phyloseq
===========
* plot_ordination() powerful, flexible ordination plots built with ggplot2
* plot_heatmap() easy, flexible heat maps built with ggplot2
* plot_tree() easy, flexible annotated tree plots built with ggplot2
* make_sample_network(), plot_sample_network() - microbiome network visualization
* plot_richness() for easy, flexible summary of species richness
* Parallel Fast UniFrac
* distance() wrapper for ecological distance calculations
* ordinate() wrapper, calculates many different ordination methods.
* General importer for all supported data formats: import()
* BIOM format import: import_biom() function
* Support for Double Principle Coordinate Analysis (DPCoA)
* Several published exampled datasets included
* Bioconductor development release updates.
* Lots of documentation updates.
* Lots and lots of fixes and improvements.

phyloseq 1.2.1
===========
- Fixed attributes fail in unit tests, affecting checks but not functionality.

phyloseq 1.2.0
===========
Bioconductor release

phyloseq 1.1.50
===========
- Fixed several compatibility issues to support latest version of ggplot2 (0.9.2).
- Also changes plot_richness_estimates() to plot_richness().

phyloseq 1.1.45
===========
- Backward compatibility for import_qiime_sampleData,
  now superseded by import_qiime_sample_data
- Added a functioning example based on the GlobalPatterns
  example sample-map file included in the package extdata.

phyloseq 1.1.44
===========
- Fixed minor bug in tax_glom function.
Thanks to Katie Shelef for the bug report. Bug only affected tax_glom behavior when the right-most rank was specified as the position for merging.

phyloseq 1.1.43
===========
- fixed distance() issue from species/taxa replacement for type argument.

phyloseq 1.1.42
===========
- fixed make_network/plot_network issue from species/taxa replacement for type argument.

phyloseq 1.1.41
===========
- Fixed documentation for `prune_taxa` and `prune_samples`
- Updated `prune_samples` method to allow for logical vectors.
- Fixed `prune_taxa` so that it properly fails with a message if the taxa argument is a logical of wrong length.
   There was some potential (and no warning) for unpredictable vector-recycling
   with short vectors in the old implementation.

phyloseq 1.1.40
===========
## Huge Update and Renaming Event.
- Made all functions use an *underscore* for English word delimiter, if they were using an abbreviation. 
- Replaced "species" in all function names with "taxa". 
- These changes are all backward compatible, for now, so your old code should work. Let me know if it doesn't and I will quickly make the adjustment. This will remain true through the next official release,
but functional references to "species" will not be supported afterward,
except in the occasions where you actually mean taxonomic species, like `tax_glom(x, "species")`.

phyloseq 1.1.33
===========
Revise taxglom() such that it handles phyloseq and taxonomyTable classes,
throws warning otherwise. It should not take a manually-produced character
vector, as this is roughly equivalent to functionality supported in other method,
especially prune_species()/merge_species().
Also added unit-tests and executable examples for taxglom().
Got rid of taxglom.internal, incorporated directly into taxglom().
taxglom() is no longer an S4-method, and 
doesn't need to be now that the character-vector argument option is omitted,
with S4-class handling delegated to merge_species().
Updated "taxTab<-" to be S4 assignment, clearer handling of taxonomy Table assignments,
especially useful for taxglom.

phyloseq 1.1.29
===========
Add unit tests and example files for import_biom (as well as import("biom",...) ).

phyloseq 1.1.28
===========
Added rarefy_even_depth() function for random subsampling of microbiome samples to the same number of reads. Default uses the minimum total reads among the samples in the dataset. This is based on the core "sample" function, which can have its random number generator fixed by set.seed for reproducibility.

phyloseq 1.1.27
===========
Fix bug in plot_ordination that caused an error rather than produce unannotated plots when sampleData absent in the input.

phyloseq 1.1.23-26
===========
Added unit tests and bugfixes

phyloseq 1.1.19-22
===========
Improving import_qiime() importer to handle large datasets,
like the HMPv35 dataset, for example, while also providing useful status messages
during non-trivial imports that might take 10 minutes or more to complete.

phyloseq 1.1.18
===========
Added replicate labels as a "Sample" factor in the soilrep dataset.

