v 0.14.4

New CRAN submission

What's Changed

• v 0.14.2 by @adrientaudiere in #114
• v 0.14.3 by @adrientaudiere in #116
• merge to dev by @adrientaudiere in #117
• Harmonize parameter names and documentation format for consistency by @Copilot in #119
• Performance improvements: optimize memory allocation and vectorize operations by @Copilot in #120
• Dev by @adrientaudiere in #121
• Fix bug introduced by ggplot2 v4.0.0 and upset_plot by @adrientaudiere in #123

New Contributors

• @Copilot made their first contribution in #119

Full Changelog: v0.14...v0.14.4

v 0.14.0

Merge pull request #113 from adrientaudiere/dev

v 0.14

v 0.13.0

Merge pull request #112 from adrientaudiere/dev

v 0.13

v 0.12.0

• Add function [assign_idtaxa()] and [learn_idtaxa()] to facilitate the taxonomic assignation using the idtaxa algorithm from the DECIPHER R package.
• Add option idtaxa to method in [add_new_taxonomy_pq()]
• Add function [tbl_sum_taxtable()] to summarize tax_table from a phyloseq object
• In function [assign_sintax()], add params too_few (default value "align_start") and too_many (default "merge") to authorize db with variable numbers of rank and parenthesis in taxonomic name,

v 0.11.0

• Add function filt_taxa_pq() to filter taxa based on the number of sequences/occurences
• Add functions no_legend() and hill_curves_pq() to plot hill diversity accumulation curves for phyloseq
• Add function umap_pq() to compute Dimensionality Reduction with UMAP
• Add function plot_complexity_pq() to plot kmer complexity of references sequences of a phyloseq object
• Add param type to ridge_pq() to plot a cumulative version (type="ecdf") version of ridge
• Introduce the idea of a pq-verse: some other packages will complete the MiscMetabar packages to make package maintenance easier. The comparpq package will facilitate the comparison of phyloseq object with different taxonomy, different clustering methods, different samples with same modality or different primers.
• Add functions [assign_vsearch_lca()], [assign_sintax()] and internal function [write_temp_fasta()]
• Add param method to add_new_taxonomy_pq() to allow the use of [dada2::assign_taxonomy()] (default, precedent only method available), [assign_sintax()] or [assign_vsearch_lca()]

v 0.10.4

v0.10.4

Merge pull request #106 from adrientaudiere/dev

v 0.10.3

v.0.10.3

Merge pull request #105 from adrientaudiere/dev

v 0.10.1

Merge pull request #101 from adrientaudiere/dev

v 0.10.1

v 0.9.3

Merge pull request #99 from adrientaudiere/dev

test: Change value in test for different version of vsearch

v 0.9.2

Merge pull request #93 from adrientaudiere/dev

style: Improve code factor notation