The special.jm.options function sets startup configurations that are peculiar to JM's work.  THESE COMMANDS SHOULD NOT CONTAIN ANY SETTINGS THAT WOULD CREATE DIFFERENCES BETWEEN JM'S R COMPUTATIONS AND THE STUDENTS' R COMPUTATIONS.  E.g., setting the R repository to Fred Hutch is ok because even without this setting, students' work will have equivalent effects.

'SSq' computes the sum of squares for a vector of numbers.
This function replaces the 'SS' function which has been removed
in order to preserve the principle that all double letters,
e.g., 'aa', 'AA', 'bb', 'BB', etc., are unused as names of
standard objects or functions in R.

Function for extracting standardized regression coefficients
(beta weights) from an 'lm' object.  This function was written by
John Fox; it was copied from his 'car' package.

'stripwhite' strips leading and trailing white space from a string.
The function was copied from a R mailing contribution by Jim Holtman,
Fri, 20 Nov 2009, http://www.mail-archive.com/r-help@r-project.org/msg76315.html.

'stu.id' adds zeroes to the start of a student id that has had its initial zeroes stripped off (usually through the stupidity of Excel).  E.g., it converts '35721' to '0035721'.  

'def.length = 7' is the default assumed length of a character string.  This is the length of a UW student id.  The user can set the def.length to a different value.  The output is a character string of length def.length.

'stu.res' displays the exam answers and correct answers for

superdiag is an MCMC convergence diagnostic function that summarizes the results of the Gelman/Rubin test, the Geweke test, the Heidelberger/Welch test and the Raftery/Lewis test.  It was written by TSUNG-HAN TSAI AND JEFF GILL. It was downloaded from:  <http://artsci.wustl.edu/~jgill/Models/superdiag.v0.4.R>  on 5/25/2013.  

ARGUMENTS:  

# mcmcoutput: input chains from jags, bugs, etc.

# confidence.gr: 1-alpha for testing with the Gelman and Rubin test

# frac1.gw: frac1 for the Geweke Test

# frac2.gw: frac2 for the Geweke Test

# eps.hw: epsilon for the Heidelberger and Welch test

# pvalue.hw: p-value for the Heidelberger and Welch test

# q.rl: q-parameter for the Raftery and Lewis Test

# r.rl: r-parameter for the Raftery and Lewis Test

# s.rl: s-parameter for the Raftery and Lewis Test

# eps.rl: convergence epsilon for the Raftery and Lewis Test