ESR Reporting Template

• ESR Reporting Template
  • Description
  • Software dependencies
  • Assumptions
  • How to use
    • Clone this github repository on ESR's production network
    • Open the reporting template in an RStudio project
    • Restore the renv environment to install software dependencies
    • Set formatting options in the yaml front matter
    • Include R code and text relevant to your analyses/report
    • "Knit" (render) the document
    • More information

Description

This repository contains templating for consistent themed ESR reports/documents using RMarkdown. Currently, knitting to a html document/report is supported.

Here's a peek at the rendered html report:

Software dependencies

• renv installed (see installation instructions)

Assumptions

• You have access to ESR's production network
• Some coding experience (command line and R)

How to use

Clone this github repository on ESR's production network

Navigate to your project directory, for example

cd /home/leah/my_project_to_report/

Clone this repository

git clone https://github.com/ESR-NZ/ESR_reporting_template.git

Open the reporting template in an RStudio project

Navigate to RStudio hosted on ESR's production network at http://rstudio.esr.cri.nz:8787, use your regular ESR login credentials to login to RStudio

Create a new RStudio project (this template was created using R version 4.1.2, use this version of R if you'd like to fully reproduce this example template, but the code should be adaptable to other versions of R with some R coding knowledge)

Open the reporting RMarkdown (RMD) file, this is the main file for the reporting template

Restore the renv environment to install software dependencies

renv::restore()

Set formatting options in the yaml front matter

Some formatting can be configured in the yaml frontmatter of the reporting_template.RMD file

title: "ANALYSIS REPORT"                                # set the main report title
author:
  # - Jane Doe^[Institution Two, [email protected]]      # add report authors (uncomment if using)
  # - John Doe^[Institution One, [email protected]]      # add a second report author (uncomment if using)
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
always_allow_html: true
output:
  bookdown::html_document2:
    toc: true                                           # create a table of contents (true or false)
    toc_depth: 2                                        # set the table of contents depth (number)
    number_sections: false                              # choose whether or not to number sections (true or false)

For example, you can set:

• Main report title
• Report authors
• Set the table of contents depth
• Choose whether or not to number report sections

Include R code and text relevant to your analyses/report

"Knit" (render) the document

More information

There is so much more you can do with RMarkdown, get started with wicked reproducible (and interactive!) documents here