1. Getting started | 2. Extracting a species list from a vegetation table | 2.1 Example data | 2.2 From plain list to taxlist | 3. Built-in data set | 3.1 Easplist | 3.2 Access to slots | 3.3 Subsets | 3.4 Hierarchical structure | 4. Applying taxlist to syntaxonomic schemes | 4.1 Example of a phytosociological classification | 4.2 Building the taxlist object
Package: taxlist 0.3.6
Miguel Alvarez
taxlist: Handling Taxonomic Lists
Handling taxonomic lists through objects of class 'taxlist'. This package provides functions to import species lists from 'Turboveg' (<https://www.synbiosys.alterra.nl/turboveg/>) and the possibility to create backups from resulting R-objects. Also quick displays are implemented as summary-methods.
Authors:
taxlist_0.3.6.tar.gz
taxlist_0.3.6.zip(r-4.7)taxlist_0.3.6.zip(r-4.6)taxlist_0.3.6.zip(r-4.5)
taxlist_0.3.6.tgz(r-4.6-any)taxlist_0.3.6.tgz(r-4.5-any)
taxlist_0.3.6.tar.gz(r-4.7-any)taxlist_0.3.6.tar.gz(r-4.6-any)
taxlist_0.3.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
taxlist/json (API)
| # Install 'taxlist' in R: |
| install.packages('taxlist', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org')) |
Reviews:rOpenSci Software Review #233
Bug tracker:https://github.com/ropensci/taxlist/issues
Pkgdown/docs site:https://docs.ropensci.org
Datasets:
- Easplist - List of vascular plants from East Africa
Last updated from:7e74a1b420 (on main). Checks:10 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 153 | ||
| pkgdown docs | OK | 155 | ||
| source / vignettes | OK | 222 | ||
| linux-release-x86_64 | OK | 169 | ||
| macos-release-arm64 | OK | 94 | ||
| macos-oldrel-arm64 | OK | 104 | ||
| windows-devel | OK | 98 | ||
| windows-release | OK | 103 | ||
| windows-oldrel | OK | 95 | ||
| wasm-release | OK | 161 |
Exports:accepted_nameaccepted_name<-add_conceptadd_leveladd_parentadd_synonymadd_traitadd_viewbackup_objectbasionymbasionym<-change_concept<-cleanclean_stringscount_taxadelete_namedf2taxlistdissect_nameget_childrenget_parentsid_generatorid_solverindented_listinsert_rowslevelslevels<-levels<-.taxlistload_lastmatch_namesmerge_taxamerge_to_parentparentsprintprint_nameprune_levelsreindexreindex<-replace_idxreplace_nareplace_viewreplace_xS4_to_listshowsort_backupssort_taxasubsetsummarysynonymstax2traitstaxlist2dftaxlist2taxmaptaxmap2taxlisttaxon_namestaxon_names<-taxon_relationstaxon_relations<-taxon_traitstaxon_traits<-taxon_viewstaxon_views<-tnrstv2taxlistupdate_conceptupdate_nameupdate_trait
Dependencies:base64encbibliobslibcachemclicommonmarkcrosstalkcrulcurldigestdplyrDTevaluatefastmapfontawesomeforeignfsgenericsgluehighrhtmltoolshtmlwidgetshttpcodehttpuvjquerylibjsonliteknitrlaterlazyevallifecyclemagrittrmemoisemimeminiUIotelpillarpkgconfigplyrpromisesR6rappdirsRcpprcrossrefrlangrmarkdownsassshinysourcetoolsstringdiststringistringrtibbletidyselecttinytextriebeardurltoolsutf8vctrswithrxfunxml2xtableyamlyamlme
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Manage accepted names, synonyms and basionyms | accepted_name accepted_name,taxlist-method accepted_name.taxlist accepted_name<- accepted_name<-,taxlist-method accepted_name<-.taxlist basionym basionym,taxlist-method basionym.taxlist basionym<- basionym<-,taxlist-method basionym<-.taxlist change_concept<- change_concept<-,taxlist-method change_concept<-.taxlist synonyms synonyms,taxlist-method synonyms.taxlist |
| Add new taxonomic concepts into taxlist objects | add_concept add_concept,taxlist,character-method add_concept,taxlist,data.frame-method add_concept,taxlist,taxlist-method update_concept |
| Coerce taxlist objects to lists. | as coerce,character,taxlist-method coerce,data.frame,taxlist-method coerce,taxlist,data.frame-method coerce,taxlist,list-method S4_to_list |
| Make and load backups of R objects | backup_object load_last sort_backups |
| Delete orphaned records | clean clean,taxlist-method |
| Cleaning character strings. | clean_strings clean_strings,character-method clean_strings,data.frame-method clean_strings,factor-method |
