
Changes in version 1.5.4 (2018-11-20)
+ Fixed bug in merge_taxa2
+ Fixed bug in Pielou's evenness
+ New functions: readcount, bfratio, aggregate_top_taxa
+ rewritten aggregate_taxa and moved the top argument in the new function aggregate_top_taxa 
+ plot_composition function: new options for sample.sort and otu.sort
+ Added Phylum level to taxonomy tables in example data sets 
* New function: dominant
+ The diversities function is now replaces by alpha function. The alpha is more
  generic and can return also other alpha diversity indices.
+ plot_frequencies function now only returns the ggplot object
+ Renamed the global function into alpha
+ Renamed arguments rarity.detection and rarity.prevalence into
  detection and prevalence in the rarity function
+ Added Chao1 index in richness function
+ In atlas1006 data set, pseudocount of +1 in otu table has been
  removed to facilitate comparison with sequencing data sets and to
  avoid confusion
+ In atlas1006 data set, only a single replicate per subject-time
  combination is chosen (at random)
+ New function collapse_replicates has been added
+ Abundance matrices (otu tables) for all example data sets now
  starting from 0 without pseudocount
+ Changed the default for the detection argument in the richness function to
  detection=0
+ removed rarity.threshold and rarity.prevalence options from the alpha function
+ Various minor fixes; see github commits for many more details
  o Color order in plot_landscape legend now follows the factor levels
    of the col argument
  o Fixed example in remove_samples
