charSubMatch takes two strings as arguments and returns TRUE if one of the strings is a part of the other string; otherwise it returns FALSE.  E.g., charSubMatch("abcdef", "cde") returns TRUE because cde is a substring of abcdef.  Similarly, charSubMatch("cde", "abcdef") returns TRUE.  charSubMatch("ace", "abcdef") returns FALSE because the string ace is not a substring of abcdef, nor is abcdef a substring of ace.  NA matches every string, including "" and NA.  

ARGUMENTS

s1.string, s2.string:  String vectors of length 1.

check.dups checks for any duplicates in a vector of names.  If duplicates are found, they are listed.  check.dups can also check whether filenames are duplicated in several different directories.    
 

ARGUMENTS:
names.vec is NA iff paths is not NA.  
If names.vec is not NA, then it is a string vector; check.dups checks for duplicate strings by the obvious method (using unique).  
If paths is not NA and and names.vec is NA, then paths must be a vector of strings that designate a series of directories (folders).  In this case, names.vec is set equal to a vector of names of all files in any of the directories specified by paths.   check.dups checks whether files have the same name in different directories.    
VALUE

'chmat.to.dframe' converts a character matrix to a dataframe.  It allows the user to designate which columns are retained as string vectors, which columns are converted to factors, and which columns are converted to numerical vectors.

'xx' is a character matrix.

'var.types' is a character vector that indicates the mode of each variable.
's' indicates a string variable; 
'f' indicates a factor variable; 
'n' indicates a numeric variable; 
'l' indicates a logical variable.

'var.names' is an optional vector of column names

ci.bugs finds the limits of an alpha level credible interval.  The input is a vector of parameter values.  The output are the lower and upper bounds of the credible interval.  The interval can be computed either as an approximate highest density interval (HDI) or with equal probability tails. 

ARGUMENTS:

parameter.vector is a vector of parameters that were sampled from the posterior distribution of a parameter.

level is the level of the credible interval (defaults to .95).

method = c("HDI", "equal.tails")[1] - the default is a highest density interval (HDI); method = "equal.tails" puts equal posterior probability in the lower and upper tails.