Homework 9

Due: 2024-04-23, 11:59pm

Submission instructions

For this homework you should submit a ZIP archive containing:

  • A single document with the answers to all the following items in HTML format only. Make sure you include plain English blocks in between the code, and its output to interpret what R is giving you.

  • Code file used to generate the answers (RMD format). There should be comments in the code blocks.

  • Jupyter notebook (IPYNB) is okay.
  • Please remember to mix your comments with code and output.
  • Do not forget acknowledgements.

1. AKI alert data (50%)

Read in the AKI alert data collected by Wilson and colleagues. The study sought to determine whether electronic health record alerts for Acute Kidney Injury (AKI) would improve patient outcomes.

  • Consult the data dictionary and read in the dataset. How many hospitals are represented in the dataset and how many patients were in each? Make a table.
  • Calculate the proportion of patients who died in 14 days in each of the hospitals.
  • Calculate the log odds ratio for the association between death in 14 days and the AKI alert intervention in each hospital along with the standard error for that estimate.

2. TB data (50%)

We will use the tuberculosis transmission data where individuals in contact with a TB patient in Peru were followed up for about three years. The event of interest was development of TB, and the primary predictor of interest was whether the index individual had drug-resistant or drug-sensitive TB.

  • Divide the data into risk sets of 30 days each with the last strata starting at 481 days. The first time period would be 1-30 days, the next one 31-60 days, and so on.
  • Calculate the log risk ratio of developing TB in a time interval for MDR vs Sensitive household, adjusting for whether the index and contaxt shared a room (Contact.Index.Roomshare).
  • Make a plot of the adjusted hazard ratio with one standard error confidence bands.

3. Project proposal (0%)

Please outline your project. Your outline should contain the following components.

  • Statement of the research problem
  • Description of the data you are going to analyze including size, complexity, and if you have it in your posssession
  • Hypothesis/goals
  • Methods to be applied to answer the question; this should include details of the statistical and computational approaches, as well as anticipated problems

It is expected that the project will use some elements from this class in terms of advanced modeling approaches and/or data manipulation.

4. Acknowledgements

Cite resources or individuals helping you.