Methods in Biostatistics
Math 150, Spring 2021
Jo Hardin
2351 Estella Laboratory
jo.hardin@pomona.edu
See Sakai for all relevant links
Office Hours (on Discord, see Sakai for link):
Tuesday 8:30-9:30am PT and 1:30 – 3pm PT
Thursday 7-8am PT and 12-2pm PT
Friday 9-10:30am PT
or by appointment
Text: Practicing Statistics, Kuiper & Sklar (CD information (datasets and R code) on Sakai.)
Important Dates:
- Exam 1 (date: Wednesday, March 17)
- Exam 2 (date: Wednesday, April 28)
- Final Data Analysis Project (date: data viz on Wednesday May 5; Final report on Thursday May 13)
Handouts:
- Class notes are here: http://st47s.com/Math150/Notes/
- Youtube videos on getting started with R and RStudio: Introduction to RStudio
- R documentation / help
- Great tutorials through the Coding Club
- swirl package
- Google for R: http://www.rseek.org/
- R tutorial
- An Introduction to R, Venables & Smith
- R Language Definition, R Core Team
- Another tutorial, with exercises & solutions
- Mosaic Reference Guide, need to install the mosaic package
- A Student’s Guide to R; Horton, Pruim, Kaplan (click on “Raw” to download)
- Data Wrangling Cheatsheet: http://www.rstudio.com/resources/cheatsheets/
| Date | Topic | Section | HW Due:
Friday (midnight PT) to Gradescope |
Handouts / article link for class discussion | Warm-ups (due by 5pm PT next day, Gradescope) |
| Mon 1/25 | Intro | Warm-up 1: 1/25 | |||
| Wed 1/27 | t-tests | 2.2 | syllabus quiz (not an actual “quiz”): syllquiz.Rmd syllquiz.pdf | just read through once (don’t need to know all the details) | Warm-up 2: 1/27 |
| Mon 2/1 | SLR | 2.3 | Warm-up 3: 2/1 | ||
| Wed 2/3 | Fisher’s Exact Test | 6.2 – 6.4 | HW1 as Rmd | Warm-up 4: 2/3 | |
| Mon 2/8 | RR & OR | What is Efficacy? | Warm-up 5: 2/8 | ||
| Wed 2/10 | Chi-sq test | 6.5 – 6.6 | HW2 as Rmd | Warm-up 6: 2/10 | |
| Mon 2/15 | Logistic regression | 7.1 – 7.3 | read (at least) the paragraph headed “Bivariate Analyses” | Warm-up 7: 2/15 | |
| Wed 2/17 | 7.4-7.6 | HW3 as Rmd | Warm-up 8: 2/17 | ||
| Mon 2/22 | Logistic regression | 7.8 | Obesity in Children Plummets
(see Table 6) |
we didn’t have time! | |
| Wed 2/24 | 7.9 – 7.10 | HW4 as Rmd | Warm-up 9: 2/24 | ||
| Mon 3/1 | Model Building | Pfizer, AstraZeneca COVID vaccines are not yet approved for kids. How are clinical trials run for children? | Warm-up 10: 3/1 | ||
| Wed 3/3 | ROC | HW5 as Rmd | Warm-up 11: 3/3 | ||
| Mon 3/8 | Spring Break | ||||
| Wed 3/10 | Spring Break | ||||
| Mon 3/15 | Cross Validation | What about the argument of restaurant owners? | Warm-up 12: 3/15 | ||
| Wed 3/17 | review | not due:
Exam 1 |
No warm-up today | ||
| Mon 3/22 | Survival Analysis: KM | 9.1-9.4 | Michalowicz et al., NEJM 2006 | Warm-up 13: 3/22 | |
| Wed 3/24 | KM CI | 9.5 | Warm-up 14: 3/24 | ||
| Mon 3/29 | Log-Rank test | 9.6 | Lamure et al. EClinical Medicine 2020 | Warm-up 15: 3/29 | |
| Wed 3/31 | Hazard Functions | 9.8 | HW7 as Rmd | Warm-up 16: 3/31 | |
| Mon 4/5 | Cox PH model | What is behind an FDA stamp? | |||
| Wed 4/7 | Multiple Cox PH model | HW8 as Rmd | Warm-up 17: 4/7 | ||
| Mon 4/12 | Assessing PH | “Why Most Published Research Findings are False“, Ioannidis, PLoS Medicine, 2005 | CHD HR tables from Dupont | ||
| Wed 4/14 | Most published research is FALSE | 1.13 | HW9 as Rmd | Warm-up 19: 4/14 | |
| Mon 4/19 | Multiple Comparisons | First project assignment due: EDA & idea for “something new” | What does “no effect” mean?
Full article (no need to read the entire thing) |
no warm-up today | |
| Wed 4/21 | q-values | HW10 as Rmd | Warm-up 20: 4/21 | ||
| Mon 4/26 | Stopping Criteria | Pausing Trials
NYT 10/14/20 |
Warm-up 21: 4/26 | ||
| Wed 4/28 | Exam 2 | ||||
| Mon 5/3 | Poisson regression | 8 | Optional rough draft of Project due | Public health, vaccines, and laws | |
| Wed 5/5 | Project Data Viz | ||||
| Thurs 5/13 | Final Project due |
