Skip to content
This repository has been archived by the owner on Aug 30, 2021. It is now read-only.

Latest commit

 

History

History
99 lines (74 loc) · 4.87 KB

CS_08.md

File metadata and controls

99 lines (74 loc) · 4.87 KB
title subtitle week type reading tasks
One Script, Many Products
RMarkdown to create dynamic research outputs. Publishing to github/word/html/etc
8
Case Study
Browse website about [RMarkdown](https://rmarkdown.rstudio.com/index.html)
Browse [R Markdown, the Definitive Guide](https://bookdown.org/yihui/rmarkdown/)
Build a RMarkdown document that downloads a dataset, produces one graph and one table, and exports to four different formats (HTML, GitHub Markdown, Word, Powerpoint).

Reading

Tasks

  • Build a RMarkdown document that downloads a dataset, produces one graph and one table, and exports to four different formats (HTML, GitHub Markdown, Word, Powerpoint).

Background

You are working on a team that needs to provide regular updates about a dataset that is regularly updated. Currently, an employee does the following steps once per week:

  1. Goes to a website with the source data
  2. Downloads the data as a text file
  3. Opens a graphing program and clicking through a set of procedures to make a particular set of graphs
  4. Saves the updated data in several formats including:
    • Powerpoint presentation
    • Website hosted on the team website
    • Word document that is included in company reports
    • A PDF document for downloading/printing

This takes the employee about 3 hours every week. You are a new member of the team and you confidently declare you could automate the procedure using R and RMarkdown (and that you could complete the automation in less than three hours!). The team looks at you with wide eyes. You realize you better get working.

Specifying multiple outputs with RMarkdown

You can specify that RMarkdown should produce multiple outputs using the following syntax in the YAML header:

output:
  html_document: default
  github_document: default
  powerpoint_presentation: default
  word_document: default

You can read more about the YAML header and all the options here. Note that you can specify many options for each output format to change the theme, structure, etc.

However, if you click the "Knit" button in RStudio, it will only make one output. To 'render' all of them, you have to use a command like this in the R Console.

rmarkdown::render("path/to/file.Rmd",output_format = "all")

Data

You will be working with the data available here. You can read it in using read_table() but you will have to look at the text file and specify how many lines to skip.

Outputs

Your objective is to automatically produce various outputs like MS Word, PPTX, and HTML.

The document should:

  1. Download the data (including correctly importing it)
  2. Make one timeseries plot (ggplot of CO2~time)
  3. Make one table. This table can summarize anything you want (top 5 years? Mean CO2 every decade?)
Show Hints

Hints

  1. Create a new RMarkdown Document (possibly starting with the template in File -> New File -> R Markdown
  2. Edit the YAML header at the top of the .Rmd file to specify the desired file types as noted above.
  3. Write code to read the "Mauna Loa CO2 annual mean data" from this website.
    • check out tidyverse::read_table() or similar to import the dataset into R directly from the URL (ftp://aftp.cmdl.noaa.gov/products/trends/co2/co2_annmean_mlo.txt)
    • after you look at the format of the text file, you will want to check out the skip parameter of read_table()
  4. Use ggplot to plot a time series of CO2 levels through time
  5. Add an additional table below the graph and format it nicely with knitr:kable() or similar.
  6. Use rmarkdown::render(file, output_format = "all") to render all the outputs specified in the YAML.
  7. Consider changing the 'chunk' settings so that the underlying code (and any messages) are hidden in the output documents. For example, consider results='hide',message=FALSE, echo=F.
  8. Tables can be a little tricky to embed in multiple formats. One approach is to use as_image() in kableExtra package which generates a png file that is easy to embed. You can use it like this:
data %>% 
  kable() %>% 
  as_image(width = 10,file = "table.png")
  1. Save the outputs in your repository.

Explore my version of the html output here.

Reflection

Think about how you could use this "one document, several outputs" approach in a project.