Package index • taxinfo

Data Verification & Quality Control

Functions for verifying, cleaning, and standardizing taxonomic names using authoritative databases and verification services.

gna_verifier_pq(): Verify (and fix) scientific names (Genus species) of a phyloseq object.
tax_crosscheck_pq(): Cross-check taxonomic names using GBIF backbone and GNA Verifier

Core functions to retrieve and integrate taxonomic information from various external databases and APIs.

tax_info_pq(): Get information from a custom csv file using taxonomic names present in a phyloseq object

tax_gbif_occur_pq(): Get number of occurrences for each taxa of a phyloseq object
tax_gbif_alt(): Get altitude range statistics for each taxa from GBIF

tax_globi_pq(): Get biotic interactions for taxa present in a phyloseq object using rglobi

Functions to access Wikipedia, Wikidata, and other knowledge bases for taxonomic information, page statistics, and content analysis.

tax_get_wk_info_pq(): Retrieve information about taxa from wikipedia
tax_get_wk_lang(): Retrieve the wikipedia pages for a given Wikidata taxon identifier
tax_get_wk_pages_info(): Retrieve information about wikipedia pages for a given taxon id

fungal_traits_guilds(): Add FungalTraits and FUNGuild information to a phyloseq object

tax_iucn_code_pq(): Get iucn conservation status through gbif
tax_spores_size_pq(): Extract spore size from mycoDB
extract_spores_mycodb(): Extract spore size from mycoDB for a single species

Functions for validating, checking, and cross-referencing taxonomic names.

tax_occur_check(): Taxa occurrences check within a radius using GBIF data
tax_occur_check_pq(): Check for taxa occurrences within a radius around samples using GBIF data
tax_occur_multi_check_pq(): Check for taxa occurrences within a radius around multiple samples using GBIF data
tax_check_ecoregion(): Check whether GPS points fall in ecoregions occupied by a set of taxa
tax_gbif_occur_coords(): Get GBIF occurrence coordinates for a vector of taxa
tax_ecoregion_occur(): Count GBIF occurrences of taxa in each WWF/TNC terrestrial ecoregion
tax_ecoregion_occur_pq(): Count GBIF occurrences per ecoregion for the taxa of a phyloseq object
points_to_ecoregions(): Map GPS points to WWF/TNC terrestrial ecoregions

tax_retroblast_pq(): Verify taxonomic assignment using BLAST against NCBI nucleotide database

Tools for analyzing geographic distributions, biogeographic ranges, and creating distribution maps from occurrence data.

range_bioreg_pq() plot_range_bioreg_pq(): Get and plot the range of taxa within a bioregion using gbif.range package
plot_tax_gbif_pq(): Plot the taxa occurrence using gbif.range package
calculate_bbox(): Calculate Bounding Box Around a Point

Functions to retrieve and manage taxonomic images, photographs, and other media content.

Utilities for selecting, filtering, and manipulating taxonomic data within phyloseq objects.

select_taxa_pq(): Select taxa in a phyloseq object based on names in a given column of the tax_table
taxonomic_rank_to_taxnames(): Extract taxonomic names from a phyloseq object

Functions for analyzing genetic distances among taxa with the same taxonomic names and clustering into species bound cluster (SBC).

intra_taxnames_dist(): Compute intra-taxanames distances for each taxa names
cluster_sbc(): Create Species-Bound Clusters using SWARM algorithm

Helper functions for package management, data validation, and ggplot2 themes.

check_package(): Check package availability and propose installation instructions
taxa_summary_text(): Text summary for a taxonomic rank
idest_colors(): IdEst colors for ggplot theme_idest
idest_pal: IdEst color palettes
scale_color_idest_c(): IdEst continuous color scales for ggplot2
scale_color_idest_d(): IdEst discrete color scales for ggplot2
scale_fill_idest_c(): IdEst continuous fill scales for ggplot2 <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle"> <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>
scale_fill_idest_d(): IdEst discrete fill scales for ggplot2 <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle"> <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>
theme_idest(): ggplot theme for IdEst
label_italic_species(): Format taxon labels with species names in italic
scale_x_italic_species(): Discrete x-axis scale with species names in italic
scale_y_italic_species(): Discrete y-axis scale with species names in italic

Package documentation and metadata.