Syllabus

Biostatistical Methods for Clinical Research II BIOSTAT208   

Location Codes: Courses noted as being at "CB" are located at China Basin Landing. Courses noted with other location codes (e.g. HSW, HSE, S, N, C, CL) are located at the UCSF Medical Center Parnassus campus

Date/Time Activity Topic/Content Faculty Locations
Tues 1/5/2010
10:30 AM-12:00 PM
Lecture

Introduction and Exploratory Analysis

Class organization; importance of data exploration; regression overview

Required Reading:

  1. Chapters 1-2, VGSM

Note/Slide Files: Biostat_208_duedates_2010.pdf (28 KB) Biostat_208_Syllabus-10.pdf (94 KB) lecture1-handout-4up.pdf (2208 KB) lecture1-handout.pdf (2243 KB)

Assignment:
Homework #1: Due Date: 01/26/10

Assignment Files: hw1-VGSM-problems.pdf (55 KB) hw1.pdf (55 KB)

Dataset Files: problem2-4.dta (1 KB) problem2-5.dta (1 KB) wcgs.dta (64 KB)

S ShiboskiCB 6702
Thurs 1/7/2010
10:30 AM-12:30 PM
Lab

Introduction

Assignment Files: lab1.pdf (137 KB)

Dataset Files: lab1.dta (2 KB)

S ShiboskiCB 6704
Tues 1/12/2010
10:30 AM-12:00 PM
Lecture

Multiple Linear Regression

Regression with a single binary or continuous predictor; Multiple regression

Required Reading:

  1. Chapter 3.2-3.3, VGSM
  2. Chapter 4.1-4.2, VGSM

Note/Slide Files: lecture2-handout-4up.pdf (424 KB) lecture2-handout.pdf (452 KB)

S ShiboskiCB 6702
Thurs 1/14/2010
10:30 AM-12:30 PM
Lab

Multiple Linear Regression

Assignment Files: lab2.pdf (100 KB)

Dataset Files: lab2.dta (3 KB)

S ShiboskiCB 6704
Tues 1/19/2010
10:30 AM-12:00 PM
Lecture

Categorical Predictors

Ordinal and nominal predictors; tests for trend

Required Reading:

  1. Chapter 4.3, VGSM

Note/Slide Files: lecture3-handout-4up.pdf (803 KB) lecture3-handout.pdf (785 KB)

S ShiboskiCB 6702
Thurs 1/21/2010
10:30 AM-12:30 PM
Lab

Categorical Predictors

Assignment Files: lab3-stata10.pdf (80 KB) lab3.pdf (81 KB)

Dataset Files: lab3.dta (7 KB)

S ShiboskiCB 6704
Tues 1/26/2010
10:30 AM-12:00 PM
Lecture

Confounding and Mediation

Confounding and mediation and adjustment

Required Reading:

  1. Chapter 4.4-4.5, VGSM

Optional Reading:

  1. Cole & Hernan, IJE, 2002
  2. Hernan, Epidemiology, 2004

Note/Slide Files: lecture4.4up.pdf (302 KB) lecture4.pdf (233 KB)

E VittinghoffCB 6702
Tues 1/26/2010
12:00 PM-1:00 PM
Other

Homework session

S ShiboskiCB 6702
Thurs 1/28/2010
10:30 AM-12:30 PM
Lab

Confounding and Mediation

Assignment Files: lab4.pdf (58 KB)

STATA Files: lab4.dta (153 KB)

E VittinghoffCB 6704
Tues 2/2/2010
10:30 AM-12:00 PM
Lecture

Interaction

Conceptual introduction, product terms, testing for interactions, lincom statements

Required Reading:

  1. Chapter 4.6, VGSM

Note/Slide Files: lecture5-4up.pdf (306 KB) lecture5.pdf (228 KB)

Assignment:
Homework #2: Due Date 2/9/10

Assignment Files: hwk2.pdf (42 KB)

STATA Files: hwk2.dta (39 KB)

E VittinghoffCB 6702
Thurs 2/4/2010
10:30 AM-12:30 PM
Lab

Interaction

Assignment Files: lab5.pdf (81 KB)

STATA Files: lab5.dta (61 KB)

E VittinghoffCB 6704
Tues 2/9/2010
10:30 AM-12:00 PM
Lecture

Model Diagnostics

Linearity, normality, constant variance; influential points

Required Reading:

