Now requires minimum version of R instead of exact match, see issue #624
Merge branch 'master' of github.com:qiime/qiime
Merge branch 'master' of github.com:qiime/qiime
Fixes issue #798
RExecutor tests now respect qiime temp dir.
Alternative hypothesis is now explicitly stated.

Alternative hypothesis is now stated in the output stats file. Affects make_distance_boxplots.py and make_distance_comparison_plots.py. Also updated script usage example output.

Verified this using the overview tutorial dataset, as well as with smaller examples in R and using PyCogent's t_two_sample.

Fixes #657.
summarize_taxa.py outputs in BIOM and TSV formats.

By default, summarize_taxa.py creates output taxa summary tables in TSV (classic) and BIOM formats. This is the first step towards full BIOM taxon table integration in QIIME.

summarize_taxa.py also has two new options: --suppress_classic_table_output and --suppress_biom_table_output.

Updated the script usage example output for summarize_taxa.py and summarize_taxa_through_plots.py.

Fixes #163.
Merge pull request #911 from jrrideout/issue-163

summarize_taxa.py now writes output tables in BIOM and TSV formats.
Merge pull request #909 from jrrideout/r_tmp_dir_2

RExecutor tests now respect qiime temp dir.
Merge pull request #898 from danknights/master

Remove std dev reporting for LOO error estimates in supervised learning, fixes issue #798
Merge branch 'master' into issue-657

Conflicts:
	ChangeLog.md
Merge pull request #910 from jrrideout/issue-657

Alternative hypothesis is now explicitly stated.