$Date: 2015-05-15 12:06:44 +0200 (Friday, 15 May 2015) $

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

Version 1.2.1 (released May 15, 2015)
   
    * group.rich: fixed the labels on x axis of plot
   
    * group.spec: fixed the labels on x axis of plot

    * filter.OTU: fixed a bug in row selection

    * tax.abund: substitues spaces in names of the output dataframes
      with "_"  
   
    * phylo_taxonomy: new function to plot hierarchical 
      taxonomic tree with relative abundance of all taxa at a 
      given rank if category variables are provided. Nonsplitting 
      nodes are collapsed as ape::plot.phylo does..
 
    * phylog_taxonomy: new function to plot hierarchical 
      taxonomic tree, the leaves are taxa at a given rank, 
      nonsplitting nodes are not collapsed as ade4::plot.phylog does.

    * factor.abundance: new function to create a stacked bar plot 
       showing the abundance of all classifications at the given 
       taxonomic rank for each level of a metadata category variable.

    * seq_var: new function to calculate and plot inter/intra 
       specific variation for an alignment.

    * network_data: new function to generate a list of network nodes 
      and edges based on an otu table and associated metadata

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

    * alignment: new data for \code{\link{seq_var}

Version 1.2.0 (released December 10, 2014)

    * fread.OTU: use data.table::fread for reading in large data 
      set. 

    * filter.OTU: Fixed a bug in selecting rownames.
   
    * fread.meta: use data.table::fread for reading in large data 
      set.

    * write.data: write datasets to a csv file of a valid file
      path.

    * write.OTU: removed and replaced by write.data function

    * 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.

    * RAM.input.formatting: describe how the ecology data should 
      be used as inputs for comparison functions. 

    * 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.

    * 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.

    * get.rank: fixed a bug that keeping otus without identified 
      taxon name at a given rank; e.g. g__ or g__;

    * transpose.LCA: transpose OTU tables with each OTU being 
      annotated by its LCA.

    * theme_ggplot: provide two ggplot themes RAM.color and R.border
      for customized fancy plots.

    * read.OTU: now can import both "," or "\t" delimited files.

    * read.meta: now can import both "," or "\t" delimited files.

    * core.OTU: core.OTU in this version shows LCA of core OTUs. 

    * OTU.recap: now can handle multiple otu tables at one run and
      do a barplot to visualize the output.
  
    * combine.OTU: combine otus for the same sample. Suggested 
      to be use for bacterial 16S datasets. 

    * filter.META: Select METADATA Variables and remove the ones
      that only have one level, neither numeric nor factor and /
      or with missing data.

    * .valid.data: check whether ecology data sets have same 
 
    * assist.ado: perform ADONIS Analysis for ecology data sets. 
        
    * filter.Taxa: filter taxonomic abundance matrices by total 
      counts or maximum relative abundance.	

    * data.clust: plot hierarchical clusters of samples based on 
      ecology data set. 

    * META.clust: Plot Hierarchical Cluster Of samples based on 
      metadata

    * assist.NB: negative binomial test of seleted otuID or 
      taxon name.

    * envis.NB: plot the negative binomial model for selected 
      otuID or taxon name.

    * group.rich: Barplot of richness for a given metadata 
      variable.

    * group.spec: Boxplot of richness for a given metadata 
      variable.

    * OTU.ord: visualize cca/rda analysis on otus

    * Taxa.ord: visualize cca/rda analysis on taxa groups at a 
      given rank.

    * group.Taxa.box: boxplot of taxa distribution among groups.

    * group.Taxa.bar: barplot of taxa distribution among groups.

    * group.abunda.taxa: barplot of selected taxa in each group.

    * group.venn: venn diagrams for taxa shared by different 
      communities

    * shared.Taxa: summarize taxa shared by all samples

    * valid.taxonomy: check whether the format of the taxonomy 
      lineages in the otu tables are supported by RAM
 
    * reformat.taxonomy: reformat the taxonomy 
      lineages in the otu tables that supported by RAM

    * sample.map: plot the number of samples collected from 
      each location. For plotting distant sampling sites.

    * sample.site: alternative view of RAM functons sample.map and 
      sample.locations, suitable for plot closely located sampling 
      sites.

    * group.diversity: plot diversity indices among different 
      groups.
    
    * group.heatmap: add standardize and dis.method options

    * core.OTU.rank: changed the name of core.OTU in v1.1.0 
      to core.OTU.rank

    * group.abundance: can process more than 2 OTU tables now.

    * group.top.number: can process more than 2 OTU tables now.

    * group.top.percent: can process more than 2 OTU tables now.

    * group.indicators: can process more than 2 OTU tables now.

    * RAM.pal: generate customized color patterns.

    * The third public version.

Version 1.1.0 (released October 20, 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.