| Count taxa within a taxlist object. | count_taxa count_taxa,character,missing-method count_taxa,factor,missing-method count_taxa,formula,taxlist-method count_taxa,taxlist,missing-method |
| Deprecated functions | add_level add_parent add_trait Deprecated-functions replace_view taxlist2taxmap taxmap2taxlist tnrs |
| Convert data frames and strings into taxlist objects | df2taxlist df2taxlist,character-method df2taxlist,data.frame-method df2taxlist.character df2taxlist.data.frame |
| Dissect Scientific Names into their Elements | dissect_name |
| List of vascular plants from East Africa | Easplist Easplist-data |
| Extract or Replace Parts of taxlist Objects | $ $,taxlist-method Extract [ [,taxlist-method |
| Retrieve children or parents of taxon concepts | get_children get_children,taxlist-method get_children.taxlist get_parents get_parents,taxlist-method get_parents.taxlist |
| Generate Identifiers | id_generator id_solver |
| Print hierarchical structure in indented lists | indented_list indented_list,taxlist-method |
| Insert additional rows to a data frame. | insert_rows insert_rows,data.frame,data.frame-method |
| Set and retrieves hierarchical levels | levels levels,taxlist-method levels.taxlist levels<- levels<-,taxlist-method levels<-.taxlist |
| Search matchings between character and taxlist objects | match_names match_names,character,character-method match_names,character,missing-method match_names,character,taxlist-method |
| Names matched with a reference taxonomic list | matched_names-class |
| Merge concepts or move names | merge_taxa merge_taxa,taxlist-method merge_taxa.taxlist |
| Merge taxa to their respective parents | merge_to_parent merge_to_parent,taxlist-method merge_to_parent.taxlist |
| Retrieve parents for specific concepts | parents parents,taxlist,character-method |
| Format usage names for publications | print_name print_name,character-method print_name,taxlist-method print_name.character print_name.taxlist |
| Prune not used taxonomic ranks | prune_levels prune_levels,taxlist-method prune_levels.taxlist |
| Re-index elements of taxlist objects | reindex reindex,taxlist-method reindex.taxlist reindex<- reindex<-,taxlist-method reindex<-.taxlist |
| Data manipulation. | replace_idx replace_na replace_x |
| Sort taxa for further print | sort_taxa sort_taxa,taxlist-method sort_taxa.taxlist |
| Subset method for taxlist objects | subset subset,taxlist-method |
| Print overviews for taxlist Objects and their content | print print,taxlist-method show,taxlist-method summary summary,taxlist-method |
| Set taxonomic information as taxon traits | tax2traits tax2traits,taxlist-method tax2traits.taxlist |
| An S4 class to represent taxonomic lists. | taxlist-class |
| Coerce taxlist objects to data frames | taxlist2df taxlist2df,taxlist-method taxlist2df.taxlist |
| Handle information on taxon usage names. | add_synonym add_synonym,taxlist-method add_synonym.taxlist delete_name delete_name,taxlist-method delete_name.taxlist taxon_names taxon_names,taxlist-method taxon_names.taxlist taxon_names<- taxon_names<-,taxlist-method taxon_names<-.taxlist update_name update_name,taxlist-method update_name.taxlist |
| Retrieve or replace slot taxonRelations in taxlist objects | taxon_relations taxon_relations,taxlist-method taxon_relations.taxlist taxon_relations<- taxon_relations<-,taxlist-method taxon_relations<-.taxlist update_concept,taxlist,numeric-method |
| Manipulation of taxon traits in taxlist objects. | taxon_traits taxon_traits,taxlist-method taxon_traits.taxlist taxon_traits<- taxon_traits<-,taxlist-method taxon_traits<-.taxlist update_trait update_trait,taxlist-method update_trait.taxlist |
| Management of concept views in taxonomic lists. | add_view add_view,taxlist,data.frame-method taxon_views taxon_views,taxlist-method taxon_views.taxlist taxon_views<- taxon_views<-,taxlist-method taxon_views<-.taxlist |
| Import species lists from Turboveg databases | tv2taxlist |
