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

\section{Changes in version 1.2.1}{

   \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 Fixed the labels on x axis of plots generated by 
     \code{group.rich} & \code{group.spec}

     \item Fixed a bug in \code{filter.OTU} 

      \item Fixed a bug in \code{tax.abund} substitues spaces in 
       names of the output dataframes with "_".
   
    
    }
  } % bug fixes


  \subsection{NEW FUNCTIONS}{
    \itemize{

      \item Function \code{phylo_taxonomy} plot hierarchical 
      taxonomic tree with relative abundance of all taxa at a 
      give rank if category variables are provided. Nonsplitting 
      nodes are collapsed as ape::plot.phylo does.
 
      \item Function \code{phylog_taxonomy} This function plot 
      hierarchical taxonomic tree, the leaves are taxa at a give 
      rank, nonsplitting nodes are not collapsed.

      \item Function \code{factor.abundance} reates a stacked bar
      plot showing the abundance of all classifications at the 
      given taxonomic rank for each level of a metadata category 
      variable.

      \item Function \code{seq_var} new function calculates and 
      plots inter/intra specific variation for an alignment.

      \item Function \code{network_data} new function to generate 
      a list of network nodes and edges based on an otu table and 
      associated metadata

      \item Function \code{group.abundance.meta} an updated version 
      of \code{\link{group.abundance}}, which groups samples by 
      metadata category variables if provided.

    }
  } % NEW FUNCTIONS

  \subsection{NEW DATA}{
    \itemize{
  
     \item DATA \code{alignment} new data for \code{\link{seq_var}.

   } % NEW DATA

} % version 1.2.1


\section{Changes in version 1.2.0}{

  \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 Fixed a bug in Function \code{get.rank} that keeping 
     otus without identified taxon name at a given rank; e.g. 
     'g__' or 'g__;'
    
    }
  } % bug fixes


  \subsection{NEW FUNCTIONS}{
    \itemize{

      \item Function \code{match.data} to match samples in ecology 
      datasets and metadata set. Only samples that present in both 
      will be kept and  reordered to match all datasets.
 
      \item Function \code{OTU.revamp} returns a list to describe 
      the percent of classifed  otus and sequences at each given 
      taxonomy ranks and visualize  the output in a barplot.

      \item Function \code{transpose.LCA} transpose OTU tables with 
       each OTU being annotated with its LCA.

      \item Function \code{theme_ggplot} provide two ggplot themes 
      RAM.color and R.border for customized fancy plots.

      \item Function \code{combine.OTU} combine otus for the same 
      sample. Suggested  to be use for bacterial 16S datasets. 

      \item Function \code{filter.META} Select METADATA Variables 
      and remove the ones  that only have one level, neither numeric 
      nor factor and /  or with missing data.

      \item Function \code{.valid.data} check whether ecology data 
      sets have same  

      \item Function \code{assist.ado} perform ADONIS Analysis for 
      ecology data sets.  

      \item Function \code{filter.Taxa} filter taxonomic abundance 
      matrices by total  counts or maximum relative abundance.	

      \item Function \code{data.clust} plot hierarchical clusters 
      of samples based on  ecology data set. 

      \item Function \code{META.clust} Plot Hierarchical Cluster 
      Of samples based on  metadata

      \item Function \code{assist.NB} negative binomial test of 
      seleted otuID or  taxon name.

      \item Function \code{envis.NB} plot the negative binomial 
      model for selected  otuID or taxon name.

      \item Function \code{group.rich} Barplot of richness for a 
      given metadata  variable.

      \item Function \code{group.spec} Boxplot of richness for a 
      given metadata  variable.

      \item Function \code{OTU.ord} visualize cca/rda analysis on 
      otus 

      \item Function \code{Taxa.ord} visualize cca/rda analysis on 
      taxa groups at a  given rank.

      \item Function \code{group.Taxa.box} boxplot of taxa 
      distribution among groups.

      \item Function \code{group.Taxa.bar} barplot of taxa 
      distribution among groups.

      \item Function \code{group.abunda.taxa} barplot of selected 
      taxa in each group.

      \item Function \code{group.venn} venn diagrams for taxa 
      shared by different  communities

      \item Function \code{shared.Taxa} summarize taxa shared by 
      all samples

      \item Function \code{valid.taxonomy} check whether the format 
      of the taxonomy  lineages in the otu tables are supported by RAM

      \item Function \code{reformat.taxonomy} reformat the taxonomy  
      lineages in the otu tables that supported by RAM

      \item Function \code{sample.map} plot the number of samples 
      collected from  each location. For plotting distant sampling 
      sites.

      \item Function \code{sample.site} alternative view of RAM 
      functons sample.map and  sample.locations, suitable for plot 
      closely located sampling  sites.

      \item Function \code{group.diversity} plot diversity indices 
      among different  groups.

      \item Function \code{RAM.pal} generate customized color pattern.

    }
  } % new functions

  \subsection{NEW FEATURES}{
    \itemize{

      \item Function \code{read.OTU} now can import both "," or 
     "\t" delimited files.

      \item Function \code{read.meta} now can import both "," or 
     "\t" delimited files.

      \item Function \code{OTU.recap} returns a list to describe 
      the percent of classifed otus and sequences at each given 
      taxonomy ranks and visualize the output in a barplot.

      \item Added standardize and dist.method options to Function 
      \code{group.heatmap}.

      \item Function \code{group.abundance} can process more than 
      2 OTU tables now.

      \item Function \code{group.top.number} can process more than 
      2 OTU tables now.

      \item Function \code{group.top.percent} can process more than 
      2 OTU tables now.

      \item Function \code{group.indicators} can process more than 
      2 OTU tables now.

    }

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

%      \item Function 
      
%      \item Function 

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

    \itemize{

      \item Function \code{write.OTU} removed and replaced by 
      \code{write.data} function
      
     }   
  } % deprecated

} % version 1.2.0

\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

} % version 1.1.0

