Context

This assignment reinforces ideas in Data Wrangling I.

Due date and submission

Due: Oct 7 at 11:59pm.

Please submit (via courseworks) the web address of the GitHub repo containing your work for this assignment; git commits after the due date will cause the assignment to be considered late.

R Markdown documents included as part of your solutions must not install packages, and should only load the packages necessary for your submission to knit.

Points

Problem Points
Problem 0 20
Problem 1 –
Problem 2 40
Problem 3 40
Optional survey No points

Problem 0

This “problem” focuses on structure of your submission, especially the use git and GitHub for reproducibility, R Projects to organize your work, R Markdown to write reproducible reports, relative paths to load data from local files, and reasonable naming structures for your files.

To that end:

  • create a public GitHub repo + local R Project; we suggest naming this repo / directory p8105_hw2_YOURUNI (e.g. p8105_hw2_ajg2202 for Jeff), but that’s not required
  • create a single .Rmd file named p8105_hw2_YOURUNI.Rmd that renders to github_document
  • create a subdirectory to store the local data files, and use relative paths to access these data files
  • submit a link to your repo via Courseworks

Your solutions to Problems 1, 2, and 3 should be implemented in your .Rmd file, and your git commit history should reflect the process you used to solve these Problems.

For this Problem, we will assess adherence to the instructions above regarding repo structure, git commit history, and whether we are able to knit your .Rmd to ensure that your work is reproducible. Adherence to appropriate styling and clarity of code will be assessed in Problems 1+.

Problem 1

This problem focuses on NYC Transit data; in particular, this CSV file contains information related to each entrance and exit for each subway station in NYC. If you’re not familiar with the NYC subway system, keeping a map in mind while looking at these data might help.

Read and clean the data; retain line, station, name, station latitude / longitude, routes served, entry, vending, entrance type, and ADA compliance. Convert the entry variable from character (YES vs NO) to a logical variable (case_match function may be useful).

Write a short paragraph about this dataset – explain briefly what variables the dataset contains, describe your data cleaning steps so far, and give the dimension (rows x columns) of the resulting dataset. Are these data tidy?

Answer the following questions using these data:

  • How many distinct stations are there? Note that stations are identified both by name and by line (e.g. 125th St 8th Avenue; 125st Broadway; 125st Lenox); the distinct function may be useful here.
  • How many stations are ADA compliant?
  • What proportion of station entrances / exits without vending allow entrance?

Reformat data so that route number and route name are distinct variables. How many distinct stations serve the A train? Of the stations that serve the A train, how many are ADA compliant?

Problem 2

This problem uses the Mr. Trash Wheel dataset, available as an Excel file on the course website.

Read and clean the Mr. Trash Wheel sheet:

  • specify the sheet in the Excel file and to omit non-data entries (rows with notes / figures; columns containing notes) using arguments in read_excel
  • use reasonable variable names
  • omit rows that do not include dumpster-specific data
  • round the number of sports balls to the nearest integer and converts the result to an integer variable (using as.integer)

Use a similar process to import, clean, and organize the data for Professor Trash Wheel and Gwynnda, and combine this with the Mr. Trash Wheel dataset to produce a single tidy dataset. To keep track of which Trash Wheel is which, you may need to add an additional variable to both datasets before combining.

Write a paragraph about these data; you are encouraged to use inline R. Be sure to note the number of observations in the resulting dataset, and give examples of key variables. For available data, what was the total weight of trash collected by Professor Trash Wheel? What was the total number of cigarette butts collected by Gwynnda in June of 2022?

Problem 3

This problem uses data collected in an observational study to understand the trajectory of Alzheimer’s disease (AD) biomarkers. Study participants were free of Mild Cognitive Impairment (MCI), a stage between the expected cognitive decline of normal aging and the more serious decline of dementia, at the study baseline.

Basic demographic information were measured at the study baseline. The study monitored the development of MCI and recorded the age of MCI onset during the follow-up period, with the last visit marking the end of follow-up. APOE4 is a variant of the apolipoprotein E gene, significantly associated with a higher risk of developing Alzheimer’s disease. The amyloid \(\beta\) 42/40 ratio holds significant promise for diagnosing and predicting disease outcomes. This ratio undergoes changes over time and has been linked to the manifestation of clinical symptoms of Alzheimer’s disease.

Import, clean, and tidy the dataset of baseline demographics. Ensure that sex and APOE4 carrier status are appropriate encoded (i.e. not numeric), and remove any participants who do not meet the stated inclusion criteria (i.e. no MCI at baseline). Discuss important steps in the import process and relevant features of the dataset. How many participants were recruited, and of these how many develop MCI? What is the average baseline age? What proportion of women in the study are APOE4 carriers?

Similarly, import, clean, and tidy the dataset of longitudinally observed biomarker values; comment on the steps on the import process and the features of the dataset.

Check whether some participants appear in only the baseline or amyloid datasets, and comment on your findings. Combine the demographic and biomarker datasets so that only participants who appear in both datasets are retained, and briefly describe the resulting dataset; export the result as a CSV to your data directory.

Optional post-assignment survey

If you’d like, you can complete this short survey after you’ve finished the assignment.