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

\section{Changes in version 1.2.1.3}{

   \subsection{GENERAL}{
     \itemize{

       \item This is a release that we fixed some bugs.

     }
  } % general


  \subsection{BUG FIXES}{

    \itemize{

     \item Fixed missing link or links in documentation object 'RAM-package.Rd': ‘[ggplot2:ggplot2-package]{ggplot2}’.

     \item Fixed a bug in \code{group.rich}     
    }
  } % bug fixes
} % version 1.2.1.3


\section{Changes in version 1.2.1.2}{

   \subsection{GENERAL}{
     \itemize{

       \item This is a release that we fixed some bugs.

     }
  } % general


  \subsection{BUG FIXES}{

    \itemize{

     \item Fixed a bug in \code{shared.OTU} where an error occurs 
     when no otus are shared by all samples.

     \item Fixed a bug in \code{shared.Taxa} where an error occurs 
     when no taxa are shared by all samples.

     \item Resolved the conflit between the 'summary.cca' function 
     of 'vegan' and the one of 'ade4'. in an internal function 
     .analysis.helper

     \item Fixed seq_var to work with gridExtra version 2.0.0
    
    }
  } % bug fixes
} % version 1.2.1.2

\section{Changes in version 1.2.1.1}{

   \subsection{GENERAL}{
     \itemize{

       \item This is a release that we fixed some bugs.

     }
  } % general


  \subsection{BUG FIXES}{

    \itemize{

     \item Fixed a bug in \code{filter.OTU} for filtering by number
     of sequences per sample.
    
    }
  } % bug fixes
} % version 1.2.1.1

\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

