Course Materials: HGEN 619 [Spring 2011]

Topics for 2011 Spring Session

Website: OpenMx
Text: Methodology for Genetic Studies of Twins and Families by Neale & Cardon, 1992 revision PDF of Neale & Maes book.
Classic Mx Manual: Mx: Statistical Modeling by Neale, Boker, Xie & Maes, 2006 PDF of Mx manual.

Date Lecture Topic Lecturer Notes and Examples
Jan 18 Chapter 1: Introduction to R Hermine Maes Rintroduction.R
PlayingWithR.R
Jan 25 Chapter 2: Probability and Statistics Review Mark Reimers Stat Computing in R Demos
Feb 01 Chapter 3: Methods for Generating Random Variables Hoa Wu / Lindon Eaves Stat Comp in R Chapter 3 Presentation
Chapter3 R Code
SimulateIRTdata R Code
Geneticdrift R Code
Genetic Drift Slides (PDF)
Feb 08 Chapter 4: Visualization of Multivariate Data Elizabeth Prom-Wormley / Wigelin Stat Computing Graphing Class.R
StatCompinRvCards.csv
Traditional Graphics Reference.xls
bivgencorrsc22.txt
Mark’s R Code
FOLFAout.txt
Dr. Jacob Wegelin’s Website
Feb 15 & 17 Review of Chapters 1-4 Lindon Eaves / Michael Neale SimulateIRTdata R Code
Updated SimulateIRTdata R Code
Rasch R Code
Directory containing Dr. Mario Rizzo’s Online Scripts
Feb 22 & 24 Chapter 5: Monte Carlo and Variance Reduction Mark Reimers / Lindon Eaves introMonteCarloMethods.R R code
Network.R
Correct Network.R
Mar 01 & 03 Chapter 6: Lindon Eaves / Elizabeth Prom-Wormley Twin inits.odc
Twin Data.odc
Twin Code.odc
Mean and SD Inits.odc
Mean and SD Data.odc
Mean and SD Code.odc
Introduction to MCMC and OpenBUGS.ppt
Instructions for Running BUGS.docx
  Chapter 7: Silviu-Alin Bacanu permutation tests.txt
permutation tests correlated SNPs.txt
how.many.permutations.txt
generate.correlated.snp.genotypes.txt
more.delicate.permutations.txt
Apr 05 & 07 Chapter 8: Lindon Eaves / Elizabeth Prom-Wormley MCMC.R
Mean and SD in R.R
Mean and SD in R.txt
Mean and SD Data.csv
Mean and SD Code.bug.R
rjags in Mac OSX
rjags.pdf
Batch twin and age effects code.txt
BUGS DHEA batchtwinage resid for JAGS.R
d_t1.csv
d_t2.txt
Installing BRugs Instructions for PC Users.docx
BUGS DHEA batchtwinage resid PC.R
Cortisol batch inits 1.txt
Cortisol batch inits 2.txt
Apr 12 & 14 Chapter 10: Fazil Aliev fazilChapter10.R
Apr 19 & 21 Chapter 11: Ryne Estabrook / Hao Wu Numerical Issues.pdf
Numerical Issues.R
Apr 26 & 28 Chapter 12: Lindon Eaves SNPSim.R
May 03 Chapter 13: Mark Reimers shrinkage.r