BIOS601 Resources: 1 Intensity/Rate: Models/ Inference / Planning; 2 Intensities/Rates: Models/ Inference / Planning

1 INTENSITY/RATE  [ Go to 2 INTENSITIES/RATES, RATE DIFFERENCE and RATE RATIO  ]

Lecture Notes

• Rate / Incidence Density: Poisson
  
  
• Poisson <--> Exponential Waiting Times
  
• Poisson 'Generations' - graph
  
• Poisson 'Generations' - R code
• Accromath   Article   Diagram   R code

Examples of Variations in Counts

• Observations fitting the Poisson Distribution (from Feller's textbook)
• Horse kicks, anthrax, and the Poisson model for deaths [Gerry Hill]
• Deaths from Horsekicks--from von Bortkiewicz (1898) Data_and_Programs(.txt)
• The rate of audience fidget (Francis Galton)
• Double Trouble in Moose Jaw
   
• Births after 1965 New York City Blackout
  New York Times article
  Genesis Of A Misconception
   
• Accidents among Bus Drivers
• Postponement of Death Until Symbolically Meaningful Occasions
• Full Moon and Crime
• DAYLIGHT SAVINGS TIME AND TRAFFIC ACCIDENTS
• Impact sanitaire de la vague de chaleur en France survenue en août 2003 Rapport d'étape 29 août 2003
  1. Contexte et chronologie de la mise en place de diverses études
  2. Bref rappel des connaissances sur les effets sanitaires de la chaleur
  3. Caractéristiques de la vague de chaleur d'août 2003
  4. Evolution de l'épidémie et premi�re évaluation de son ampleur
  5. Présentation des différentes enqu�tes et des principaux résultats obtenus
  6. Bilan de l'impact de la vague de chaleur dans les autres pays
  Conclusion / Références bibliographiques / Annexes
• Number of in-hospital deaths at Edouard Herriot Hospital , and Daily Maximal Temperatures
  during summers of 2002 and 2003, Lyon, France. Vanhems P et al.
  New Eng J Med Nov 20, 2003, pp 2077-2078.
  article and
  data: heatwave_lyon.txt   heatwave_lyon.csv heatwave.sas   heatwave_lyon.do
   
  
• Extended Work Duration and Risk of Self-reported Percutaneous Injuries in Interns (2006)
    Effect on Patient Safety of a Resident Physician Schedule without 24-Hour Shifts (2020)
   
• quedata.txt
• CircumcisionHIV_Uganda.pdf
• UgandaTrial Data.txt
• chtable226.txt
• CircumcisionHIV_Kenya.pdf
   
  
• Alcohol as a risk factor for sudden infant death syndrome (SIDS) -- see New Year's Day

"Clusters" and other co-incidences

• Jumping to Co-incidences

Tables

• Poisson Probabilities
• Exact Poisson CI

Articles, Chapters, Notes - Methodological

• 'De Mensura Sortis' or 'On the Measurement of Chance' by A. de Moivre (1718,1738,1756, and 1712)
  Author(s): A. Hald, Abraham de Moivre and Bruce McClintock. International Statistical Review / Revue Internationale de Statistique, Vol. 52, No. 3 (Dec., 1984), pp. 229-262 Published by: International Statistical Institute (ISI)
• Recherches sur la probabilité des jugements en matière criminelle at en matière civile: by S.D. Poisson. 1837. See, in particular, section (81) beginning on page 205.
• On the error of counting with a haemocytometer: by STUDENT Biometrika 5(3) 1907
• (1910) LXXVI. The probability variations in the distribution of alpha particles The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science, 20:118, 698-707, DOI: 10.1080/14786441008636955. by E. Rutherford, H. Geiger & H. Bateman.
• Practical Applications of the Statistics of Repeated Events, Particularly to Industrial Accidents
  Ethel M. Newbold. Journal of the Royal Statistical Society, Vol. 90, No. 3 (1927), pp. 487-547
• Mathematical Distributions used in Common Tests, RA Fisher, 1935
• Poisson Distribution    |     Inferences from Counts Armitage et al.
• Rothman 1986. Ch 10 Fundamentals of Epidemiologic Data Analysis
• Rothman 1986. Ch 11 Analysis of Crude Data
• Rothman 2002. Chapter 7 Analyzing Simple Epidemiologic Data
• Walker Ch8: Estimation Analysis of Open Cohort Studies
• Exact confidence limits on a Poisson parameter: Notes by FDKLiddell (.gif)
• JH and AL. If Nothing Goes Wrong, Is Everything All Right? Interpreting Zero Numerators
• Randomness at the root of things 2: Poisson sequences [article from Physics Education]
• Simple exact analysis of the standardized mortality ratio FDK Liddell J Epi Comm. Health 37 85-88, 1984
  page 85 | page 86 | page 87 | page87
• The simplest statistical test: how to check for a difference between treatments SJ Pocock BMJ 2006
• Stigler, S. The Digital Approximation of the Binomial by the Poisson
  The American Statistician, February 2013, Vol. 67, No. 1 pages 57-59.
• Link between Poisson and Gamma/ChiSquare tail areas. Accromath. 2015.

