Instructor: Saanchi Shah
Slack Channel: TBD
Slack Channel Invite: TBD
Class: R 9:30 AM - 12:20 PM Covel 210
Office Hours: After class, by appointment and TBD
Here is the INSTALLATION GUIDE.
| Week | Topic | Lecture | Homework | Data |
|---|---|---|---|---|
| 1 | R/R studio set up | Lecture notes: Set up (html) | NA | NA |
| 2 | Introduction, reading files in, subsetting observations | Lecture notes: Lab 1 (html), Rmd | Download Practice set 1(Rmd), (html). Submit by the deadline before Week 3 class. | Class: HP Characters Homework: Potions |
| 3 | Filtering and selecting variables and counting observations | Lab 2 (html), Rmd | Download Practice set 2(Rmd),(html). Submit by the deadline before Week 4 class. | Class: NYC HANES - SPI NYC Homework: NYC airbnb |
| 4 | Grouping, summarizing and renaming variables | Lecture notes: Lab 3 (html), Rmd | Download Practice set 3(Rmd),(html). Submit by the deadline before Week 5 class. | Class: NYC HANES - SPI NYC Homework: NYC airbnb - you guessed it right, I love NYC! |
| 5 | Merging datasets and creation of new variables | Lecture notes: Lab 4 (html), Rmd | Download Practice Set 4 (Rmd),(html). Submit by the deadline before Week 6 class. | Class: NYC HANES - SPI NYC and NYC HANES - CAPI NYC, Homework: Travel |
| 6 | GGplot (data visualization) | Lecture notes: Lab 5 (html), Rmd | Download Practice Set 5 (Rmd),(html). Submit by the deadline before Week 7 class. | Class: Use your merged NYC HANES file or here is mine. Homework: Travel and NC Births |
| 7 | Statistical analysis (t-tests and chi squares) | Lecture notes: Lab 6 (html), Qmd | Download Practice Set 6 (Rmd),(html). Submit by the deadline before Week 8 class. | NA |
| 8 | In-class practice (recap) + TBD | TBD | Rough Draft Due | TBD |
| 9 | Workshopping | NA | NA | |
| 10 | Final Project Presentation | NA | NA |
It’s time to become an MCH researcher! Your goal is to work in a team to determine associations between environmental exposures/habits and pregnancy outcomes. Use this markdown file to get started on your final project - more details to come later. Feel free to spend time on this website in the meanwhile (highly encouraged): UniSA. For copyright reasons, I have not shared articles on github, however, I did link a couple of articles in the markdown file which I believe will be helpful as we develop some skills and try to emulate 10% of what the authors achieved using the PALS dataset.
Here is the PALS dataset in CSV format. Since this is the original dataset, it has all the variables as is (which is a lot). To make your life easier, I created a subset with a few variables and a few new variables. Should you want to use it as is, here you go: PALS SUBSET. Here is the codebook for the original dataset which can also be found online. Here is a document listing the variables I kept in the subset dataset.
My suggestion is to approach the paper/analysis in one of the 2 ways:
Association between dietary variables and birth weight
Association between term status and maternal health
a) Vitamin A Supplementation and Low Birth Weight’s Relationship with Declining Under Five Mortality Rate in Africa from 2000-2015. Feel free to take a look here.
b) Methicillin-Resistant Staphylococcus Aureus (MRSA) Infections in California Across Community Type and Years. Feel free to take a look here.
Note: Sample project submitters did NOT use PALS. If you wish to use a different dataset or the WHO data most students have worked with in the past, let me know! Further, expectations for the paper were a little different and we used a different programming language a couple of years ago. Do not worry about all the graphs (some students were also very advanced and I had to modify some of the assignments accordingly).