$Date: 2014-10-22 14:25:44 +0200 (Wednesday, 22 Oct 2014) $

RAM RELEASE VERSIONS at http://cran.r-project.org/

Version 1.1.0 (released October 22, 2014)

	* tax.abund: fixed drop.unclassified option.

	* group.abundance: plot with adjusted and aligned x axis labels. 
        
        * tax.split: previously used a function concate.split from package
           splitstackshape, which is deprecated. Replaced with new function 
           in RAM \code{split.col}.  

        * group.indicators: RAM::tax.split.   

        * tax.abund: fixed the bug that fails to remove unclassified 
          taxon groups in defined blacklist when drop.unclassified is
          set as TRUE. 

        * group.abundance: needs \code{tax.abund} when plot relative 
           abundance of top taxon groups at each ranks. Now it correctly 
           remove unclassified taxon groups when drop.unclassified option 
           is set TRUE.
      
        * tax.fill: failed to recognize unclassified taxon groups in defined
          blacklist and replace them with the OTUs lowest comman ancestor. 
      
        * OTU.diversity: calculates most used diversity indices for each samples 
          based on OTU tables.

        * core.OTU: summarizes most prevelant otus.

        * core.Taxa: summarizes most prevelant taxon groups.

        * group.OTU: plot function for the distribution of selected otus.

        * filter.OTU: function to subset OTUs by either total 
          count or relative abundance.
     
        * OTU.recap: summarizes classified OTUs at each taxonomic ranks.
     
        * .get.rank.name: internal function to generate the name 
          of a given taxonomic rank.
    
        * LCA.OTU: function to obtain LCA for each otu. Unclassified taxa 
          are removed and the lowest rank that an otu can be assigned to is 
          returned. 
      
        * correlation: plot function to display correlation coefficient 
          (or covariance) among taxa at a give rank and / or numeric variables 
          of metadata. 
            
        * col.splitup: function to split a column of a data frame by 
          predefined separator.
	

	* The second public version.

