Wiki source code of Event-history analysis, fall 2008
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| author | version | line-number | content |
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| 1 | = Event-history analysis, fall 2008 = | ||
| 2 | |||
| 3 | === Lecturers === | ||
| 4 | |||
| 5 | [[Kari Auranen>>doc:mathstatHenkilokunta.Auranen, Kari]] | ||
| 6 | [[Sangita Kulathinal>>doc:mathstatHenkilokunta.Kulathinal, Sangita]] | ||
| 7 | |||
| 8 | === Scope === | ||
| 9 | |||
| 10 | 6-8 cu. | ||
| 11 | |||
| 12 | === Type === | ||
| 13 | |||
| 14 | Advanced studies. | ||
| 15 | |||
| 16 | === Prerequisites === | ||
| 17 | |||
| 18 | Basic skills in statistics and programming. | ||
| 19 | |||
| 20 | === Lectures === | ||
| 21 | |||
| 22 | Weeks 36-38, September 1-5, 8-10, 15-16 from 09.00 to 13.00. | ||
| 23 | |||
| 24 | Place: September 1, 2, 4, 5, 8, 9, 15, 16 room B120; September 3, 10 room C323. Computer class exercises in room C128. | ||
| 25 | |||
| 26 | === Lecture summaries === | ||
| 27 | |||
| 28 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/day1-l1.pdf>>url:http://www.rni.helsinki.fi/~~kja/day1-l1.pdf||shape="rect"]] | ||
| 29 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/day2-l2.pdf>>url:http://www.rni.helsinki.fi/~~kja/day2-l2.pdf||shape="rect"]] | ||
| 30 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/day3-l3.pdf>>url:http://www.rni.helsinki.fi/~~kja/day3-l3.pdf||shape="rect"]] | ||
| 31 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/day4-l4.pdf>>url:http://www.rni.helsinki.fi/~~kja/day4-l4.pdf||shape="rect"]] | ||
| 32 | |||
| 33 | Friday (Sep 5): See Course works below. | ||
| 34 | |||
| 35 | Monday (Sep 8): Please read articles by Bull et al. ("Tutorial in biostatistics") and Andersen (Competing risks). The links to these articles you can find below. | ||
| 36 | |||
| 37 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/day7-l7.pdf>>url:http://www.rni.helsinki.fi/~~kja/day7-l7.pdf||shape="rect"]] | ||
| 38 | |||
| 39 | Wednesday (Sep 10) : Please read articles by Andersen and Keiding (Sections 1, 2, 3, 4, 5.1.1, 5.1.2, and 5.6) and Hougaard (Sections 1, 2 and 5.3). | ||
| 40 | |||
| 41 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/lecture9.pdf>>url:http://www.rni.helsinki.fi/~~kja/lecture9.pdf||shape="rect"]] | ||
| 42 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/lecture10.pdf>>url:http://www.rni.helsinki.fi/~~kja/lecture10.pdf||shape="rect"]] (Tuesday, Sep 16) | ||
| 43 | |||
| 44 | |||
| 45 | \\ | ||
| 46 | |||
| 47 | === Computer class exercises (room C128) === | ||
| 48 | |||
| 49 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/ex1.pdf>>url:http://www.rni.helsinki.fi/~~kja/ex1.pdf||shape="rect"]] | ||
| 50 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/answers1.r>>url:http://www.rni.helsinki.fi/~~kja/answers1.r||shape="rect"]] | ||
| 51 | |||
| 52 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/ex2.pdf>>url:http://www.rni.helsinki.fi/~~kja/ex2.pdf||shape="rect"]] | ||
| 53 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/answers2.pdf>>url:http://www.rni.helsinki.fi/~~kja/answers2.pdf||shape="rect"]] | ||
| 54 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/cervix.dat>>url:http://www.rni.helsinki.fi/~~kja/cervix.dat||shape="rect"]] | ||
| 55 | |||
| 56 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/ex3.pdf>>url:http://www.rni.helsinki.fi/~~kja/ex3.pdf||shape="rect"]] | ||
| 57 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/answers3.r>>url:http://www.rni.helsinki.fi/~~kja/answers3.r||shape="rect"]] | ||
| 58 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/melanoma.csv>>url:http://www.rni.helsinki.fi/~~kja/melanoma.csv||shape="rect"]] | ||
| 59 | |||
| 60 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/ex4.pdf>>url:http://www.rni.helsinki.fi/~~kja/ex4.pdf||shape="rect"]] | ||
| 61 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/answers4.r>>url:http://www.rni.helsinki.fi/~~kja/answers4.r||shape="rect"]] | ||
| 62 | |||
| 63 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/practical5.pdf>>url:http://www.rni.helsinki.fi/~~kja/practical5.pdf||shape="rect"]] | ||
| 64 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/answers5.r>>url:http://www.rni.helsinki.fi/~~kja/answers5.r||shape="rect"]] | ||
| 65 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/dataSI.dat>>url:http://www.rni.helsinki.fi/~~kja/dataSI.dat||shape="rect"]] | ||
| 66 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/dataIR.dat>>url:http://www.rni.helsinki.fi/~~kja/dataIR.dat||shape="rect"]] | ||
| 67 | |||
| 68 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/practical6.pdf>>url:http://www.rni.helsinki.fi/~~kja/practical6.pdf||shape="rect"]] | ||
| 69 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/answers6.R>>url:http://www.rni.helsinki.fi/~~kja/answers6.R||shape="rect"]] | ||
