Course Files and Examples, Stat141
Class 9/26
1. Course Introduction and Overview
2. In the news:
Opening Day Exemplars
a. Was Darwin just messin' with us? Public Acceptance of Evolution, Science 11 August 2006
Vol. 313. no. 5788, pp. 765 - 766 Jon D. Miller, Eugenie C. Scott, Shinji Okamoto supplemental materials
Topics: ordered categorical data, regression for explanation?
b. Can Bees tell time? Interval Timing by an Invertebrate, the Bumble Bee Bombus impatiens
Current Biology 16, 1636–1640, August 22, 2006
Topics: waiting time data, two-group comparisons (t or F tests)
c. Plan B contraception. Direct access to emergency contraception through pharmacies and effect on unintended pregnancy and STIs: a randomized controlled trial. Raine et al. JAMA.2005; 293: 54-62.
Topics: randomized controlled field trials, odds ratio outcomes
d. Couch potatoes and rats. Elevated hypothalamic orexin signaling, sensitivity to
orexin A, and spontaneous physical activity in obesity-resistant rats.
Am J Physiol Regul Integr Comp Physiol 291: R889–R899, 2006.
Topics: comparing groups (phenotypes)
e. Reduced Antibody Responses to Vaccinations in Children Exposed to Polychlorinated Biphenyls
PLoS Medicine www.plosmedicine.org August 2006 | Volume 3 | Issue 8 | e311
Topics: regression, dose-response
3. Getting started. Describing Distributions: SW text Chap 2; esp secs 2.3, 2.4, 2.5, 2.6, 2.7
Class handouts:
Brain weight data from SW text ex 2.12, pp.22-23
MAO data from SW text ex 1.4, pp.3-4
Class 9/28
Continue: Describing distributions (handouts and content from 9/26)
SW text Chap 2; esp secs 2.3, 2.4, 2.5, 2.6, 2.7. Verzani 2.2, 2.3, 3.2 (comparing groups)
Also, Transformations to change shape (SW 2.7); Count and Category Data SW ex1.5, sec 2.1, exs 2.1,2.2,2.5; Verzani 2.1
In the news:
College weight gain: time 1, time 2 data
College: A weighty endeavor? 'Freshman 15' may be a myth, but many students pack on pounds. San Francisco Chronicle Tuesday, September 26, 2006
Empirical studies (available through pubmed)
Changes in body weight and fat mass of men and women in the first year of college: A study of the "freshman 15".
Hoffman DJ, Policastro P, Quick V, Lee SK
J Am Coll Health. 2006 Jul-Aug;55(1):41-5. Rutgers press release
Freshman 15: valid theory or harmful myth? Graham MA, Jones AL. J Am Coll Health. 2002 Jan;50(4):171-3.
Susan Albers, cited as "a former postdoctoral fellow at Stanford" Mindful Eating
Class handouts:
Cricket Singing Times data from SW text ex 2.19, pp.29
Biological aside: pigeons do logs, so can you. Pigeon-brained birds can think in logarithms
Evidence that pigeons represent both time and number on a logarithmic scale
Behavioural Processes Volume 72, Issue 3 , 1 June 2006, Pages 207-214
Class 10/3
Count and Category Data SW ex1.5, sec 2.1, exs 2.1,2.2,2.5; Verzani 2.1
In the news:
1. Scientists explain why insects don't get fat Fat, thin caterpillars are studied
Evolving resistance to obesity in an insect Proceedings of the National Academy of Science, Warbrick-Smith et al. 103 (38): 14045.
2. HIV measurement is questioned
Predictive value of plasma HIV RNA level on rate of CD4 T-cell decline in untreated HIV infection.
JAMA. 2006 Sep 27;296(12):1498-506.
3. Stanford scientist shares Nobel Prize in medicine Nobel Prize for Medicine: Silence is golden for US laureates
Nobel site (primer on RNAi)
Class handouts and materials:
Count Data--Prussian Army Horse Kicks.