Cancer Screening Trials

• Breast Cancer
  
  
• Lung Cancer
  
  ... X-Ray
  
  
  • Biometric design of the Mayo Lung Project for early detection and localization of bronchogenic carcinoma.
    Taylor WF, Fontana RS. Cancer. 1972 Nov;30(5):1344-7.
  • Some Results of Screening for Early Lung Cancer
    W.F. Taylor, R.S. Fontana, M.A. Uhlenhopp, and C.S. Davis. Cancer 47:1114-1120, 1981.
  • Lung Cancer Screening: The Mayo Program.
    R.S. Fontana; D.R. Sanderson; L.B. Woolner; W.F. Taylor; W.E. Miller; and J.R. Muhm.
    Journal of Occupational Medicine/Volume 28 No. 8/August 1986.
  • Lung Cancer Mortality in the Mayo Lung Project: Impact of Extended Follow-up
    P.M. Marcus, E.J. Bergstralh, R.M. Fagerstrom, D.E. Williams, R. Fontana, W.F. Taylor, P.C. Prorok.
    J Natl Cancer Inst 2000;92:1308-16.
    
    Statistical Exercises based on Mayo Lung Project
    See Exercises 0.1 part 2 (p.11); 0.12 (p.16); and 0.13 (p.16);
    
    
  ... CT
  
  
  • Early Lung Cancer Action Project: overall design and findings from baseline screening.
    Claudia Henschke et al. The Lancet. 1999.
  • Survival of patients with stage I lung cancer detected on CT screening.
    International Early Lung Cancer Action Program Investigators. NEJM. 2006.
  • The National Lung Screening Trial (NLST): Overview and Study Design
    Gatsonis et al. Radiology: Volume 258: Number 1, 2011.
  • Reduced Lung-Cancer Mortality with Low-Dose Computed Tomographic Screening NEJM 2011.
  • Lung Cancer Incidence and Mortality with Extended Follow-up in the National Lung Screening Trial.
    The National Lung Screening Trial Research Team, 2019.
  • Reduced Lung Cancer Mortality with Volume CT Screening in a Randomized Trial
    The Dutch-Belgian lung-cancer screening trial (Nederlands-Leuvens Longkanker Screenings Onderzoek [NELSON]). Published on January 29, 2020, at NEJM.org.
    
    
• Prostate Cancer
• Ovarian Cancer

Software, Data, Demos, Simulations, ...

• Poisson Process: Excel Macro
  { 'unprotect' Excel sheets if you wish to alter the layout .. under Tools menu -> Protection}
• Tire Ruptures during 7500Km Trip... R code     Java Applet
• Cell Occupancy... Randomly selected visits to 1000 cells [java applet]    
  1000 visits (mean 1/cell)    
  2000 visits (mean 2/cell)    
  6000 visits (mean 6/cell)    
  
• Exact confidence limits on a Poisson parameter: Excel worksheet
• Power for test of E = E_null vs E = E=_alt: Excel worksheet
• Analysis of Count data using SAS (PROC GENMOD) and Stata
• Rates_regressionR.txt [needlestick injuries, Que. death rates, Uganda RCT, CH table 22.6 via R, SAS and Stata]

2 INTENSITIES/RATES, RATE DIFFERENCE and RATE RATIO  [ Go to 1 INTENSITY/RATE  ]

Lecture Notes

• Comparisons of 2 Intensities: - models / inference / planning
  
  
• Notes on C&H Chapter 13 (Likelihoods for the Rate Ratio)
  
  
• R Code for 'Women are Safer Pilots' questions
  
   

Articles

• Cancer Risk among Children Born after Assisted Conception
  N Engl J Med 2013;369:1819-27.
  
  
• Cancer Incidence and Survival among Children and Adolescents
  United States SEER Program 1975-1995