Package: taxinfo 0.1.2

taxinfo: Augment 'Phyloseq' Objects with Taxonomy-Based Information

Augments 'phyloseq' objects with taxonomy-based information retrieved from multiple external data sources. Provides functions to query 'GBIF' (Global Biodiversity Information Facility), 'Wikipedia', 'GLOBI' (Global Biotic Interactions), 'OpenAlex', and other databases to verify taxonomic names, retrieve occurrence data, access species interaction networks, and fetch scientific literature metadata. Designed to work with the 'phyloseq' data structure common in metabarcoding analyses. Most functions support both 'phyloseq' objects and plain taxonomic name vectors as input.

Authors:Adrien Taudiere [aut, cre, cph]

taxinfo_0.1.2.tar.gz
taxinfo_0.1.2.zip(r-4.7)taxinfo_0.1.2.zip(r-4.6)taxinfo_0.1.2.zip(r-4.5)
taxinfo_0.1.2.tgz(r-4.6-any)taxinfo_0.1.2.tgz(r-4.5-any)
taxinfo_0.1.2.tar.gz(r-4.7-any)taxinfo_0.1.2.tar.gz(r-4.6-any)
taxinfo_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
taxinfo/json (API)
NEWS

# Install 'taxinfo' in R:
install.packages('taxinfo', repos = c('https://adrientaudiere.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adrientaudiere/taxinfo/issues

Pkgdown/docs site:https://adrientaudiere.github.io

On CRAN:

Conda:

3.78 score 1 stars 1 packages 19 scripts 40 exports 177 dependencies

Last updated from:c66182e101. Checks:8 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR406
source / vignettesERROR445
linux-release-x86_64ERROR426
macos-release-arm64ERROR262
macos-oldrel-arm64ERROR219
windows-develERROR367
windows-releaseERROR352
windows-oldrelERROR355
wasm-releaseOK274

Exports:check_packagecluster_sbcextract_spores_mycodbfungal_traits_guildsgna_verifier_pqidest_colorsidest_palintra_taxnames_distplot_range_bioreg_pqplot_tax_gbif_pqpoints_to_ecoregionsrange_bioreg_pqscale_color_idest_cscale_color_idest_dscale_fill_idest_cscale_fill_idest_dselect_taxa_pqtax_check_ecoregiontax_crosscheck_pqtax_ecoregion_occurtax_ecoregion_occur_pqtax_gbif_alttax_gbif_occur_coordstax_gbif_occur_pqtax_get_wk_info_pqtax_get_wk_langtax_get_wk_pages_infotax_globi_pqtax_info_pqtax_iucn_code_pqtax_oa_pqtax_occur_checktax_occur_check_pqtax_occur_multi_check_pqtax_photos_pqtax_retroblast_pqtax_spores_size_pqtaxa_summary_texttaxonomic_rank_to_taxnamestheme_idest

Dependencies:abindade4alphahullapeaskpassBHBiobaseBiocGenericsBiocParallelbiomformatBiostringsbitbit64bitopscigarilloclassclassIntclicliprclustercodetoolscpp11crayoncrulcubaturecurldada2data.tableDBIdbmssDelayedArraydeldirdigestdiventdoFuturedplyre1071EntropyEstimationfarverfastmatchforeachformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicAlignmentsGenomicRangesggplot2globalsgluegoftestgtablehmshttpcodehttrhwriterigraphinterpIRangesisobanditeratorsjpegjsonliteKernSmoothlabelinglambda.rlatticelatticeExtralazyevallifecyclelistenvmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimeMiscMetabarmulttestnatservnlmeoaiopensslparallellypermutephangornphyloseqpillarpixmappkgconfigplyrpngpolyclipprettyunitsprogressprogressrproxypurrrpwalignquadprogR.methodsS3R.ooR.utilsR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRCurlRdpackreadrrentrezreshape2rgbifrglobiRhtslibritisrlangrnclrotlrredlistRsamtoolss2S4ArraysS4VectorsS7scalesSeqinfosfsgeostatShortReadsnowsolriumspSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilssplancsstringistringrSummarizedExperimentsurvivalsystaxizetensortibbletidyrtidyselecttriebeardtzdbunitsurltoolsutf8vctrsveganviridisLitevroomwhiskerWikipediRwikitaxawithrwkworrmsXMLxml2XVectorzoo

Readme and manuals

Help Manual

Help pageTopics
'taxinfo' packagetaxinfo-package
Check package availability and propose installation instructionscheck_package
Create Species-Bound Clusters using SWARM algorithmcluster_sbc
Extract spore size from mycoDB for a single speciesextract_spores_mycodb
Add FungalTraits and FUNGuild information to a phyloseq objectfungal_traits_guilds
Verify (and fix) scientific names (Genus species) of a phyloseq object.gna_verifier_pq
IdEst colors for ggplot theme_idestidest_colors
IdEst color palettesidest_pal
Compute intra-taxanames distances for each taxa namesintra_taxnames_dist
Format taxon labels with species names in italiclabel_italic_species
Plot the taxa occurrence using gbif.range packageplot_tax_gbif_pq
Map GPS points to WWF/TNC terrestrial ecoregionspoints_to_ecoregions
Get and plot the range of taxa within a bioregion using gbif.range packageplot_range_bioreg_pq range_bioreg_pq
IdEst continuous color scales for ggplot2scale_color_idest_c
IdEst discrete color scales for ggplot2scale_color_idest_d
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_c
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>scale_fill_idest_d
Discrete x-axis scale with species names in italicscale_x_italic_species
Discrete y-axis scale with species names in italicscale_y_italic_species
Select taxa in a phyloseq object based on names in a given column of the tax_tableselect_taxa_pq
Check whether GPS points fall in ecoregions occupied by a set of taxatax_check_ecoregion
Cross-check taxonomic names using GBIF backbone and GNA Verifiertax_crosscheck_pq
Count GBIF occurrences of taxa in each WWF/TNC terrestrial ecoregiontax_ecoregion_occur
Count GBIF occurrences per ecoregion for the taxa of a phyloseq objecttax_ecoregion_occur_pq
Get altitude range statistics for each taxa from GBIFtax_gbif_alt
Get GBIF occurrence coordinates for a vector of taxatax_gbif_occur_coords
Get number of occurrences for each taxa of a phyloseq objecttax_gbif_occur_pq
Retrieve information about taxa from wikipediatax_get_wk_info_pq
Retrieve the wikipedia pages for a given Wikidata taxon identifiertax_get_wk_lang
Retrieve information about wikipedia pages for a given taxon idtax_get_wk_pages_info
Get biotic interactions for taxa present in a phyloseq object using rglobitax_globi_pq
Get information from a custom csv file using taxonomic names present in a phyloseq objecttax_info_pq
Get iucn conservation status through gbiftax_iucn_code_pq
Get scientific works about taxa present in a phyloseq objecttax_oa_pq
Taxa occurrences check within a radius using GBIF datatax_occur_check
Check for taxa occurrences within a radius around samples using GBIF datatax_occur_check_pq
Check for taxa occurrences within a radius around multiple samples using GBIF datatax_occur_multi_check_pq
Find photos of taxa from GBIF or Wikitaxatax_photos_pq
Verify taxonomic assignment using BLAST against NCBI nucleotide databasetax_retroblast_pq
Extract spore size from mycoDBtax_spores_size_pq
Text summary for a taxonomic ranktaxa_summary_text
Extract taxonomic names from a phyloseq objecttaxonomic_rank_to_taxnames
ggplot theme for IdEsttheme_idest