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Context

As part of a strategy for Knowledge Management and using code for reproducible research and addressing global challenges, the integration of data standardisation, formatting and visualisation code with reporting and the communication of results is a powerful extension of R.

The development of rmarkdown and the production of static and dynamic documents greatly facilitates the integration of data, code & reporting. For the routine monitoring of coral reefs, this means that once new data are obtained, they can be readily put into format, plotted and incorporated into standardised reports.

This wiki page provides an overview of the Project documentation & reporting module and a brief introduction to rmarkdown and approaches to standardised reporting.

Combining data, code & documentation

As part of a general workflow for data management of coral reef monitoring data, the reporting element integrates the data importing, cleaning & standardisation, mapping and plotting of status & trends.

Using rmarkdown provides functionality to imbed sections of code into a working document that can be “rendered” into different formats (e.g. *.pdf, *.html, *.docx, *.pptx and others).

As one can imagine from the image above, there are many ways to use rmarkdown for the production of static & dynamic (i.e. allowing readers to explore data) documents.

For this training course, we will focus on the production of a static *.pdf document which aims to “harvest” the outputs from the data cleaning & plotting. In further exercises, we will demonstrate the use of modifications of markdown (i.e. *.Rmd and *.md) documents to create slide presentations using reveals (as an example of how to do this) and maintain a project wiki.

As part of the course exam, we will be creating an example report to evidence the course participants’ R skills and Homework completion:

The strategy of separating the data cleaning, standardisation, mapping and plotting and producing intermediate *.rda and *.png outputs in separate scripts means that the binary outputs of the coding can be used for multiple purposes (e.g. static report document, presentation, wiki).

As the workflow is controlled through integrate.R, we can also recreate the analysis and creation of multiple dissemination materials.

Next steps

To begin this module, we will have a look at ways of how to structure a markdown document and the knitr::render() function.