Week 4 Material (read if you have never used R Markdown)

[eeholmes]

On Friday, I will cover using R Markdown for reports. This lecture will be intermediate material geared towards the kind of reports that we prepare as part of our NOAA Fisheries work. I am going to focus quite a bit on how to output nice Word documents. The fact is that for many of us Word (or Word uploaded to Google Drive) is part of our workflow, particularly within teams. I personally use LaTeX and would love to use something other than Word, but within teams I use Word and actually the Track features aspect of Word is pretty great.

You'll get a lot more out of this lecture if you have played around with R Markdown. And it is super easy in RStudio.

Instructions for making your first R Markdown document

1. Open RStudio. You can do this on your computer if you have RStudio installed or click on this LINK and use RStudio Cloud. You can use RStudio Cloud from anywhere (e.g. your phone).
2. Click File > New File > R Markdown...
3. Click Ok at bottom of the pop-up window. You don't need to change anything.
4. Click the Knit button. It is in the nav bar just below the file name. Icon is a ball of yarn.

5. It'll ask you to save the document. Give it a name and save. 6. The first time you Knit a document, you'll see a pop-up window telling you you need to install some packages. Just click Install on that and let it install the packages you need.

That's it! The html doc should pop up. You can click the Knit drop down (the Knit button) and Knit to a Word doc or a PDF too.

Learning R Markdown basics

The basics are really simple. R Markdown is designed that way.

1. Read the Rmd document from above, edit the file and re-Knit to see the changes.
2. If you want, go through the RStudio tutorials: https://rmarkdown.rstudio.com/lesson-1.html