\name{NEWS}
\title{RAM News}
\encoding{UTF-8}

\section{Changes in version 1.1.0}{

  \subsection{GENERAL}{
     \itemize{

       \item This is a release with new functions and features. In
       the same we also fix some issues of plot functions.

     }
  } % general


  \subsection{BUG FIXES}{

    \itemize{

     \item Function \code{tax.split} previously used a function 
      \code{splitstackshape::concat.split}, which is deprecated. Replaced 
      with new function in RAM \code{split.col}.  

     \item Function \code{group.indicators} fix the bug caused by previous
      version of tax.split, which call function 
      \code{splitstackshape::concat.split}, which is not required any more.   

      \item Function \code{tax.abund} failed to remove unclassified 
      taxon groups in defined blacklist when drop.unclassified is
      set as TRUE. 

      \item Function \code{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.
      
      \item \code{tax.fill} failed to recognize unclassified 
      taxon groups in defined blacklist and replace them with the OTUs 
      lowest comman ancestor. 

      \item \code{...} 
    
    }
  } % bug fixes


  \subsection{NEW FUNCTIONS}{
    \itemize{

      \item Function \code{OTU.diversity} calculates most used 
      diversity indices for each samples based on OTU tables.

      \item Function \code{core.OTU} summarizes most prevelant otus.

      \item Function \code{core.Taxa} summarizes most prevelant taxon 
      groups.

      \item \code{group.OTU} plot function for the distribution of 
      selected otus.

      \item \code{filter.OTU} function to subset OTUs by either total 
      count or relative abundance.
     
      \item \code{OTU.recap} summarizes classified OTUs at each taxonomic
      ranks.
     
      \item \code{.get.rank.name} internal function to generate the name 
      of a given taxonomic rank.
    
      \item \code{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. 
      
      \item \code{correlation} plot function to display correlation 
       coefficient (or covariance) among taxa at a give rank and / or 
      numeric variables of metadata. 
            
      \item \code{col.splitup} function to split a column of a data frame by 
      predefined separator.

    }
  } % new functions

%  \subsection{NEW FEATURES}{
%    \itemize{

%      \item 

%      \item 

%      \item 

%    }

%  } % new features
  
%  \subsection{INSTALLATION AND BUILDING}{
%    \itemize{

%      \item 
      
    }
  } % installation and building
  
%  \subsection{DEPRECATED}{

%    \itemize{

%      \item 

%    }   
%  } % deprecated

} % version 1.1.0