Horseshoe Crab Satellites data from Agresti
Verzani text, Albotross count data downloading packages
Extra calcs 10/3 cricket dichotomization, moments for grouped crab data, evolution categorical data
Class 10/5
Introduction to probability calculations, SW text secs 3.1-3.5; Verzani 5.1
In the news:
1. Parasitic Weed Seems to Smell Its Prey
Parasitic Weed Uses Chemical Cues to Find Host Plant, Elizabeth Pennisi
Science 29 September 2006 313: 1867 (in News of the Week)
Volatile Chemical Cues Guide Host
Location and Host Selection by
Parasitic Plants Science 29 September 2006
Supporting Online Material for
Volatile Chemical Cues Guide Host Location and Host Selection by Parasitic Plants Justin B. Runyon, Mark C. Mescher, Consuelo M. De Moraes
2. Mother's Voice Better Than Smoke Alarm Noise.
Comparison of a Personalized Parent Voice Smoke Alarm With a Conventional Residential Tone Smoke Alarm for Awakening Children
Gary A. Smith, MD, DrPH, Mark Splaingard, MD, John R. Hayes, PhDa and Huiyun Xiang, MD, PhD, MPH, Pediatrics Vol. 118 No. 4 October 2006, pp. 1623-1632
3. another Stanford Nobel (chem).... US scientist Roger Kornberg wins Nobel, 47 years after his father
Nobel site (Molecular basis of eukaryotic transcription)
Class handouts and materials:
Random samples and Probability
false-positive, false negative Medical Diagnosis see SW text section ex3.17
Class 10/10
Discrete Random Variables: Bernoulli Trials and Binomial Distribution; Poisson Distribution and Count Data; SW text 3.7-3.8; Verzani 5.1.1, 5.2.2
In the news:
1. Study says no video games on school nights Association Between Television, Movie, and Video Game Exposure and School Performance Iman Sharif, MD, MPHa, James D. Sargent, MDb PEDIATRICS Volume 118, Number 4, October 2006.
2. Estimated Prevalence of Compulsive Buying Behavior in the United States Koran LM, Faber RJ, Aboujaoude E, Large MD, Serpe RT. Am J Psychiatry. 2006 Oct;163(10):1806-12
Class handouts and materials:
1. Binomial Distribution Examples and Binomial-Poisson approximation
2. Poisson Distribution for Count Data. link1 link2 link3
Class Handout was an annotated "link 2" plus Poisson fit to horsekick data
3. Discrete Distribution examples
Class 10/12
Continuous Distributions for measured data (Normal, Uniform, Exponential). SW text 3.6, 4.1-4.3; Verzani 5.1.2, 5.2.1-5.2.2
Probability calculations with Normal distribution. SW text 4.3.
Binomial approximation, SW text 4.5 and 5.5; Verzani 6.1
In the news:
1. Just say, what? Marijuana's Active Ingredient May Slow Progression Of Alzheimer's Disease
Scripps Institute press release: Marijuana's Active Ingredient Shown to Inhibit Primary Marker of Alzheimer's Disease
A Molecular Link Between the Active Component of Marijuana and Alzheimer's Disease Pathology, Molecular Pharmaceutics
2. It's not easy being random.
Oh no, not Steely Dan again Slashdot discussion The Perception of 'Random' on the iPod
3. Another reason to avoid Chemo. Chemotherapy linked to lasting brain change
Altered frontocortical, cerebellar, and basal ganglia activity
in adjuvant-treated breast cancer survivors 5-10 years after
chemotherapy Breast Cancer Res Treat
Class handouts:
1. Continuous Distributions (including keepsake)
2. Calculation of Moments for Discrete and Continuous Distributions: Mathematica notebook pdf of notebook
3. Normal Distribution calculations, Assessing Normality including qq-plots
4. normal approximation to discrete distrib, continuity correction
Class 10/17
Review: probability calculations, continuous distributions
Assessing normality, q-q plots. SW text 4.4, Verzani 3.2.4;
Sampling Distributions of sample means: dichotomous (proportions) and quantitative observations. Central Limit Theorem
SW text 5.1-5.4; Verzani book, 5.1.3, 5.1.4, 5.3, 6.1
In the news:
Don't blame the prof, blame the pork rinds:
The greater your weight, the lower your IQ, say scientists Obese people lose IQ through 'Homer Simpson effect'
Slashdot discussion: French Scientists Link Higher BMI with Lower IQ
Relation between body mass index and cognitive function in healthy middle-aged men and women
Neurology 2006 67: 1208-1214.
Class handouts:
Exponential distribution materials: Wolfram Mathworld Wikipedia
data for qqplot example fruit moisture, SW ex 4.8
Distribution of Sample Means: How do sample means behave?
Class 10/19
Continue Central Limit Thm examples and calculations;
Begin: Inference for a single mean (including proportions): Confidence Intervals and Hypothesis tests.
