Lab report module 8

The purpose of this assignment is for you to demonstrate basic familiarity with importing, inspecting, cleaning, manipulating, visualising, and interpreting archaeological data.

We are investigating a variety of archaeological and environmental datasets to understand why the Mayan civilisation collapsed. Please review the lecture slides Download lecture slides to see the specific questions that your report needs to answer. 

Here's what you need to do:

1. Create a new RStudio project (New Project -> New Directory -> New Project), and
   • save it as archy-208-module-8-bmarwick (replace my UW ID with yours), you will get a new, empty folder, ready to work in
2. Download the zip file of the datasets here Download zip file of the datasets here, these files come from Kennett et al (2012) Links to an external site., Hoggarth et al (2016) Links to an external site., and Lentz et al. (2020). Links to an external site.
   • use your desktop folders to move this zip file into your RStudio project directory that you just created.
   • If you upload the zip file to RStudio in your web browser, it will auto-unzip, that is ok. It you're working on the desktop, we will write R code to unzip, do not do this manually or you might create a confusing situation
   • File names are vital here: do not rename the data files. We can't grade your assignment if the file names are not exactly as specified here (check for numbers magically appearing at the end of the filename, that means you've downloaded it multiple times, you should delete the other copies).
3. In your new project, create a new Quarto file (File -> New file -> Quarto Document -> click "Create"), and
   • save your qmd file as archy-208-module-8-bmarwick.qmd (replace my UW ID with yours),
   • delete all the template content
   • Ensure your YAML front matter has:
     • an effective title (how?), e.g. in the form of a question or statement
     • your name, hint: author: "Ben Marwick"
     • the date automatically inserted, hint: date: now
     • the output format set as html, hint: format: html: self-contained: true
     • warnings and messages suppressed in the output, hint: execute: warning: false
     • increase the image quality of the plots, hint: fig-dpi: 600
     • customize the date label, hint: title-block-published: "Last updated"
4. In your qmd file, use these headings, and write a total 8-12 fully-formed sentences containing specific details and concrete nouns that answers these questions:
   • Introduction: What is the aim of your report? See Thursday's lecture slides Download Thursday's lecture slides for the specific aims to mention here (1-2 sentences containing specific details and concrete nouns).
   • Data: What type of data are you analyzing and where does it come from? (2-3 sentences containing specific details and concrete nouns, e.g. name of the location and time period that the data represents)
     • use at least one examples of inline R code to get a meaningful summary value (do not hard-code any values, e.g. 'two')
     • your text must cite the publication that originally presented the data in APA style (how?). Do not include the title of the article in your sentence). Do include the full reference in your reference section.
   • Exploratory data visualisation: What do you observe when you visualise the data? (3-4 sentences)
     • you need to write R code that produces a panel of plots (using cowplot) that shows Mercury concentrations over time, and inscription numbers over time
     • you need to write R code that produces a plot to show Oxygen isotope values over time.
     • you need a captions and cross-references for each figure or panel of figures
     • Each visualisation needs at least one complete sentence describing your observations of what you see in the plot, and how it relates to the questions you need to answer in this lab report.
   • Conclusion: What is your conclusion about the cause of the collapse of the Maya? (3-4 sentences) 
     • you need a statement that answers the questions presented in the Thursday lecture and cross-references at least one of your plots.

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

• • Check that in your qmd file your data file names are exactly the same as ours.

6. Upload to Canvas your two files (please do not zip them):

• • your qmd file, correctly named, with correct YAML, with code and text, and
  • your HTML file, containing the output of your code and text, with no warnings or messages from the code visible

If you get stuck at any point here please let us know at any time by posting a message to our Discord workspace. We want you to succeed!