Longitudinal data-analysis, fall 2013

What's new

It is possible to gain 1 or 2 extra credit points by doing a course work. The work is based on the following article: http://www.rni.helsinki.fi/~kja/lda13/coursework/article.pdf. For instructions (in Finnish for the time being), see: http://www.rni.helsinki.fi/~kja/lda13/coursework/HT1.pdf. For 1 credit point read chapters up to the end of age 1215 in the article (up to the sub-section titled "Imperfect detectability") and do the first 4 tasks in the exercise paper. For 2 credit points, there are two options: (a) continue reading the article and implement the method for estimating the transition hazards when the detection of infection is imperfect; (b) continue with the rest of tasks in the exercise paper. These consider estimation of the hazard rates (still assuming perfect detectability) using Bayesian modelling and computational methods. 

The data for the course work (see Nagelkerke et al.): http://www.rni.helsinki.fi/~kja/lda13/coursework/giardia.txt

The second course exam will be on December 12 (Thursday), starting at 4:00 p.m. sharp. The exam covers the following material: (A) Lectures 11-16; (B) Textbook (Diggle et al.), Chapters 2, 8.1, 8.2, 8.4., 9 (except for those examples not covered in the lectures or practicals), 13.1 - 13.7; (C) Exercises 6-7. (N.B. Regarding the computer class exercise, it will not be required to produce R code during the exam).

On Thursday (Dec 12), there is also possibility to do a final exam covering the whole course. For more information about the material included from the first part of

the course, see "Exams" below. The material from the second part of the course is listed above (as well as under "Exams" below).

Answers to Exercise 6: http://www.rni.helsinki.fi/~kja/lda13/exercise6/answers6.pdf

http://www.rni.helsinki.fi/~kja/lda13/exercise6/testMCAR.R

There will be no actual lecture On Tuesday (Dec 10). Those interested will be distributed course practicals

for extra credits points.

Lecturer

Kari Auranen (1st part)
Jukka Jokinen (2nd part)

Scope

8 sp.

Type

Advanced studies

Prerequisites

Linear models, Statistical inference

Lectures

Weeks 36-42 and 44-50, Tuesday 16-18 and Thursday 16-18 in room B120. Two hours of exercise classes per week.

There are no lectures in week 38 (Tue, Sep 17, and Thu, Sep 19).

Exams

The first course exam was on Thursday, October 17, starting at 4:00 p.m. (sharp). The exam covered the following material: A. Lectures 1-10; B. Textbook (Diggle et al.), Chapters 1, 3, 4, 5, 7, 8.1-8.2., 9.2-9.3; C. Exercises 1-5.

The second course exam will be on December 12 (Thursday), starting at 4:00 p.m. sharp. The exam covers the following material: (A) Lectures 11-16; (B) Textbook (Diggle et al.), Chapters 2, 8.1, 8.2, 8.4., 9 (except for those examples not covered in the lectures or practicals), 13.1 - 13.7; (C) Exercises 6-7. (N.B. Regarding the computer class exercise, it will not be required to produce R code during the exam).

Lecture summaries

http://www.rni.helsinki.fi/~kja/lda13/lecture1/lecture1.pdf (Lecture 1, September 3)

http://www.rni.helsinki.fi/~kja/lda13/lecture2/lecture2.pdf (Lecture 2, September 5)

http://www.rni.helsinki.fi/~kja/lda13/lecture3/lecture3.pdf (Lecture 3, September 10)

http://www.rni.helsinki.fi/~kja/lda13/lecture4/lecture4.pdf (Lecture 4, September 12)

http://www.rni.helsinki.fi/~kja/lda13/lecture5/lecture5.pdf (Lecture 5, September 24)

http://www.rni.helsinki.fi/~kja/lda13/lecture6/lecture6.pdf (Lecture 6, September 26)

http://www.rni.helsinki.fi/~kja/lda13/lecture7/lecture7.pdf (Tuesday, October 1)

