Package: taxa 0.4.3

Zachary Foster

taxa: Classes for Storing and Manipulating Taxonomic Data

Provides classes for storing and manipulating taxonomic data. Most of the classes can be treated like base R vectors (e.g. can be used in tables as columns and can be named). Vectorized classes can store taxon names and authorities, taxon IDs from databases, taxon ranks, and other types of information. More complex classes are provided to store taxonomic trees and user-defined data associated with them.

Authors:Scott Chamberlain [aut], Zachary Foster [aut, cre]

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taxa/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/ropensci/taxa/issues

On CRAN:

taxonomybiologyhierarchydata-cleaningtaxon

55 exports 48 stars 3.17 score 20 dependencies 451 downloads

Last updated 4 months agofrom:9f2353a3d7871b576b5f7b18877d236c1478e977 (via master)

Exports:%>%%in%as_data_frameas_taxonclassificationcontainsdb_refends_witheverythinginternodesis_classificationis_internodeis_leafis_rootis_stemis_taxonis_taxon_authorityis_taxon_dbis_taxon_idis_taxon_rankis_taxonomyleavesmatchesn_leavesn_subtaxan_supertaxanum_rangeone_ofrootsstarts_withstemssubtaxasupertaxatax_authtax_auth<-tax_authortax_author<-tax_citetax_cite<-tax_datetax_date<-tax_dbtax_db<-tax_idtax_id<-tax_nametax_name<-tax_ranktax_rank<-taxontaxon_authoritytaxon_dbtaxon_idtaxon_ranktaxonomy

Dependencies:clicrayondplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigR6rlangstringistringrtibbletidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Value matching for taxa package%in%
Convert a taxa object to a 'data.frame'as_data_frame
Convert to a taxon vectoras_taxon
Taxon classclassification
Valid taxonomy databasesdb_ref
Get internodesinternodes
Check if is a classificationis_classification
Check if taxa are internodesis_internode
Check if taxa are leavesis_leaf
Test if taxa are rootsis_root
Check if taxa are stemsis_stem
Check if something is a taxon objectis_taxon
Check if is a taxon_authorityis_taxon_authority
Check if something is a taxon_dbis_taxon_db
Check if something is a taxon_id objectis_taxon_id
Check if something is a taxon_rankis_taxon_rank
Check if something is a taxonomyis_taxonomy
Get leavesleaves
Number of leaves per taxonn_leaves
Number of subtaxa per taxonn_subtaxa
Number of supertaxa per taxonn_supertaxa
Get root taxaroots
Get stemsstems
Get subtaxasubtaxa
Get supertaxasupertaxa
Set and get taxon authoritiestax_auth tax_auth.taxa_classification tax_auth.taxa_taxon tax_auth.taxa_taxonomy tax_auth<- tax_auth<-.taxa_classification tax_auth<-.taxa_taxon tax_auth<-.taxa_taxonomy
Set and get taxon authorstax_author tax_author.taxa_classification tax_author.taxa_taxon tax_author.taxa_taxonomy tax_author.taxa_taxon_authority tax_author<- tax_author<-.taxa_classification tax_author<-.taxa_taxon tax_author<-.taxa_taxonomy tax_author<-.taxa_taxon_authority
Set and get taxon authority citationstax_cite tax_cite.taxa_classification tax_cite.taxa_taxon tax_cite.taxa_taxonomy tax_cite.taxa_taxon_authority tax_cite<- tax_cite<-.taxa_classification tax_cite<-.taxa_taxon tax_cite<-.taxa_taxonomy tax_cite<-.taxa_taxon_authority
Set and get taxon authority datestax_date tax_date.taxa_classification tax_date.taxa_taxon tax_date.taxa_taxonomy tax_date.taxa_taxon_authority tax_date<- tax_date<-.taxa_classification tax_date<-.taxa_taxon tax_date<-.taxa_taxonomy tax_date<-.taxa_taxon_authority
Set and get taxon ID databasestax_db tax_db.taxa_classification tax_db.taxa_taxon tax_db.taxa_taxonomy tax_db.taxa_taxon_id tax_db<- tax_db<-.taxa_classification tax_db<-.taxa_taxon tax_db<-.taxa_taxonomy tax_db<-.taxa_taxon_id
Set and get taxon IDstax_id tax_id.taxa_classification tax_id.taxa_taxon tax_id.taxa_taxonomy tax_id<- tax_id<-.taxa_classification tax_id<-.taxa_taxon tax_id<-.taxa_taxonomy
Set and get taxon namestax_name tax_name.taxa_classification tax_name.taxa_taxon tax_name.taxa_taxonomy tax_name<- tax_name<-.taxa_classification tax_name<-.taxa_taxon tax_name<-.taxa_taxonomy
Set and get taxon rankstax_rank tax_rank.taxa_classification tax_rank.taxa_taxon tax_rank.taxa_taxonomy tax_rank<- tax_rank<-.taxa_classification tax_rank<-.taxa_taxon tax_rank<-.taxa_taxonomy
Taxon authority classtaxa_taxon_authority taxa_taxon_authority-class
Taxon database classtaxa_taxon_db taxa_taxon_db-class
Taxon ID classtaxa_taxon_id taxa_taxon_id-class
Taxon rank classtaxa_taxon_rank taxa_taxon_rank-class
Taxon classtaxa_taxon taxa_taxon-class
Taxonomy classtaxa_taxonomy taxa_taxonomy-class
Taxon classtaxon
Taxon authority classtaxon_authority
Taxon database classtaxon_db
Taxon ID classtaxon_id
Taxon rank classtaxon_rank