/usr/lib/R/site-library/taxize/INDEX is in r-cran-taxize 0.9.0-1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 | apg Get APG names
apg_families MOBOT family names
apg_lookup Lookup in the APGIII taxonomy and replace
family names
apg_orders MOBOT order names
bold_search Search Barcode of Life for taxonomic IDs
children Retrieve immediate children taxa for a given
taxon name or ID.
class2tree Convert list of classifications to a tree.
classification Retrieve the taxonomic hierarchy for a given
taxon ID.
col_children Search Catalogue of Life for for direct
children of a particular taxon.
col_downstream Use Catalogue of Life to get downstream taxa to
a given taxonomic level.
col_search Search Catalogue of Life for taxonomic IDs
comm2sci Get scientific names from common names.
downstream Retrieve the downstream taxa for a given taxon
name or ID.
eol_dataobjects Given the identifier for a data object, return
all metadata about the object
eol_pages Search for pages in EOL database using a
taxonconceptID.
eol_search Search for terms in EOL database.
eubon EUBON taxonomy search
eubon_capabilities EUBON capabilities
eubon_children EUBON children
eubon_hierarchy EUBON hierarchy
fungorum Index Fungorum
gbif_downstream Retrieve all taxa names downstream in hierarchy
for GBIF
gbif_name_usage Lookup details for specific names in all
taxonomies in GBIF.
gbif_parse Parse taxon names using the GBIF name parser.
genbank2uid Get NCBI taxonomy UID from GenBankID
get_boldid Get the BOLD (Barcode of Life) code for a
search term.
get_colid Get the Catalogue of Life ID from taxonomic
names.
get_eolid Get the EOL ID from Encyclopedia of Life from
taxonomic names.
get_gbifid Get the GBIF backbone taxon ID from taxonomic
names.
get_id_details Details on 'get_*()' functions
get_ids Retrieve taxonomic identifiers for a given
taxon name.
get_iucn Get a IUCN Redlist taxon
get_natservid Get NatureServe taxonomic ID for a taxon name
get_nbnid Get the UK National Biodiversity Network ID
from taxonomic names.
get_tolid Get the OTT id for a search term
get_tpsid Get the NameID codes from Tropicos for
taxonomic names.
get_tsn Get the TSN code for a search term.
get_ubioid Get the uBio id for a search term
get_uid Get the UID codes from NCBI for taxonomic
names.
get_wiki Get the page name for a Wiki taxon
get_wormsid Get Worms ID for a taxon name
gni_details Search for taxonomic name details using the
Global Names Index.
gni_parse Parse scientific names using EOL's name parser.
gni_search Search for taxonomic names using the Global
Names Index.
gnr_datasources Get data sources for the Global Names Resolver.
gnr_resolve Resolve names using Global Names Resolver.
ion ION - Index to Organism Names
iplant_resolve iPlant name resolution
ipni_search Search for names in the International Plant
Names Index (IPNI).
itis_acceptname Retrieve accepted TSN and name
itis_downstream Retrieve all taxa names or TSNs downstream in
hierarchy from given TSN.
itis_getrecord Get full ITIS record for one or more ITIS TSN's
or lsid's.
itis_hierarchy ITIS hierarchy
itis_kingdomnames Get kingdom names
itis_lsid Get TSN from LSID
itis_name Get taxonomic names for a given taxonomic name
query.
itis_native Get jurisdiction data, i.e., native or not
native in a region.
itis_refs Get references related to a ITIS TSN.
itis_taxrank Retrieve taxonomic rank name from given TSN.
itis_terms Get ITIS terms, i.e., tsn's, authors, common
names, and scientific names.
iucn_getname Get any matching IUCN species names
iucn_id Get an ID for a IUCN listed taxon
iucn_status Extractor functions for 'iucn'-class.
iucn_summary Get a summary from the IUCN Red List
lowest_common Retrieve the lowest common taxon and rank for a
given taxon name or ID
names_list Get a random vector of species names.
nbn_classification Search UK National Biodiversity Network
database for taxonomic classification
nbn_search Search UK National Biodiversity Network
nbn_synonyms Return all synonyms for a taxon name with a
given id from NBN
ncbi_children Search NCBI for children of a taxon
ncbi_downstream Retrieve all taxa names downstream in hierarchy
for NCBI
ncbi_get_taxon_summary
NCBI taxon information from uids
phylomatic_format Get family names to make Phylomatic input
object, and output input string to Phylomatic
for use in the function phylomatic_tree.
phylomatic_tree Query Phylomatic for a phylogenetic tree.
ping Ping an API used in taxize to see if it's
working.
plantGenusNames Vector of plant genus names from ThePlantList
plantNames Vector of plant species (genus - specific
epithet) names from ThePlantList
plantminer Search for taxonomy data from Plantminer.com
rank_ref Lookup-table for IDs of taxonomic ranks
rankagg Aggregate data by given taxonomic rank
resolve Resolve names from different data sources
sci2comm Get common names from scientific names.
scrapenames Resolve names using Global Names Recognition
and Discovery.
status_codes Get HTTP status codes
synonyms Retrieve synonyms from various sources given
input taxonomic names or identifiers
tax_agg Aggregate species data to given taxonomic rank
tax_name Get taxonomic names for a given rank
tax_rank Get rank for a given taxonomic name.
taxize-defunct Defunct functions in taxize
taxize-package Taxonomic Information from Around the Web
taxize_capwords Capitalize the first letter of a character
string.
taxize_cite Get citations and licenses for data sources
used in taxize
theplantlist Lookup-table for family, genus, and species
names for ThePlantList
tnrs Phylotastic Taxonomic Name Resolution Service.
tnrs_sources TNRS sources
tol_resolve Resolve names using Open Tree of Life (OTL)
resolver
tp_accnames Return all accepted names for a taxon name with
a given id.
tp_dist Return all distribution records for for a taxon
name with a given id.
tp_refs Return all reference records for for a taxon
name with a given id.
tp_search Search Tropicos by scientific name, common
name, or Tropicos ID.
tp_summary Return summary data a taxon name with a given
id.
tp_synonyms Return all synonyms for a taxon name with a
given id.
tpl_families Get The Plant List families.
tpl_get Get The Plant List csv files.
tpl_search A light wrapper around the taxonstand fxn to
call Theplantlist.org database.
ubio_classification uBio classification
ubio_classification_search
This function will return ClassificationBankIDs
(hierarchiesIDs) that refer to the given
NamebankID
ubio_id Search uBio by namebank ID.
ubio_ping uBio ping
ubio_search This function will return NameBankIDs that
match given search terms
ubio_synonyms Search uBio for taxonomic synonyms by
hierarchiesID.
upstream Retrieve the upstream taxa for a given taxon
name or ID.
vascan_search Search the CANADENSYS Vascan API.
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