| 70 | |||
| 71 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/practical7.pdf>>url:http://www.rni.helsinki.fi/~~kja/practical7.pdf||shape="rect"]] | ||
| 72 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/baboon.csv>>url:http://www.rni.helsinki.fi/~~kja/baboon.csv||shape="rect"]] | ||
| 73 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/answer7.R>>url:http://www.rni.helsinki.fi/~~kja/answer7.R||shape="rect"]] | ||
| 74 | |||
| 75 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/practical8.pdf>>url:http://www.rni.helsinki.fi/~~kja/practical8.pdf||shape="rect"]] | ||
| 76 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/answer8.R>>url:http://www.rni.helsinki.fi/~~kja/answer8.R||shape="rect"]] | ||
| 77 | |||
| 78 | === Discussion articles === | ||
| 79 | |||
| 80 | Bull and Spigelhalter: Tutorial in biostatistics | ||
| 81 | Andersen: Competing risks as a multi-state model | ||
| 82 | Andersen and Keiding: Multistate models for event history analysis | ||
| 83 | Hougaard: Multi-state models: a review | ||
| 84 | |||
| 85 | === Course works === | ||
| 86 | |||
| 87 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/coursework1.pdf>>url:http://www.rni.helsinki.fi/~~kja/coursework1.pdf||shape="rect"]] | ||
| 88 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/coursework2.pdf>>url:http://www.rni.helsinki.fi/~~kja/coursework2.pdf||shape="rect"]] | ||
| 89 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/coursework3.pdf>>url:http://www.rni.helsinki.fi/~~kja/coursework3.pdf||shape="rect"]] | ||
| 90 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/coursework4.pdf>>url:http://www.rni.helsinki.fi/~~kja/coursework4.pdf||shape="rect"]] | ||
| 91 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/melanoma.pdf>>url:http://www.rni.helsinki.fi/~~kja/melanoma.pdf||shape="rect"]] A background article for course work 4. | ||
| 92 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/Bonemarrow.pdf>>url:http://www.rni.helsinki.fi/~~kja/Bonemarrow.pdf||shape="rect"]] How to compute (non-parametric) cumulative incidence functions. | ||
| 93 | |||
| 94 | The data sets: | ||
| 95 | |||
| 96 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/diet.dat>>url:http://www.rni.helsinki.fi/~~kja/diet.dat||shape="rect"]] data for course work 1 | ||
| 97 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/mouse.dat>>url:http://www.rni.helsinki.fi/~~kja/mouse.dat||shape="rect"]] data for course work 2 | ||
| 98 | [[http:~~/~~/www.rni.helsinki.fi/~~~~kja/smallpox.dat>>url:http://www.rni.helsinki.fi/~~kja/smallpox.dat||shape="rect"]] data for course work 3 | ||
| 99 | The data set for course work4 is available in R. | ||
| 100 | |||
| 101 | === Bibliography === | ||
| 102 | |||
| 103 | Andersen, P. K., Borgan, O, Gill, R. D., Keiding, N. Statistical Models Based on Counting Processes. Springer-Verlag, (1993). | ||
| 104 | |||
| 105 | Kalbfleisch, J. D., and R. L. Prentice. The Statistical Analysis of Failure Time Data. 2nd ed. New York: Wiley, (2002). | ||
| 106 | |||
| 107 | Per Kragh Andersen and Niels Keiding. Multi-state models for event history analysis. Statistical Methods in Medical Research 2002; 11: 91-115. | ||
| 108 | |||
| 109 | Per Kragh Andersen, Steen Z Abildstrom, Susanne Rosthøj. Competing risks as a multi-state model. Statistical Methods in Medical Research 2002; 11: 203-215. | ||
| 110 | |||
| 111 | === Exercises === | ||
| 112 | |||
| 113 | There will be one exercise class every day illustrating event history analysis using R. | ||
| 114 | |||
| 115 | === Course content === | ||
| 116 | |||
| 117 | * Monday (Sep 1) Introduction to survival and event history analysis. Practical I (Intro to R and basics to survival analysis in R). | ||
| 118 | * Tuesday (Sep 2) Estimation of survival functions and the construction of likelihood functions. Parametric survival distributions. Practical II. | ||
| 119 | * Wednesday (Sep 3) Parametric, semiparametric and nonparametric inference in survival models. Practical III. | ||
| 120 | * Thursday (Sep 4) Model checking, stratified analysis. Practical IV. | ||
| 121 | * Friday (Sep 5) Introduction to course works. Practical V. | ||
| 122 | * Monday (Sep 8) Discussion article I (Choice of time scale,open and closed cohorts etc.). | ||
| 123 | Discussion article II (Competing risks). | ||
| 124 | * Tuesday (Sep 9) Discussion article III (Event history analysis). More on event history models. Practical VI. | ||
| 125 | * Wednesday (Sep 10) Counting process formulations. Practical VII. | ||
| 126 | * Monday (Sep 15) Special topics (late entry, truncation, cross-sectional sampling etc.). Practical VIII. | ||
| 127 | * Tuesday (Sep 16) Bayesian analysis of survival models. Practical IX. | ||
| 128 | |||
| 129 | === Registration at the first lecture. === |