R script demonstrates a simple start-to-finish analysis (using the Morrison 2010 data included in the package).

In either approach, the steps are:

1. develop fit(s) for local serological data (e.g., use the fit.R script in Rstudio, write your own script with the denvax::serofit function, or use make with the target %-fit.json in Makefile).
2. use a fit to synthesize a population (e.g., synthesize.R script, the denvax::synthetic.pop function, or the target %-lh.rds in Makefile)
3. use the synthetic population to estimate the lifetime outcome probabilities (e.g., digest.R script, the denvax::npxa function, or the target %-npxa.rds in Makefile)
4. combine the probabilities with the desired boundaries for interventions (initial testing age and maximum number of tests) and to compute the ROI equation coefficients (denvax::ROIcoeffs function)
5. finally, combine the coefficients with desired cost fraction ranges (i.e., the cost of vaccination and testing as fractions of the estimated burden of secondary infection, or $\nu$ and $\tau$ respectively), to determine the threshold region for positive ROI (denvax::ROI function).

The pub/ folder includes all the scripts necessary to generate the figures associated with the original publication of the analysis.

denvax documentation built on Dec. 2, 2019, 1:09 a.m.