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# Hens, N., Shkedy, Z., Aerts, M., Faes, C., Van Damme, P., Beutels, P. 2012 
# Modeling Infectious Disease Parameters Based on Serological and Social Contact Data
# Springer-Verlag New York
# R programs and data files
# Last update: 26 August 2012
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Summary:
The material provided here covers the data and R-code used throughout the book. The relevant SAS-code and WinBugs-code can be obtained from the authors.

A few notes:
Chapter 6: not all results as mentioned in the book are explicitly coded here, however these results are easily obtained from the code
Chapter 12: the combination of R 2.14.0 and the VGAM-library results in errors. We are currently sorting out these errors with the author of the library (Thomas Yee). The current version of the code works perfectly using an old R-version (R 2.9.2) and the current version of the VGAM-library
Chapter 13: the bivariate spline s(a,b) can be replaced by te(a,b) allowing for different smoothness parameters for the two components

Future: 
We are working hard at CenStat and Chermid to extend the presented work in various directions. We will be sharing code at www.simid.be and the institutes' websites.

Contact: 
Any mistake in the code is completely ours. We therefore appreciate any feedback related to the code. Please send us an email at: niel.hens@uhasselt.be

Overview of the material:
Chapter 1: no code
Chapter 2: chapter2.r - aids1.txt - aids2.txt - aids3.txt
Chapter 3: chapter3.r - HAV-BUL.dat - VZV-B19-BE.dat
Chapter 4: chapter4.r
		hepatitis A Belgium 1993: HAV-BE.dat 
		hepatitis A Belgium 1993 & 2002: hepatitis1993-2002.dat
		hepatitis A Bulgaria: HAV-BUL.dat
		hepatitis B incidence: incidencedataHepB.txt
		hepatitis B serology: seroprevalencedataHepB.txt
		hepatitis C: hcvdat.txt 
		mumps UK: MUMPSUK.dat & Rubella-Mumps-UK.dat
		parvovirus B19: 5 countries: B19-countries.dat & 
		parvovirus B19 Belgium: VZV-B19-BE.dat
		rubella UK: Rubella-UK.dat & Rubella-Mumps-UK.dat
		TB Netherlands: tb.dat
		varicella Flanders: VZV-Flanders.dat
		varicella Belgium: VZV-B19-BE.dat
		St-Petersburg: data1999.txt & population St Petersburg.txt		
Chapter 5: chapter5.r
Chapter 6: chapter6.r - hcv.txt
Chapter 7: chapter7.r
Chapter 8: chapter8.r - chapter8_casestudy.r - GLM functions Eilers and Marx.R - glmm_model'2-5'.txt
Chapter 9: chapter9.r - monotone psplinefit.R
Chapter 10: chapter10.r - chapter10_nonparametrics.r - bball.txt - fubbb04.txt - mumps'1-2'.txt - rubella1.txt
Chapter 11: chapter11.r - monotone logistic and gaussian psplinefit.R - clasify.txt - foii.txt - mix1.txt - pii.txt - pii7.txt
Chapter 12: chapter12.r
Chapter 13: chapter13.r - additive monotone psplinefit.R - monotone logistic and gaussian psplinefit.R 
Chapter 14: chapter14.r
Chapter 15: chapter15.r - folder: 'contacts belgium' (10 files + subfolder location with 6 files)
Chapter 16: chapter16.r - psplinefoihatvzv.txt - SIR age-structured 'core - vaccination' - finer grid.R
Appendix: appendix.r & Bayeslogistic.txt

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