Renamed function to read QIIME mapping files, added tests.
Renamed parse_otu_table to read_qiime_otu_table, detect metadata column in OTU tables according to conventions in QIIME source code.  Counts table was returned as data frame despite the documentation, now returned as matrix.

Improved interface to parse_assignments and renamed as split_assignments.

Introduced new function, simplify_assignments, to create taxa labels for plots.  Eliminated prettyprint_assignments in favor of simplify_assignments.

Function otu_heatmap now invisibly returns the matrix of data displayed in the plot, and has a flag to suppress plotting.

Improved and simplified the implementation of the saturated_rainbow palette.

Eliminated the otu_barplot function.

Added tests for all functions listed above.
Improved documentation for read_qiime_sample_mapping
Renamed parse_otu_mapping to read_qiime_otu_mapping.

Added names for dimensions of table returned by make_otu_table.

Added tests for read_qiime_otu_mapping and make_otu_table.
Forgot to add OTU table tests in earlier commit.
Renamed parse_distmat to read_qiime_distmat.

Fixed bug in dist_get if diagonal elements are selected.

Fixed bug of inconsistent labels in dist_groups if groups were not pre-sorted.

Added tests for all functions.
Renamed parse_blast_table to read_blast_table.

Added tests for read_blast_table.
Renamed raw_biom_data to biom_raw_data.

Bypassed bug in biom package where row or column names are sometimes not returned correctly.

Added tests for biom_raw_data and biom_taxonomy.
Renamed parse_rarefaction to read_qiime_rarefaction.

Changed implementation to eliminate dependency on reshape2 and plyr.

Added tests for read_qiime_rarefaction and rarefaction_stats.
Updated DESCRIPTION, removed extra man files.