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.

v.0.0.3

This is a checkpoint release of metagMisc as of 2017-11-08.
New in v.0.0.3:

New functions:

• phyloseq_phylo_div - for phylogenetic diversity estimation
• phyloseq_phylo_ses - standardized effect size for phylogenetic diversity
• phyloseq_randomize - randomization of abundance table and phylogeny in phyloseq objects (for null model testing and simulation)
• mult_dissim - compute beta diversity for each rarefaction iteration
• mult_dist_average - average multiple distance matrices
• dissimilarity_to_distance - transform (non-metric) dissimilarity matrix to a weighted Euclidean distance (metric), as in Greenacre 2017
• add_metadata - wrapper to add sample metadata to data frames
• uc_to_sumaclust - convert UC files (from USEARCH or VSEARCH) to Sumaclust OTU observation maps

Enhancements:

• phyloseq_mult_raref is able to run in parallel now; custom seeds option and rarefaction attributes were added, fixed auto-detection of rarefaction depth
• phyloseq_compare was completely rewritten to allow for one or multiple input phyloseq objects; additional abundance statistics were added; fixed bug with percentage estimation
• prevalence - mean and median OTU abundance were added

++ Documentation updates and some other improvements.

Side notes: this version was used on a SLURM cluster.

v.0.0.2

This is a checkpoint release of metagMisc as of 2017-10-03.
New in v.0.0.2:

New functions:

• prepare_inext
• phyloseq_filter_sample_wise_abund_trim
• make_utax_taxonomy
• make_utax_taxonomy_batch
• check_tax_uniqueness

Enhancements:

• phyloseq_group_dissimilarity - generalized to more than 2 groups
• phyloseq_filter_prevalence - added conditional option (AND/OR) for abundance and prevalence filtering

++ Documentation updates.

v.0.0.1

This is a checkpoint release of metagMisc as of 2017-08-23.
New in v.0.0.1:

Data-handling functions:

• phyloseq_filter_prevalence
• phyloseq_prevalence_plot
• physeq_rm_na_tax
• phyloseq_sep_variable

Functions for dissimilarity analysis:

• phyloseq_group_dissimilarity
• MultSE

Functional diversity related functions:

• predict_metagenomes
• metagenome_contributions
• filter_cazy

General purpose functions:

• some
• dist2list

++ Documentation updates and bug fixes.

v.0.0.0.9000

The first alpha release of metagMisc.