SW text 6.1-6.3, 6.5-6.7; paired samples (including nonparametric tests) SW Ch.9;
Verzani book, 7.1-7.3, 7.5.3, 7.6 ; 8.1-8.4, 8.6.2
In the news:
1. Another reason not to spring break in North Korea: Study finds thyroid damage from nuke tests
2. Does Television Cause Autism?
Class handouts:
Inference for a single mean (including paired data) squirrel data, SW ex 9.6
Inference for a single mean: paired data, virus example mengovirus SW ex 9.10 data
Class 10/24
Continue: Inference for a single mean (including proportions): Confidence Intervals and Hypothesis tests.
inference for single mean: SW text 6.1-6.3, 6.5, 6.7, Verzani, 7.1, 7.3 8.2,8.3; paired samples SW Ch.9, Verzani, 7.5.3; 8.6.2.
proportions: SW 6.6 (ignore "p-tilda"), Verzani 7.2,8.1
In the news:
1. Complete Darwin works put online The Complete Work of Charles Darwin Online - University of Cambridge
2. Job at PC plant may raise risk of cancer death
Mortality among US employees of a large computer manufacturing company: 1969-2001, Richard W Clapp, Environmental Health 2006, 5:30
Class handouts:
Inference for a single mean and proportions squirrel data, SW ex 9.6
Class 10/26
Single mean: nonparametric alternatives
Begin two sample (treatment/control) comparisons, inference procedures, SW Ch 7, Verzani 7.5.2, 8.6.
In the news:
Scientists prove that parts of cell nuclei are not arranged at random
The Transcriptional Regulator CBP Has Defined Spatial Associations within Interphase Nuclei
Kirk J. McManus, David A. Stephens, Niall M. Adams, Suhail A. Islam, Paul S. Freemont, Michael J. Hendzel , PLoS Computational Biology, Published October 20, 2006.
Class handouts:
Inference for two-sample comparisons Two-sample(treatment/control)inference: t-test, nonparametric alternatives (Mann-Whiney, Duckworth)
ancy data SW ex7.7
Additional data sets: rats sniffing glue,
tuolene data SW ex 7.9-7.11 soil respiration SW ex 7.17
Short description of Duckworth and history (Dick Deveaux text pp.29-30)
Slides recapping nonparametric methods Courtesy of Department of Environmental and Plant Biology, Ohio University, Athens Ohio
Class 10/31
Further examples: two sample (treatment/control) comparisons, inference procedures, SW Ch 7, Verzani 7.5.2, 8.6, 9.3.1 (Kolmogorov-Smirnov)
Research Design: Overview, value of experiments, Causal inference, Association vs Causation, SW Ch 8. (esp 8.1-8.3, easy reading)
Research Design: Sample Size Calculations. SW 6.4, 7.8, App7.1.
In the news:
1. Supply your own tagline. Testosterone Tumbling in American Males Men's Testosterone Levels Down: Levels Are Still Within the Normal Range, Boston Study Shows
Thomas G Travison, Andre B Araujo, Amy B O'Donnell, Varant Kupelian, and John B McKinlay
A population-level decline in serum testosterone levels in American men
J Clin Endocrinol Metab October 24, 2006 doi:10.1210/jc.2006-1375
2. Study Sees Gain on Lung Cancer NY Times 10/26
Survival of Patients with Stage I Lung Cancer Detected on CT Screening, New England Journal of Medicine Volume 355:1763-1771 October 26, 2006
Class Materials:
Class handout materials Oct 31
Research paper for urea synthesis data: Comparative Analyses of Pretest-Posttest Research Designs,
Donna R. Brogan; Michael H. Kutner, The American Statistician, Vol. 34, No. 4. (Nov., 1980), pp. 229-232. JSTOR link
urea synthesis, BK data
another nonparametric test: ks.test(): Kolmogorov-Sminorv test (stats)
A general document that includes K-S examples: Fitting distributions with R
Background reading on research design.
1. Classic paper on Medical experimentation.
Statistics and Ethics in Surgery and Anesthesia. John P. Gilbert; Bucknam McPeek; Frederick Mosteller Science, New Series, Vol. 198, No. 4318. (Nov. 18, 1977), pp. 684-689.
JTSOR link
2. From Stat209 Cause and Effect Examples:
a. Prayer, more harm than good?
