vmikk/metagMisc: v.0.0.4

This is a checkpoint release of metagMisc as of 2018-02-13. New in v.0.0.4:

New functions:

• phyloseq_mult_raref_div - for averaging of diversity metrics across multiple rarefaction iterations
• phyloseq_to_MetaCommunity - converter of phyloseq class to MetaCommunity object from entropart package
• phyloseq_otu_occurrence - estimates taxa occurrence or occurrence frequency
• phyloseq_standardize_otu_abundance - wrapper of decostand function from vegan package
• phyloseq_filter_top_taxa - extracts the most abundant taxa from phyloseq-objects
• phyloseq_add_max_tax_rank - adds the lowest level of taxonomic classification to the taxonomy table
• taxonomy_to_qiime - prepares taxonomy in QIIME-style

Experimental functions:

• phyloseq_average
• phyloseq_mult_raref_avg This functions implements OTU abundance averaging following compositional data analysis workflow.

Bug fixes:

• phyloseq_mult_raref - multithreading fix
• phyloseq_to_df - fix bug with taxonomy order
• parse_taxonomy_amptk_batch - fix column reordering
• phyloseq_transform_vst_blind - add workaround for excessive zeros

++ Documentation and some minor updates.