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Changelog

Source: NEWS.md

taxinfo 0.1.2

Major Changes

  • Changed default behavior: The add_to_phyloseq parameter now defaults to TRUE when a phyloseq object is provided, and FALSE when using the taxnames parameter. This makes the workflow more intuitive - when working with phyloseq objects, the enriched object is returned by default.

New Features

  • tax_photos_pq() now works correctly with gallery = TRUE regardless of the add_to_phyloseq value: when add_to_phyloseq = TRUE the gallery is printed as a side-effect and the updated phyloseq object is returned invisibly. The pixture package dependency has been removed; the gallery is now built with htmltools (available on CRAN). Two new parameters img_height and img_width replace the previous h/w arguments passed via ... to pixture::pixgallery().

  • Add fungal_traits_guilds() to enrich a phyloseq tax_table with guild and trait information from both the FungalTraits and FUNGuild databases in a single call. The function automatically calls [gna_verifier_pq()] when currentCanonicalSimple is absent, and optionally produces consensus columns (cons_trophicMode, cons_trophicMode_agreement) comparing the two sources.

  • All main functions (gna_verifier_pq(), tax_gbif_occur_pq(), tax_get_wk_info_pq(), tax_globi_pq(), tax_info_pq(), tax_iucn_code_pq(), tax_oa_pq(), tax_occur_check_pq(), tax_photos_pq()) now support the taxnames parameter, allowing users to query information for specific taxonomic names without a phyloseq object.

  • Added comprehensive tests for taxnames parameter usage across all functions.

  • Add functions extract_spores_mycodb() and tax_spores_size_pq() to retrieve spore size information from MycoDB.

  • Add params year_col and authorship_col to gna_verifier_pq() to output year of publication and authorship information for each taxa.

  • Add function intra_taxnames_dist() to compute pairwise DNA distances among taxa with the same taxonomic names.

  • Add function cluster_sbc() to (post)cluster taxa into SBC (Species bound cluster) defined as “clusters that include all and only ESVs assigned to one species, the sequence similarity threshold can vary between these clusters” by Riley et al. 2025 (https://doi.org/10.1186/s12915-025-02284-x). Also add a new vignette to illustrate the use of cluster_sbc().

  • Print information when using tax_info_pq() with add_to_phyloseq = TRUE to inform users that the phyloseq object is being updated.

  • Add an example in tax_info_pq() manual with the EPPO database to determine if pest species regulated in France are found in the example phyloseq object.

  • Change the result column genus into genusEpithet from the gna_verifier_pq() function to avoid confusion between “Genus” and “genus” columns and to debug the use of duckdb in taxinfo_pq().

Bug fix

Documentation

  • Updated documentation for all functions to clarify the new default behavior of add_to_phyloseq.
  • Added examples showing both phyloseq and taxnames usage patterns.
  • Updated vignettes to demonstrate the dual-input capability (phyloseq objects vs. taxonomic name vectors).
  • Updated README to highlight the flexible input options.

taxinfo 0.1.1

  • Add list_keywords and n_citation columns in the return of tax_oa_pq().

taxinfo 0.1.0

  • Initial github submission.