From Harvard Study calls prayer for sick people ineffective Rate of problems after surgery unchanged by act
Study of the Therapeutic Effects of Intercessory Prayer (STEP) in cardiac bypass patients: A multicenter randomized trial of uncertainty and certainty of receiving intercessory prayer American Heart Journal, Volume 151, Issue 4, Pages 934-942 (April 2006). [compliance note]
Prior Duke flip flop
b. Carbonated soft drinks and Cancer Yale press release News report: Soda-Cancer Link Revealed as Myth
Journal of the National Cancer Institute JNCI paper Carbonated Soft Drink Consumption and Risk of Esophageal Adenocarcinoma
Mayne et al. J Natl Cancer Inst.2006; 98: 72-75
c. Is TV bad or is it bad parenting? Attention Deficit Disorder and TV
2004 version : Pediatrics. 2004;113:708-713. Christakis DA, Zimmerman FJ, DiGiuseppe DL, McCarty CA. Early television exposure and subsequent attentional problems in children. Publication summary press release news report audio NPR interview interview transcript and publication
2006 reversal? Pediatrics. March 2006. Stevens T and Mulsow M. There is no meaningful relationship between television exposure and symptoms of attention-deficit hyperactivity disorder. Pediatrics. 2006; 117(3):665-672. News Reports: TV may not cause kids' attention disorders Researchers say TV is not to blame for ADHD TV may not cause kids' attention disorders: study. Good general commentary in Slate Feb '06
3. Another textbook treatment (Dick DeVeaux)
Power and Sample Size Calculations: Some resources:
JAMA review article: Statistical Power, Sample Size, and Their Reporting in Randomized Controlled Trials (JAMA. 1994;272:122-124)
Resources on power calculations:
Graphpad R-helpfile: Power calculations for one and two sample t tests R Tutorial: Calculating The Power Of A Test
Class 11/2
Comparing Many Means: Introduction to Analysis of Variance, single classification. SW Ch. 11.1-11.5, 11.8 .
One way anova and post-hoc multiple pairwise comparisons
In the news:
1. fat drunk mice. Big doses of red wine extract help obese mice stay fat and happy
11/1/2006 USA TODAY
Resveratrol improves health and survival of mice on a high-calorie diet Nature, Advance online publication.
2. more testosterone. Guns Up Testosterone, Male Aggression
Guns, Testosterone, and Aggression: An Experimental Test of a Mediational Hypothesis
Klinesmith, Jennifer; Kasser, Tim; McAndrew, Francis T,
Psychological Science. Vol 17(7), Jul 2006, pp. 568-571.
note: if that link doesn't work from your machine, go through SU libraries using
PsycArticles and PsycInfo search
Class Materials:
Class handout Nov 2, One-way anova examples
Data for Nov2 Oberlin dance data
Full Moon mental health
Class 11/7
Continue: Comparing Many Means: Introduction to Analysis of Variance, single classification. SW Ch. 11; Verzani Ch 11.
One way anova and post-hoc multiple pairwise comparisons; SW 11.4,11.8, Verzani
Power and sample size calculations
Nonparametric alternatives, Verzani 11.1.4
In the news:
1. Be cool, especially if you are a mouse. Cool down -- you may live longer
Transgenic Mice with a Reduced Core Body Temperature Have an Increased Life Span Science 3 November 2006: 825-828.
2. Eat fish, now. 90% of the ocean's edible species may be gone by 2048
Impacts of Biodiversity Loss on Ocean Ecosystem Services
Science 3 November 2006: 787-790.
Class Materials:
Class handouts Nov 7, One-way anova examples
squid respiration power calculations nonparametric alternative, Kruskal-Wallis
Data for Nov7 Squid respiration data Clergy mental health
Power and sample size resources:
JAMA review article: Statistical Power, Sample Size, and Their Reporting in Randomized Controlled Trials (JAMA. 1994;272:122-124)
Resources on power calculations:
Graphpad R-helpfile: Power calculations for balanced one-way analysis of variance tests Lesson 21: Power and Sample Size in ANOVA courtesy of West Point
Class 11/9
Randomized Blocks and Factorial Designs. SW 8.4, 11.6, Verzani 11.4 (end TH2)
Introduction to analysis of categorical data, 1 X c tables (univariate) SW text Ch. 10, Verzani 9.1
In the news:
1. Go Darwin? Japanese Researchers Find Dolphin With 'Remains of Legs'
2. not statististical, but fun. iGEM, international genetically engineered machines competition.
3. Sapolsky and stress. Scientists use gene therapy to improve memory and learning in animals Nov. 8 issue of the Journal of Neuroscience
4. more mouse abuse. Antioxidants: New Kid On The Block For Pain Relief?