phyloseq 1.1.17
===========
Fix possible bug that results from the latest version (0.6+) of igraph not being backward compatible. A stable igraph0 package is available on CRAN as a stop-gap, and so all igraph dependencies were migrated to "igraph0" until the phyloseq-source can be updated to match the igraph latest.

phyloseq 1.1.15
===========
plot_heatmap: Added default (but adjustable) threshold to omit taxa/sample labels

phyloseq 1.1.14
===========
Update import_qiime() function to import latest non-BIOM qiime output files.
	Also added check for presence of taxonomy information (consensus lineage).

phyloseq 1.1.10
===========
* Add plot_heatmap() function, for easy flexible heat maps built with ggplot2

phyloseq 1.1.8-9
===========
* Fix bug for some variants of new BIOM format
* Add import_RDP_otu() import function for new RDP pipeline export format

phyloseq 1.1.7
===========
* Removed the old plot_tree_phyloseq() function, in favor of the new ggplot2-based plot_tree()
* Uncommented / tested formal examples in documentation of plot-functions
* Updated variable names and doc for the plot_taxa_bar() function

phyloseq 1.1.6
===========
* Update vignette with plot_tree() example, replacing the 
   old base-graphics function, plot_tree_phyloseq().
* Fix bug in legend for trees with size mapped to abundance

phyloseq 1.1.5
===========
* Add initial version of tree_plot(), built with ggplot2
* Adds several internal functions borrowed from devel version of ggphylo

phyloseq 1.1.4
===========
* Add errorIfNULL option to auxiliary accessors
  (e.g. sample.variables(), rank.names())

phyloseq 1.1.1-3
===========
* R version updated to match Bioconductor, R-2.15.0+
* ape-package version updated to 3.0+
* ape-package now import dependency
* ggplot2-package version updated to 0.9.0+
* ggplot2-package now import dependency

v0.99.48
===========
* Updated README.md

v0.99.47
===========
* Add support for ordinate() to take dist-object instead of distance-method string.
* Update the documentation for ordinate() to reflect change.
* Updated README.md to describe new tools, distance() and ordinate()
* Update JSD documentation.

v0.99.46
===========
* Added support and documentation for Jensen-Shannon Divergence to distance().
* Some updates to distance() function and its documentation.

v0.99.45
===========
* Completely remove vegdist documentation from phyloseq by omitting all roxygen2
  headers except for 
  #' keywords internal
  This finally fixes it, without build warnings/errors, once and for all.

v0.99.44
===========
* Make the phyloseq::vegdist() wrapper an internal function. Documentation updated as well.
  This is a solution to Issue 87
  https://github.com/joey711/phyloseq/issues/87
* Remove rda.phyloseq and cca.phyloseq from exported methods.
  Documentation had already been removed when these were first attempted to be converted
  to internal methods in v0.99.42
* Modify make_sample_network to use the new distance() function, and be able to pass on
  additional parameters to distance().
* Re-order arguments to make_sample_network to better represent the stability of defaults.
* Removed redundant parameters from make_sample_network(). Transformations to abundance
  tables should be performed upstream using phyloseq tools, not embedded in this function.
* Modify vignettes to reflect these changes.
* Rebuild vignette.
* Update import() documentation to reflect support for BIOM format, import_biom() function.

v0.99.43
===========
* Revise component assignment operators, e.g. "sampleData(physeq)<-" to coerce/access
  from more diverse objects based on context. Documentation for these operators updated.
  This is a more general solution to Issue 68
  https://github.com/joey711/phyloseq/issues/68

v0.99.42
===========
* purge rda.phyloseq and cca.phyloseq from documentation, vignettes. Internal functions.
* analysis vignette revisions

v0.99.41
===========
* Added ordinate() function, general ordination wrapper.

v0.99.40
===========
* Fixed case issues with source filenames. 
  Required multiple commits, break in versioning for source files that had improper letter case (e.g. ".r")

v0.99.37 - 0.99.39
===========
* Vignette updates.

v0.99.36
===========
* Added general distance calculation wrapper, distance()
* Consolidated it with unifrac.R code in a new "distance-methods.R" source file.

