2016-11-15  Scott Ritchie <sritchie73@gmail.com>

   * DESCRIPTION: Release 1.0.4
   
   * Restructured and curated documentation: Rd files are no longer generated
     for internal functions, and functions intended to extend basic package 
     usage have been removed from the package manual.

2016-10-20  Scott Ritchie <sritchie73@gmail.com>

   * DESCRIPTION: Release 1.0.3
   
   * README: updated to reflect publication in Cell Systems and package 
     publication on CRAN (as of version 1.0.2).

   * R/NetRep.R: fixed spelling mistake in package documentation.
   * man/NetRep.Rd: compilation of R/NetRep.R spelling fix.
   
   * R/check-user-input.R: in processInput() improved handling of user input 
     arugments 'modules', 'moduleAssignments', 'backgroundLabel' and 'test'
     to handle cases where user code has overwritten a necessary list element 
     with 'NULL'.
  
   * R/check-user-input.R: numeric labels in 'modules' are now returned as 
     "character", fixing a bug where the incorrect modules would be reported
     in the 'contigency' table list element returned by contigencyTable() in
     R/contingency.R

   * R/contingency.R: fixed bug where ratios returned in the 'propVarsExplained'
     list element by contingencyTable() were greater than 1 due to mismatch in
     in module order of the vectors when calculating the ratios (one ordered 
     as text, one numerically).
     
   * R/contingency.R: improved the 'contingency' table list element returned by 
     contigencyTable() so that it now reports module sizes in their discovery
     datasets, the number of nodes present in the other dataset in the 
     contigency table comparison, and includes modules with no nodes present in
     the other dataset.

   * R/networkProperties.R: in netPropsInternal() improved progress reporting
     messages so that the module discovery dataset is listed as well as the
     dataset in which the module properties are being calculated.