  1. Chapter 4.7, VGSM

Note/Slide Files: lecture6-4up.pdf (3734 KB) lecture6.pdf (2854 KB)

E VittinghoffCB 6702
Tues 2/9/2010
12:00 PM-1:00 PM
Other

Homework session

Note/Slide Files: hwk2.review.pdf (189 KB)

S ShiboskiCB 6702
Thurs 2/11/2010
10:30 AM-12:30 PM
Lab

Model Diagnostics

Assignment Files: lab6.pdf (92 KB)

STATA Files: lab6.dta (18 KB)

E VittinghoffCB 6704
Tues 2/16/2010
10:30 AM-12:00 PM
Lecture

Predictor Selection

Causal diagrams, three inferential goals; number of predictors, colinearity

Required Reading:

  1. Chapter 5, VGSM

Optional Reading:

  1. Hernan et al, Epidemiology, 2004
  2. Altman & Royston, Statistics in Medicine, 2000
  3. Pencina et al, Statistics in Medicine, 2008
  4. Vickers et al, Medical Decision Making, 2006
  5. Harrell et al, Statistics in Medicine, 1996
  6. Peduzzi et al, Journal of Clinical Epidemiology, 1996

Note/Slide Files: lecture7-4up.pdf (331 KB) lecture7.pdf (291 KB)

Assignment:
Homework #3: Due Date 2/23/10

Assignment Files: hwk3.pdf (54 KB)

STATA Files: hwk3.dta (15 KB)

E VittinghoffCB 6702
Thurs 2/18/2010
10:30 AM-12:30 PM
Lab

Predictor Selection

Assignment Files: lab7.pdf (76 KB)

STATA Files: lab7.dta (153 KB)

E VittinghoffCB 6704
Tues 2/23/2010
10:30 AM-12:00 PM
Lecture

Binary Outcome Data

Contingency tables; binary outcomes; measures of association; logistic model

Required Reading:

  1. Chapter 3.4, VGSM
  2. Chapter 6.1, VGSM

Note/Slide Files: lecture8-handout-4up.pdf (856 KB) lecture8-handout.pdf (880 KB)

Assignment:
Homework #4: Due Date 3/9/10

Assignment Files: hwk4.pdf (96 KB)

STATA Files: icu.dta (17 KB)

S ShiboskiCB 6702
Tues 2/23/2010
12:00 PM-1:00 PM
Other

Homework session

S ShiboskiCB 6702
Thurs 2/25/2010
10:30 AM-12:30 PM
Lab

Binary Outcome Data

Assignment Files: lab8.pdf (94 KB)

STATA Files: lab8.dta (174 KB)

S ShiboskiCB 6704
Tues 3/2/2010
10:30 AM-12:00 PM
Lecture

Multiple Logistic Regression

Multiple logistic regression; confounding; interaction

Required Reading:

  1. Chapter 6.2.1-6.2.3, VGSM

Note/Slide Files: lecture9-handout-4up.pdf (667 KB) lecture9-handout.pdf (692 KB)

S ShiboskiCB 6702
Thurs 3/4/2010
10:30 AM-12:30 PM
Lab

Multiple Logistic Regression

Assignment Files: lab9.pdf (103 KB)

S ShiboskiCB 6704
Tues 3/9/2010
10:30 AM-12:00 PM
Lecture

Prediction and Model Diagnostics

Prediction; model assessment; outliers; goodness of fit

Required Reading:

  1. Chapter 6.2.4-6.2.5 & Chapter 6.4, VGSM

Note/Slide Files: lecture10-handout-4up.pdf (2143 KB) lecture10-handout.pdf (2154 KB)

Assignment:
Homework #5: Due Date 3/16/10

Final Exam Due Date: 3/19/10

S ShiboskiCB 6702
Tues 3/9/2010
12:00 PM-1:00 PM
Other

Homework session

S ShiboskiCB 6702
Thurs 3/11/2010
10:30 AM-12:30 PM
Lab

Prediction and Model Diagnostics

Assignment Files: lab10.pdf (113 KB)

S ShiboskiCB 6704
Tues 3/16/2010
10:30 AM-12:00 PM
Lecture

Case Control Studies

Case-control study; conditional logistic regression; generalized linear models

Required Reading:

  1. Chapter 6.3 & 6.5 VGSM

Note/Slide Files: lecture11-handout-4up.pdf (520 KB) lecture11-handout.pdf (544 KB)

S ShiboskiCB 6702