v0.99.35
===========
* Added tool to retain user-defined subset of points from an ordination, subset_ord_plot
* Updates to vignette
* Remove a poorly-documented, unpublished example dataset, ex1 -> and all references to it in documentation

v0.99.34
===========
* Updates to vignette

v0.99.33
===========
* Allow color specification for "biplot" type in plot_ordination()
* bug fix for certain combinations of biplot options.

v0.99.32
===========
* Remove plot_ordination_biplot() from phyloseq -> replaced by: plot_ordination()
*  |-> also removed from vignette.
* Remove calcplot(). -> Will be replaced by pipeline_() methods
* plot_ordination() shown in vignette for "species" plot type.
* Fix - Allow flexible axis labels for plot_ordination()

v0.99.31
===========
* Aesthetic fixes in plot_ordination()
* Remove plot_ordination_samples() -> redundant, covered by plot_ordination().

v0.99.30
===========
* Added plot_ordination -> general ordination plotting function

v0.99.29
===========
* Added first-draft of analysis vignette to package
* Total package-space and build/check times tested

v0.99.28
===========
* Fixed bug when specifying alternative axes in plot_ordination_samples()

v0.99.27
===========
* Added DPCoA() function for Double Principle Coordinate Analysis, relies heavily on ade4.
* Added ade4 dependency. Some masking, but no errors apparent.
* Added dpcoa extension for scores()
* minor bugfix in plot_ordination_biplot().

v0.99.26
===========
* Add plot_ordination_samples() for convenient ordination plotting
* Renamed plot_ordination_phyloseq to more precise, plot_ordination_biplot()
* Added extension to vegan::scores for ape:pcoa results, scores.pcoa()

v0.99.25
===========
* Fix build warning from duplicate import in namespace
* Update README.md

v0.99.24
===========
* Advanced network/graph plotting/visualization wrappers: make_sample_network(), plot_sample_network()
* Advanced alpha diversity wrappers: plot_richness_estimates(), estimate_richness()
* Added taxafilter() function for even more convenient filtering of species/taxa
* Added reshape dependency for explicit use of melt() function.

v0.99.23
===========
* Added a rooted tree to "GlobalPatterns" dataset
* Allow multi-class tests with mt()

v0.99.20
===========
* Added "GlobalPatterns" dataset, and some other minor improvements
* added "GlobalPatterns" dataset, with doc and some analysis
  examples. More examples will be added to the vignette.
* add getVariable accessor function, for streamlining access
  to values/vectors/factors/etc of the variates contained in
  the sampleData component
* revise documentation about parallelization of import_biom()
* revise documentation for enterotype dataset

v0.99.19
===========
* fixed a bug in general import() function in which it properly processed import command, but then failed to return result.

v0.99.18
===========
* Added import_biom() function to import BIOM format OTU-clustered data / metadata
* Added (direct) dependency for plyr, as well as RJSONIO 


phyloseq 0.4.2 - 0.4.7
===========

* Improvements to import_mothur() via import_mothur_otulist().
* merge_samples() function added, in preparation for hypergeometric (fisher.test) test wrapper.
* Fixed bug in merge_phyloseq() for certain combinations of objects. 
* Various other fixes and improvements.

phyloseq 0.4.1
===========

* First official submission to Bioconductor
* Includes many build-fixes, bug-fixes
* Final tweaks to conform to Bioconductor guidelines

phyloseq 0.3
===========

* Added Importers for mothur, RDP-pipeline, and PyroTagger
* Lots of new plotting and analysis support
* Parallelized UniFrac calculations using foreach package
* Some improvements to the class inheritance structure to simplify method extension and future development.
* Function-level documentation
* Vignette-level documentation
* Package dependencies achieved via import for all packages with a namespace. Depends (full load) otherwise.

phyloseq 0.2.4
===========

* Added ordination and plotting pipeline, calcplot() and plot.ordination.phyloseq()
* All trees converted to phylo4 by default. Support for phyla achieved by coercion to phylo4.

phyloseq 0.2
===========

* Modifications for proper build, and bug tests.

phyloseq 0.1
===========

* basic data structure in place.
* some support for phylo4 objects
* import_qiime(): A Qiime input wrapper