Tuesday, October 3, Computes class practical (see Exercise 4)

http://www.rni.helsinki.fi/~kja/lda13/lecture8/lecture8.pdf (Tuesday, October 8)

http://www.rni.helsinki.fi/~kja/lda13/lecture9/lecture9a.pdf (Thursday, October 10)

http://www.rni.helsinki.fi/~kja/lda13/lecture9/lecture9b.pdf (Thursday, October 10)

http://www.rni.helsinki.fi/%7Ekja/lda13/lecture10/lecture10.pdf (Tuesday, October 15)

http://www.rni.helsinki.fi/~kja/lda13/lecture11/lecture11.pdf (Tuesday, October 29)

http://www.rni.helsinki.fi/~kja/lda13/lecture11/lecture11b.R (Thursday, October 31)

http://www.rni.helsinki.fi/~kja/lda13/lecture12/lecture12.pdf (Tuesday, November 5)

http://www.rni.helsinki.fi/~kja/lda13/lecture12/lecture12b.R (Thursday, November 7)

http://www.rni.helsinki.fi/~kja/lda13/lecture13/lecture13.pdf (Tuesday, November 19)

http://www.rni.helsinki.fi/~kja/lda13/lecture14/lecture14.pdf (Thursday, November 21)

http://www.rni.helsinki.fi/~kja/lda13/lecture15/lecture15.pdf (Tuesday, November 26, and Thursday, November 28)

http://www.rni.helsinki.fi/~kja/lda13/lecture15/samplesize.pdf (background for sample size calculation, Tuesday, Nov 26)

http://www.rni.helsinki.fi/~kja/lda13/lecture16/lecture16.pdf (Tuesday, December 3)

Exercises and Answers

http://www.rni.helsinki.fi/~kja/lda13/exercise1/exercise1.pdf

http://www.rni.helsinki.fi/~kja/lda13/exercise1/answers1.pdf

http://www.rni.helsinki.fi/~kja/lda13/exercise1/lehmaresid.R

http://www.rni.helsinki.fi/~kja/lda13/exercise1/variogram.R

http://www.rni.helsinki.fi/~kja/lda13/exercise2/exercise2.pdf

http://www.rni.helsinki.fi/~kja/exercise2/answers2.pdf

http://www.rni.helsinki.fi/~kja/lda13/exercise3/exercise3.pdf

http://www.rni.helsinki.fi/~kja/lda13/exercise3/answers3.pdf

http://www.rni.helsinki.fi/~kja/lda13/exercise4/exercise4.pd (A computer class practical)

http://www.rni.helsinki.fi/~kja/lda13/exercise5/exercise5.pdf

http://www.rni.helsinki.fi/~kja/lda13/exercise5/answers5.pdf

http://www.rni.helsinki.fi/~kja/lda13/exercise6/exercise6.pdf

http://www.rni.helsinki.fi/~kja/lda13/exercise6/answers6.pdf

http://www.rni.helsinki.fi/~kja/lda13/exercise6/testMCAR.R

http://www.rni.helsinki.fi/~kja/lda13/exercise7/exercise7.pdf (A computer class practical)

Data sets

http://www.rni.helsinki.fi/~kja/lda13/exercise1/cd4.dat (cd4 data)

http://www.rni.helsinki.fi/~kja/lda13/exercise1/info_cd4.txt (instruction to task 4 in Exercise 1)

http://www.rni.helsinki.fi/~kja/lda13/exercise1/cows.dat (cow data)

http://www.rni.helsinki.fi/~kja/lda13/exercise1/info_cows.txt

http://www.rni.helsinki.fi/~kja/lda13/exercise2/bindata1.dat

http://www.rni.helsinki.fi/~kja/lda13/exercise4/pigs.dat

http://www.rni.helsinki.fi/~kja/lda13/exercise6/cows_long.dat

http://www.rni.helsinki.fi/~kja/lda13/exercise7/seizures.dat

Bibliography

Diggle, Heagerty, Liang, Zeger: Analysis of Longitudinal Data (Oxford Statistical Science Series, 2002) and

material from the lecturers.

Registration

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Laskuharjoitukset

rni.helsinki.fi/~kja/lda13/exercise1/exercise1.pdf