Lab report module 1

The purpose of this assignment is for you to demonstrate basic familiarity with using R, Quarto, and RStudio (FAQ: why are we using R?

Before starting this assignment, you need access to RStudio. You can do this assignment by logging into RStudio with your UW Net ID in your web browser here. Or you can download and install R and RStudio to your computer by following my instructions here. If you are not sure which option is best for you, read our FAQ on this. Remember that you are warmly welcome to ask for help at any time by posting a message to our Discord Links to an external site. workspace. 

When you use RStudio for the first time this quarter, ensure that you optimize the program by changing some of the default settings by following my instructions here. This will make the software more efficient and safer for you (i.e. less likely to lose unsaved work or contaminate your working environment and get the wrong results). 

For this lab we are using data from an interesting paper by Benjamin et al (2020) Links to an external site. about stone artefacts found in underwater archaeological sites in one of my favourite parts of the world, north-western Australia. This is just a paper with a convenient dataset that is suitable to demonstrate the basics of getting started writing R code. Unlike subsequent labs, we are not going to be discussing this paper in detail in class (if you're interested in Australian archaeology, please join me in my class ARCHY 319 'Archaeology of Australia').  The aim of your report is to briefly explore the stone artefact data found at the underwater sites.

Your tasks are: 

1. Create a new RStudio project (New Project -> New Directory -> New Project),
   • call it archy-208-module-1-bmarwick (replace my UW ID with yours).
   • You should get a new, empty folder, ready to work in
   • Download the Benjamin et al (2020) Links to an external site. data file from here Download here on our Canvas site. Do not download the data directly from the journal article because I changed the format to keep this lab simple. 
   • Move the data file into your RStudio project directory that you just created in this step. File names are vital here, it must keep its original name: do not rename the data file. Do not download it multiple times because your computer will automatically change the filename it by adding (1) to the end of the filename, and can cause confusion, and will cause you to lose points when your assignment is graded.
2. In your new project, create a new Quarto file (File -> New file -> Quarto Document -> click "Create"), and:
   • call it archy-208-module-1-bmarwick.qmd (replace my UW ID with yours), and
   • ensure the YAML front matter has an effective title (how?), e.g. in the form of a question or statement
   • ensure the YAML front matter has your name
   • ensure the YAML front matter has the date.
   • ensure the YAML front matter has html set as the output format
3. In your new qmd file:
   • delete all the template content
   • create a code block that imports the data you downloaded in step 1, in your code block, use the function read.csv() to import the CSV file.
   • create a second code block that uses the hist() function to visualise the distribution of artefact length 

 5. In your qmd file, write 3-4 fully-formed sentences that include inline R code Links to an external site. and answer these questions:

• • What is the aim of your report? (hint: look at the text below "What is your conclusion...")
  • What type of data are you analysing and where is it from? Cite the source of the data (how?).
  • What are the basic details of the data? Use inline R code to get these summary values in your sentence: the total number of artefacts in the sample, the maximum and minimum lengths, and the average length of the artefacts. 
  • What is the distribution that you see in the plot? For example, your sentence might look this: "The histogram above shows that most artefacts are between X and Y mm long",  and you replace X and Y with numbers you see on your plot
  • What is your conclusion about whether or not the artefacts represent an intact, undisturbed archaeological site? Feel free to draw on your intuition here and make what you think are reasonable assumptions to make a logical argument. You may also reference what Benjamin et al (2020) Links to an external site. argued in their conclusion. Keep it brief, just a sentence or two is all we're looking for here. 

7. Render your qmd file to output a HTML document.

8. Upload to Canvas your three files, one at a time (please do not zip them into one file), and only upload each file once (Canvas auto-renames files if you upload the same file multiple times):

• your data file, correctly named, check that your data file name is exactly the same as ours
• your qmd file, correctly named, with correct YAML, with code and text, and
• your HTML file, containing the output of your code and text

Additional resources: 

• Before We Start (Data Carpentry Lesson) Links to an external site. (article)
• Introduction to R Links to an external site. (article)
• An opinionated tour of RStudio (R-Ladies Sydney) Links to an external site. (15 min video)