0.5.0

metagMisc v.0.5.0 (git 621e9cf, March 20, 2024)

• New functions

  • phyloseq_num_shared_otus.R - estimation of the number of shared and non-shared OTUs between all pairwise combinations of samples
  • phyloseq_bootstrap - bootstraps samples in phyloseq object
  • phyloseq_combine_samples - sums OTU abundances of replicates or sample groups into a single sample
  • phyloseq_coverage - estimates the observed abundance-based sample coverage
  • coverage_to_samplesize - estimates the required sample size for a particular coverage
  • phyloseq_coverage_raref - coverage-based rarefaction
  • phyloseq_effort_div - computes OTU diversity for a particular sample size or coverage
  • phyloseq_effort_div_rangeplot - vizualization of OTU diversity and richness for a particular sequencing depth or sample coverage ranges
  • phyloseq_otu_appearance - determines which OTUs appeared or disappeared in comparison with reference sample group
  • phyloseq_richness_filter - removes samples from phyloseq object that have less than n taxa
  • phyloseq_inext - estimates interpolated and extrapolated Hill numbers and sample coverage and constructs rarefaction curve
  • phyloseq_merge_samples - merges samples by name
  • phyloseq_mult_raref_dist - performs multiple rarefactions and averages sample dissimilarity across rarefactions
  • phyloseq_rename_with_tax - renames phyloseq OTUs or species with taxonomy ranks
  • phyloseq_sep_pairwise - splits phyloseq-class object for pairwise comparisons by sample-level variable
  • phyloseq_taxonomic_resolution - summarizes taxonomic resolution of the data
  • phyloseq_taxonomy_imputation - replaces missing taxonomy with higher ranks
  • phyloseq_replace_zero - replaces zeros in OTU abundance with psudocount or min observed abundnce
  • phyloseq_transform_aldex_clr - performs ALDEx2-based centred log-ratio transformation of OTU table
  • get_max_taxonomic_rank_DT - determines the lowest level of taxonomic classification (with data.table)
  • prepare_breakaway - prepares frequency counts for breakaway package
  • raref_rtk - RTK-based rarefaction
  • read_m8 - reads the standard BLAST m8 format (-outfmt 6)
  • blast_to_wide - converts BLAST results to a wide table
  • SES - standardized effect size estimation
  • centroid_coords - coordinates of centroids and medoids
  • chunk - split vector into chunks of equal size
  • chunk_table - split data.table into chunks
  • count_primers - counts number of reads in which the primer is found
  • jaccard_bray - converts between Bray-Curtis and Jaccard dissimilarity indicies
  • leading_zero - adds or removes leading zeros
  • zero_pad - pads a number with leading zeros
  • package_availability - checks the availability of dependencies
  • vegdist_zero - Bray-Curtis index with double-zero support

• Bug fixes

  • phyloseq_extract_shared_otus and phyloseq_extract_non_shared_otus - issue warning in the case if no OTUs were found
  • get_max_taxonomic_rank - data types bug
  • phyloseq_average - progress bar fixed
  • parse_uc - fixed a column name problem
  • prevalence was added to NAMESPACE (thanks @LukDrey for reporting the issue)

• The other updates

  • phyloseq_to_df - handles taxa as rows case and checks the presence of taxonomy in phyloseq object
  • parse_uc - is much faster now with data.table
  • parse_uc - new option to remove duplicated rows
  • parse_taxonomy_amptk rewritten
  • parse_taxonomy_amptk_batch - supports multithreading now
  • phyloseq_standardize_otu_abundance - added wisconsin and rhea methods
  • phyloseq_filter_prevalence - informative error messages added
  • phyloseq_sep_variable - informative error messages added
  • phyloseq_summary - add OTU occurrence stats
  • eig_perc - added plots of explained variance percentages
  • adonis_pairwise
  • phyloseq_ntaxa_by_tax
  • some - works with phyloseq now
  • taxonomy_to_qiime - supports Domain rank and performs validation of user-supplied ranks
  • phyloseq_otu_occurrence - added counts
  • phyloseq_filter_sample_wise_abund_trim - added relative abundance option
  • phyloseq_phylo_ses - added VPD metric
  • phyloseq_group_dissimilarity - added comparison types (between/within group)
  • phyloseq_extract_shared_otus - estimates percentage of shared OTUs
  • prevalence is now much faster with data.table

• New logo, designed by Olesya Dulya

• Documentation updates

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.