Welcome to this report factory!

The factory will help you handle multiple rmarkdown reports at the same time. Put your .Rmd files in report_sources, refer to any external files in the .Rmd using here::here(), and you’re sorted.

How the default factory is organised

• report_sources: (mandatory) put your .Rmd documents there (subfolders are OK)

• data/: (recommended) put your data in this folder (subfolders are OK)

  • data/raw: to store raw data, as read-only
  • data/clean: to store cleaned data

• R/: (recommended) put your external R scripts and functions, used in your .Rmd reports, in this folder (subfolders are OK)

• outputs/: (automatically created) the factory will store report outputs there, using named and time-stamped folders

How to run the factory: useful commands

• list_reports(): lists reports currently stored in the factory (only .Rmd source files)

• compile_reports(): compiles one or more reports: An individual report can be compiled using the exact file name or a non-ambiguous match; multiple reports can be compiled by using a regular expression to match report names; all reports can be compiled if the argument is left empty. Compiled reports will be stored in outputs/.

Basic workflow

Below is a basic workflow to get you started. For more information consult [https://www.repidemicsconsortium.org/reportfactory/]

1. create a new factory using new_factory() and move into this new folder

2. go to report_sources/, write your .Rmd report, using the provided examples as inspiration; remove the examples files.

3. check your report by compiling the .Rmd manually if needed, e.g. rmarkdown::render("foobar.Rmd"); once you are happy with the results, make sure you remove all output files from the source folder

4. run compile_reports() to generate all outputs, or compile_reports("foobar") if you just want to produce time-stamped outputs for reports that can be matched via regular expressions by "foobar"; check results in the folder outputs/.