IGP 304: Statistics for Biomedical Research (Spring 2010)

Instructors

Grading Assistant

Lectures

  • Tuesdays 10:00-11:30; D-2221 Medical Center North
  • Thursday 10:00-11:30; D-2221 Medical Center North
  • Exceptions:

Help sessions: by request to instructor

Class News

Prerequisites

  • Good command of standard algebra
  • Excellent skills in storing, moving, and organizing computer files and using a text editor

Discussion Board | Biostatistics Clinics (Friday is for basic science)

Syllabus | http://biostat.mc.vanderbilt.edu/survey/?94085624 Pre-course Survey

Textbook and reading materials

Software

Datasets for homework assignments

Homework and exams

  • Note: send your work directly to the grading assistant by e-mail or campus mail. See above for addresses.
  • Homework 1 using Rosner's FEV data
    • Questions 1-3 are due Friday, Jan 23
    • Questions 4-6 are due Friday, Jan 30
  • Homework 2 (Due Friday, Feb 13)
  • Homework 3 (Due Friday, Feb 27)
  • Homework 4 (Assigned 20Mar09 due 27Mar09)
  • NEW Homework 5 (due Apr 24)
  • Assignments from last year
    • Homework 3 (assigned Feb 19 due Feb 26)
    • Midterm Exam (assigned Feb 28 due Mar 13 9am in S-2323 Medical Center north or e-mailed directly to grading assistant)
    • Quiz 3 (take home handed out Mar 20 due 10a Apr 1 to grading assistant)
    • Homework 4 (due 4/15)
    • Some solutions to homework problems and to the midterm. Note: The computer code provided in the solutions is meant just to show how to do certain "manual" calculations in R. You can do these calculations any way you want.
    • Final Exam (due 9am 28 April to Chris; questions to discussion board only)
    • Extra Project

Lectures

  Date To read/do before class Topics Instructor
1 01/07 (Th) Get the textbook and optionally download R and install the Rcmdr package or RExcel Course description and overview; software FH
2 01/12 (Tu) H 1-2.2; EMS 1-2; SN 15 Presentation of numerical data; Data import and entry; data types; spreadsheets from hell and heaven; 10 Data Entry Commandments FH
3 01/14 (Th) H 2.2-2.5; EMS 3-4; LHSP Is statistics hard? Descriptive/exploratory analysis; graphics FH
4 01/19 (Tu) R 3.1-3.4, 3.8; EMS 5; normal distribution calculator Intro to probability; normal distribution FH
5 01/21 (Th) R 5.5;R 6.1-6.4 The normal distribution Normal distribution; estimation; intro to study design; regression to the mean FH
6 01/26 (Tu) R 6.5-6.7; H 3.4.3; demonstration; CI applet Estimating the sample mean; t distribution; confidence interval for a mean; sampling distribution of the sample standard deviation FH
7 01/28 (Th) R 6.4,13.10 Experimental Design Presentation Experimental Design; Quiz 2 FH
8 02/04 (Th) R 6.5, 6.11, CI applet, H 3.4.3-3.4.4 Distributions; Experimental Design; Sample size for a given precision (1-sample mean); Interpreting confidence intervals FH
9 02/9 (Tu) R 7.1-7.8, H 3.1-3.4.1 Hypotheses; branches of statistics; Hypothesis tests: Introduction, errors, and one-sample inference FH
10 02/11 (Th) R 7.10, 7.12-7.13, 8-8.5, H 3.4.2, 3.6-3.7.1 [skip 3.5 for now] Power and sample size; more about confidence intervals; paired data; two-sample test for means FH
11 02/16 (Tu) R 8.8, 8.10, H 3.7 Two-sample tests for means, continued; FH
12 02/26 (F) H 3.8-3.10, H 3.5, R 6.8, 7.10 Problems with hypotheses and P-values; how to present results; extended examples of two-sample and one-sample t-tests; one-sample methods for proportions/probabilities FH
13 03/05 (F) H 4, R 10.1-10.3, 10.5-10.6, 10.9, 13.3 PS software; Sample size for two proportions using PS Two-sample methods for proportions/probabilities; Quiz 3 FH
14 03/12 (F) H 4.9; H 5, R 9 Comprehensive example comparing 2 proportions; Non Parametric Methods; Wilcoxon Signed rank test; Wilcoxon-Mann-Whitney two-sample rank sum test FH
15 03/19 (F) H 6; R 11.1, 11.7, 11.8, 11.12; observer variability Linear and rank correlation; assessing agreement FH
16 03/26 (F) R 12; H 8 Analysis of Variance (ANOVA) FH
17 04/02 (F) H 7; R 11 Simple and multiple regression models FH
18 04/9 (F) H 10; MeasureChange Quiz 4 ; Measuring change and transformations FH
19 04/16 (F) ManuscriptChecklist Last Class Review, answer questions related to final homework FH
  04/23 (F) No class Homework 5 Due FH


Topic attachments
I Attachment Action Size Date Who Comment
PSforProportions.pdfpdf PSforProportions.pdf manage 317.5 K 27 Mar 2008 - 07:31 ChrisSlaughter Using the PS software to calculate sample size for two proptions example
SampleSizePrecisionExample.pdfpdf SampleSizePrecisionExample.pdf manage 33.5 K 15 Apr 2008 - 09:27 ChrisSlaughter Example of sample size and precision for binary outcomes
binomial.pdfpdf binomial.pdf manage 226.5 K 25 Mar 2008 - 11:53 ChrisSlaughter Binomial probabilities for n=3 or 6 and p=.9
chisqr-Rcmdr.pdfpdf chisqr-Rcmdr.pdf manage 206.6 K 01 Apr 2008 - 09:10 ChrisSlaughter Screenshots for using R commander to do Chi2 and Fisher's tests
dox.rm.jcs.pdfpdf dox.rm.jcs.pdf manage 198.9 K 01 Apr 2008 - 12:47 ChrisSlaughter Experimental Design presentation
extranotes-proportions.pdfpdf extranotes-proportions.pdf manage 284.7 K 26 Mar 2008 - 15:36 ChrisSlaughter Scan of hand-written notes to cover CIs and hypothesis tests for a single proportion
logistic.linear.compare.pdfpdf logistic.linear.compare.pdf manage 1003.6 K 03 Apr 2008 - 12:21 ChrisSlaughter Comparison of interpretation for linear regression and logistic regression model
logistic.output.pdfpdf logistic.output.pdf manage 61.5 K 01 Apr 2008 - 09:11 ChrisSlaughter Output from a logistic regression model examining low birth weight
sepsis.csvcsv sepsis.csv manage 113.4 K 05 Feb 2008 - 14:47 ChrisSlaughter sepsis dataset for homework
Topic revision: r133 - 08 Mar 2015, FrankHarrell
 

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