2.2 Main folders and files

The main components are:

  • data/: a folder where raw and clean data are stored; the content of this folder is not stored on github to minimize the size of the git archive

  • report_sources/: a folder containing the sources of the Rmd reports doing the data gathering and cleaning, and all analyses; see the reports chapter for more information

  • scripts/: a folder containing R scripts used in the various reports; this includes small helper functions to load the latest versions of the data, help with bits of analysis, and code for installing packages not on CRAN, which cannot be handled automatically by reportfactory::install_deps()

  • outputs/: a folder containing all compiled reports and associated outputs, in timestamped folders; this content is automatically generated when using reportfactory::compile_reports(), and is only stored locally (i.e. on your machine), and not on github (to keep the git archive to a minimal size)

  • css/: a folder containing styling for the reports

  • asmodee_outputs/: a folder containing outputs of the main analysis, shared on github; this includes images (pinplots and tadpoles), R objects (rds files) containing re-usable analysis results (e.g. for inclusion in websites or dashboards), and analysis notes (indicating excluded countries, and reasons for their exclusions)

  • docs/: a folder containing the sources and compiled versions of this handbook

Other useful files and folders to know of include:

  • README.Rmd: the source of the README.md file, which is displayed on the landing package of the github project, and shows the latest tadpoles figures by WHO region and also provides links to the corresponding rds files

  • run_factory.R: the main R script for updating data, and running analysis reports for every WHO regions; also used by github actions

  • run_synthesis.R: an R script used in github actions to generate a synthesis report for all countries, including a classification into levels of risk based on incidence, growth and trend acceleration, and for sending an email to a list of recipients with these documents attached

  • .github/workflows/: a (hidden) folder storing the files used to define the github actions; see the automation chapter for more information

  • factory_config: a simple text file containing some information about the name of key directories of the factory; normally will not need editing, unless you rename the folder containing the factory (see 2.3.1)