We computed the analysis in this publication in a series of steps, each dependent on the next, linked together via the traditional development tool
gnu make. We fit some example serological data sets (Morrison 2010 and L’Azou 2016, both collected from published studies and available as part of this package), and then use those fits to simulate populations.
All of the scripts mentioned in this vignette are included in the
inst/extdata of this package, and can be located wherever your R packages are installed, or accessed via the
build.project tool to make a skeleton, or by using
list.files(system.file("extdata/pub", package="denvax"), pattern=".R", full.names = T) to get the paths.
The skeleton includes a ‘Makefile’ that defines a general set of dependencies, as well as the specific steps used to generate the figures in the published manuscript. 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:
build.projectin Rstudio, write your own script with the
denvax::serofitfunction, or use make with the target
denvax::synthetic.popfunction, or the target
denvax::npxafunction, or the target
pub/ directory, we have another makefile and scripts which cover the specific analyses used in the publication.