README.org

Tajikistan poliomyelitis analysis

• Look at these notes for material relating to the model.
• Look at these notes for material relating to the manuscript.
• IMPORTANT there is a configuration file for the analysis.
• There is a ANT build script which coordinates this analysis.

Data

• Figure fig:data-plot is produced by ./R/preprocessing-1.R.

Results

• This file containing the strings used to describe the time series in the XML is produced by ./R/preprocessing-2.R.
• This file containing the timed sequences is produced by ./R/preprocessing-2.R.
• This BEAST2 XML was produced by BEAUti.
• Figure fig:estimates-plot is produced by ./R/postprocessing-1.R and shows the reproduction number alongside previous estimates.
• Figure fig:data-and-estimates is produced by ./R/postprocessing-1.R.
• There are a couple of prior/posterior plots produced by ./R/postprocessing-2.R
• A table summarising the parameter estimates is produced by by ./R/postprocessing-2.R.
• NOTE that this uses the HDPI as computed by bayestestR for the credible intervals.