NEWS.md
In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

metagMisc v.0.5.0 (git xxxx; Mar xx, 2023)

New functions
make rarefaction based on RTK
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

metagMisc v.0.0.4 (git b0802ea; Feb 13, 2018)

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
New 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

metagMisc v.0.0.3 (git 924976f; Nov 8, 2017)

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

metagMisc v.0.0.2 (git fd2697b; Oct 4, 2017)

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