Antioxidants attenuate multiple phases of formalin-induced nociceptive response in mice Behavioural Brain Research, Volume 173, Issue 2, 16 October 2006, Pages 211-216
A. Hacimuftuoglu, C.R. Handy, V.M. Goettl, C.G. Lin, S. Dane and R.L. Stephens, Jr.
Class Materials:
factorial design analysis of fullmoon data (class 11/7)
randomized blocks, factorial designs
Randomized blocks ex: alfalfa data factorial design ex soybean data interaction plot for soybean
Class 11/14
Introduction to analysis of categorical data, 1 X c tables (univariate) ; r X c tables (bivariate); chi-square tests, Fisher's exact test.
SW text Ch. 10, sections 10.1-10.7, 10.10; Verzani 9.1,9.2
In the news:
Could our big brains come from Neanderthals?
Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage PNAS published November 7, 2006
Class handouts:
Introduction to analysis of categorical data
Comparing proportions (2x3 table) ex: villi data
Readings on Phillips and death dates:
Can the Famous Really Postpone Death? JAMA, 1990 Postponement of death until symbolically meaningful occasions
Class 11/16
Categorical Data continued. SW text 10.8, 10.9.
Odds ratios and relative risks;
Paired data (McNemar);
Bayes Thm calculations;
Simpson's paradox and higher dimensional tables.
In the news:
1. Angioplasty no help for heart attack victims who wait
Coronary Intervention for Persistent Occlusion after Myocardial Infarction New England Journal of Medicine
2. Doctors using Google to diagnose illnesses
Googling for a diagnosis--use of Google as a diagnostic aid: internet based study
Hangwi Tang, Jennifer Hwee Kwoon Ng
BMJ, (published 10 November 2006)
3. Beware: 'Tis the season to fall from ladders
Class handouts:
Trends in proportions; Odds ratios and relative risks; Paired data (McNemar's test); Simpson's paradox and higher dimensional tables,
1971 Draft Lottery data, 12x3 table chi-square test (in Minitab)
The vcd Package Visualizing Categorical Data. November 2, 2006 Version 1.0-0
R-Session example: installing and loading vcd package
Class 11/28
Association among measured variables
Introduction to correlation (for measuring associations) and regression (for fitting, and prediction).
SW text 12.1-12.6, Verzani Ch.3, Ch.10
In the news:
1. Evolution experiments. Evolution's "Driving Force" Shifts Based on Behavior, Study Says
Rapid Temporal Reversal in Predator-Driven Natural Selection Science 17 November 2006: 1111.
2. Speed dating. In speed-dating, size really matters
Can Anyone be "The" One? Evidence on Mate Selection from Speed Dating, Michele Belot, Marco Francesconi, University of Essex
3. Panda porn. Porn sparks panda baby boom in China
Class handouts:
Introduction to correlation and regression figures for examples
data sets: platelet.dat SW p.550 ratspeed.dat amphetamine data SW ex 12.1
Class 11/30
Regression and prediction cont'd.
Measured outcomes (straight-lines and ploynomials) and Dichotomous outcome (logistic regression). SW text, sec 12.7, Verzani 10.3, 12.1
In the news:
1. Don't believe everything you read, in Science Panel recommends changes at Science
Responding to Fraud, 1 December 2006, Science 314, 1353 (2006)
2. Fly-fighting. fruitless regulates aggression and dominance in Drosophila, Nature Neuroscience Advance Online Publication
Eleftheria Vrontou, Steven P Nilsen, Ebru Demir, Edward A Kravitz & Barry J Dickson
Published online: 19 November 2006 | doi:10.1038/nn1809
3. Nerve fibers need specific growth factor chemical to form connections within the brain
A role for neurotrophin-3 in targeting developing cholinergic axon projections to cerebral cortex Neuroscience, Volume 143, Issue 2 , 1 December 2006, Pages 523-539
Class handouts:
Inference for regression models, Logistic regression logistic model fit
data sets: donner.dat Donner Party Survival by Gender and Age
Dead Week Tuesday, class 12/5
Consolidation and Review: Additional examples for Correlation and Regression, Odds Ratios.
In the news:
Stealthy Insect Sensor Project, Los Alamos Trained bees can sniff bombs, scientists say
Class handouts:
Additional examples of regression models: More logistic regression; Data transformations and fitting polynomials.
plots for tumor data ex
plots for Esophageal cancer data ex
data sets: tumor.dat Tumor growth data
lymph.dat Esophageal cancer data , SW ex 12.44, table 12.9 p.583.
Dead Week Thursday, class 12/7
Course Review and Summary. SW Chap 13 examples. Discuss HW6, Exam 3 for Finals Week.
SW chapter 13 data examples:
Example 13.1 plant growth hormones
Example 13.2 whale swimming, tail-beating
Example 13.4 fried fruit flies