smri2020

My first awesome chromebook edit!

My first awesome README

Weekly Digest

April 21st

• Tasks:
  • Finish Q1 and Q2
    • Look into other appropriate hypothesis tests for Q2
  • Read chapters on matplotlib to generate some plots to include in final results slides
    • https://jakevdp.github.io/PythonDataScienceHandbook/

April 14th

• Tasks:
  • Start Project presentation slides that will contain all the results (numbers/figures/etc.) from answering the Qs and testing the hypotheses.
  • Read the multiple comparisons chapter in the online handbook
  • Run fisher drug and reaction tests for all drugs and reactions
  • Get the number of drugs and reactions above and below a bonferroni value of 0.05
    • write those numbers in your slides
  • Read paired ttest chapter in handbook

April 7th

• Tasks:
  • Finish tasks from the 2nd

April 2nd

• Tasks
  • Finish count and frequency tabulation of males and females per reaction
  • Read http://www.biostathandbook.com/fishers.html and write pseudocode for testing hypotheses with this test for all concepts.

March 17th

• Tasks
  • Practice presentation so as to be ready to presentt it over your laptop via Google Hangouts
  • Do 2 more examples for hypothesis 1 using less code than the firs example
  • Read here: http://www.biostathandbook.com/linearregression.html
    • Focus on understtanding correlation and r squared.

March 12th

• Tasks
  • Practice presentation
    • practice it like you would give it on the 24th.
    • Understand why we set up both questions and hypotheses
    • Understand why we form both a null and alternative hypothesis.
  • Try extracting the data necessary to answer all three questions

March 10th

• Tasks
  • Finish any unfinished tasks from last week.
  • Go through presentation slides
    • Read through a few times what you have written and practice speaking in front of friends/family. Ideally, you should be able to communicate to them what are adverse drug reactions, why they are a problem to individuals and society, and how data can help us address the problem (e.g. raise awareness of the issue).
    • When we meet again, you will present your slides as you would on the actual presentation day.
  • Write down 3 questions about how adverse drug reactions vary between patients of different age and different sex.
    • Write down both a null and alternative hypothesis for each question.
    • This exercise will help identify the questions/hypotheses to be investigated for the rest of the project.

March 5th

• Tasks
  • Read more about
    • the problem (why and how adverse drug reactions are bad),
      • Look here for research articles https://www.ncbi.nlm.nih.gov/pubmed/
    • what contributes to the problem (specifically, age and sex),
    • why we need to address the problem (increase awareness, influence policy, etc.), and
    • why this data will help us address the problem (read about the openfda and why consumer reports would be useful to address the problem)
  • Write down what you would say as you present your slides in the presenter notes
  • Read this again http://www.biostathandbook.com/hypothesistesting.html

March 3

• Outline
  • Write down (>5) questions about consumer drug reporting you are interested in.
  • (when nick puts up the consumer data) Ask and answer atleast 5 questions in the new dataset that you are interested in.
    • Drugs, reactions, sex, age, date

-Tasks

• Do the above.
• Also, think of 3 larger questions, that you may not be able to answer now, but would like to know about adverse drug effects and how consumers report them.
• Also, write down 3 null hypotheses that underly your questions. In other words, what are the statements that you want to argue are NOT the case. For example, if you want to know the relationship of A and B, your null hypothesis is there is no relationship between A and B.

February 27th

• Outline
  • Go through asking and answering more questions.
  • Go through hypothesis testing
  • Assign reading/videos on hypothesis testing

February 25th

• Tasks:

  • Ask and try to answer 5 questions

  • Identify 3 pandas tutorials and read through as well as implement some of their examples (if you are able to with their instructions).

February 19th

• Tasks for next week:

  • Try to answer the two questions in thhe notebook

  • Read the hypothesis testing chapter in the biological statistics handbook

February 11th

• Went over basic commands of how to go through the terminal

• We learned simple commands to work with Git directories

• I learned how to edit this file!

February 4th

• Created GitHub repository to use throughout internship -- Woohoo!

• Went over the drug event data available from the FDA https://open.fda.gov/

• Went over basics of computer servers, programming, and drug safety questions

For next time:

• Try to follow and run the commands in https://realpython.com/python-first-steps/

• Set up proper applications on laptop

Reading

The Handbook for Biological Statistics

http://www.biostathandbook.com/index.html

Resources

Project Jupyter https://jupyter.org/

Python https://www.python.org/

Pandas tutorials and notebooks

https://pandas.pydata.org/pandas-docs/stable/getting_started/tutorials.html https://github.com/guipsamora/pandas_exercises

Pandas videos

https://www.youtube.com/watch?v=pu3IpU937xs&list=PLgJhDSE2ZLxaY_DigHeiIDC1cD09rXgJv

Git https://git-scm.com/book/en/v2

Athena - standardized drug and side effect names athena.ohdsi.org

Pandas tutorial https://www.learndatasci.com/tutorials/python-pandas-tutorial-complete-introduction-for-beginners/