Chapter 3 Overview of the reports

This chapter provides some additional informations about the different Rmarkdown reports. For details of data processing and analyses, we refer to the respective documents, as we attempted to document all code in each report. We recommend compiling the reports first and looking at the html outputs generated as a more user-friendly alternative to inspecting the source code directly.

Reports can be compiled by two ways:

1. using reportfactory::compile_reports(...) where ... is a character string matching the name(s) of the reports to be processed (regular expression accepted); outputs will be stored in time-stamped folders inside outputs/

2. using the usual rmarkdown::render(...) where ... is the path of the Rmd document to process; outputs will be stored inside report_sources/

Some reports accept parameters, i.e. variables set at compilation time which can impact the results generated. This is typically used, for instance, to indicate which WHO region the analyses are to be performed on, and is a more sustainable alternative to handling separate reports for every region. For both compilation methods the way to specify parameters to a report is the same; passing a list called param when compiling documents. For instance:

library(reportfactory)
compile_reports(report = "analyses",
                params = list(who_region = "AFRO")

will compile the analysis report regional_analyses.Rmd (only match for the word "analyses") for the AFRO region.

Default values of parameters are set in the YAML headers of the respective reports.