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:
taxa_0.4.3.tar.gz
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taxa.pdf |taxa.html✨
taxa/json (API)
NEWS
| # Install 'taxa' in R: |
| install.packages('taxa', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ropensci/taxa/issues
taxonomybiologyhierarchydata-cleaningtaxon
Last updated 5 months agofrom:9f2353a3d7 (on 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 page | Topics |
|---|---|
| Value matching for taxa package | %in% |
| Convert a taxa object to a 'data.frame' | as_data_frame |
| Convert to a taxon vector | as_taxon |
| Taxon class | classification |
| Valid taxonomy databases | db_ref |
| Get internodes | internodes |
| Check if is a classification | is_classification |
| Check if taxa are internodes | is_internode |
| Check if taxa are leaves | is_leaf |
| Test if taxa are roots | is_root |
| Check if taxa are stems | is_stem |
| Check if something is a taxon object | is_taxon |
| Check if is a taxon_authority | is_taxon_authority |
| Check if something is a taxon_db | is_taxon_db |
| Check if something is a taxon_id object | is_taxon_id |
| Check if something is a taxon_rank | is_taxon_rank |
| Check if something is a taxonomy | is_taxonomy |
| Get leaves | leaves |
| Number of leaves per taxon | n_leaves |
| Number of subtaxa per taxon | n_subtaxa |
| Number of supertaxa per taxon | n_supertaxa |
| Get root taxa | roots |
| Get stems | stems |
| Get subtaxa | subtaxa |
| Get supertaxa | supertaxa |
| Set and get taxon authorities | tax_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 authors | tax_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 citations | tax_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 dates | tax_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 databases | tax_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 IDs | tax_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 names | tax_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 ranks | tax_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 class | taxa_taxon_authority taxa_taxon_authority-class |
| Taxon database class | taxa_taxon_db taxa_taxon_db-class |
| Taxon ID class | taxa_taxon_id taxa_taxon_id-class |
| Taxon rank class | taxa_taxon_rank taxa_taxon_rank-class |
| Taxon class | taxa_taxon taxa_taxon-class |
| Taxonomy class | taxa_taxonomy taxa_taxonomy-class |
| Taxon class | taxon |
| Taxon authority class | taxon_authority |
| Taxon database class | taxon_db |
| Taxon ID class | taxon_id |
| Taxon rank class | taxon_rank |
