R: Handling Taxonomic Lists

# Handling Taxonomic Lists

## Documentation for package ‘taxlist’ version 0.3.5

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

A B C D E G I L M P R S T U misc

## -- A --

accepted_name | Manage accepted names, synonyms and basionyms
accepted_name-method | Manage accepted names, synonyms and basionyms
accepted_name.taxlist | Manage accepted names, synonyms and basionyms
accepted_name<- | Manage accepted names, synonyms and basionyms
accepted_name<--method | Manage accepted names, synonyms and basionyms
accepted_name<-.taxlist | Manage accepted names, synonyms and basionyms
add_concept | Add new taxonomic concepts into taxlist objects
add_concept-method | Add new taxonomic concepts into taxlist objects
add_level | Deprecated functions
add_parent | Deprecated functions
add_synonym | Handle information on taxon usage names.
add_synonym-method | Handle information on taxon usage names.
add_synonym.taxlist | Handle information on taxon usage names.
add_trait | Deprecated functions
add_view | Management of concept views in taxonomic lists.
add_view-method | Management of concept views in taxonomic lists.
as | Coerce taxlist objects to lists.

## -- B --

backup_object | Make and load backups of R objects
basionym | Manage accepted names, synonyms and basionyms
basionym-method | Manage accepted names, synonyms and basionyms
basionym.taxlist | Manage accepted names, synonyms and basionyms
basionym<- | Manage accepted names, synonyms and basionyms
basionym<--method | Manage accepted names, synonyms and basionyms
basionym<-.taxlist | Manage accepted names, synonyms and basionyms

## -- C --

change_concept<- | Manage accepted names, synonyms and basionyms
change_concept<--method | Manage accepted names, synonyms and basionyms
change_concept<-.taxlist | Manage accepted names, synonyms and basionyms
clean | Delete orphaned records
clean-method | Delete orphaned records
clean_strings | Cleaning character strings.
clean_strings-method | Cleaning character strings.
coerce-method | Coerce taxlist objects to lists.
count_taxa | Count taxa within a taxlist object.
count_taxa-method | Count taxa within a taxlist object.

## -- D --

delete_name | Handle information on taxon usage names.
delete_name-method | Handle information on taxon usage names.
delete_name.taxlist | Handle information on taxon usage names.
Deprecated-functions | Deprecated functions
df2taxlist | Convert data frames and strings into taxlist objects
df2taxlist-method | Convert data frames and strings into taxlist objects
df2taxlist.character | Convert data frames and strings into taxlist objects
df2taxlist.data.frame | Convert data frames and strings into taxlist objects
dissect_name | Dissect Scientific Names into their Elements

## -- E --

Easplist | List of vascular plants from East Africa
Easplist-data | List of vascular plants from East Africa
Extract | Extract or Replace Parts of taxlist Objects

## -- G --

get_children | Retrieve children or parents of taxon concepts
get_children-method | Retrieve children or parents of taxon concepts
get_children.taxlist | Retrieve children or parents of taxon concepts
get_parents | Retrieve children or parents of taxon concepts
get_parents-method | Retrieve children or parents of taxon concepts
get_parents.taxlist | Retrieve children or parents of taxon concepts

## -- I --

id_generator | Generate Identifiers
id_solver | Generate Identifiers
indented_list | Print hierarchical structure in indented lists
indented_list-method | Print hierarchical structure in indented lists
insert_rows | Insert additional rows to a data frame.
insert_rows-method | Insert additional rows to a data frame.

## -- L --

levels | Set and retrieves hierarchical levels
levels-method | Set and retrieves hierarchical levels
levels.taxlist | Set and retrieves hierarchical levels
levels<- | Set and retrieves hierarchical levels
levels<--method | Set and retrieves hierarchical levels
levels<-.taxlist | Set and retrieves hierarchical levels
load_last | Make and load backups of R objects

## -- M --

matched_names-class | Names matched with a reference taxonomic list
match_names | Search matchings between character and taxlist objects
match_names-method | Search matchings between character and taxlist objects
merge_taxa | Merge concepts or move names
merge_taxa-method | Merge concepts or move names
merge_taxa.taxlist | Merge concepts or move names
merge_to_parent | Merge taxa to their respective parents
merge_to_parent-method | Merge taxa to their respective parents
merge_to_parent.taxlist | Merge taxa to their respective parents

## -- P --

parents | Retrieve parents for specific concepts
parents-method | Retrieve parents for specific concepts
print | Print overviews for taxlist Objects and their content
print-method | Print overviews for taxlist Objects and their content
print_name | Format usage names for publications
print_name-method | Format usage names for publications
print_name.character | Format usage names for publications
print_name.taxlist | Format usage names for publications
prune_levels | Prune not used taxonomic ranks
prune_levels-method | Prune not used taxonomic ranks
prune_levels.taxlist | Prune not used taxonomic ranks

## -- R --

reindex | Re-index elements of taxlist objects
reindex-method | Re-index elements of taxlist objects
reindex.taxlist | Re-index elements of taxlist objects
reindex<- | Re-index elements of taxlist objects
reindex<--method | Re-index elements of taxlist objects
reindex<-.taxlist | Re-index elements of taxlist objects
replace_idx | Data manipulation.
replace_na | Data manipulation.
replace_view | Deprecated functions
replace_x | Data manipulation.

## -- S --

S4_to_list | Coerce taxlist objects to lists.
show-method | Print overviews for taxlist Objects and their content
sort_backups | Make and load backups of R objects
sort_taxa | Sort taxa for further print
sort_taxa-method | Sort taxa for further print
sort_taxa.taxlist | Sort taxa for further print
subset | Subset method for taxlist objects
subset-method | Subset method for taxlist objects
summary | Print overviews for taxlist Objects and their content
summary-method | Print overviews for taxlist Objects and their content
synonyms | Manage accepted names, synonyms and basionyms
synonyms-method | Manage accepted names, synonyms and basionyms
synonyms.taxlist | Manage accepted names, synonyms and basionyms

## -- T --

tax2traits | Set taxonomic information as taxon traits
tax2traits-method | Set taxonomic information as taxon traits
tax2traits.taxlist | Set taxonomic information as taxon traits
taxlist-class | An S4 class to represent taxonomic lists.
taxlist2df | Coerce taxlist objects to data frames
taxlist2df-method | Coerce taxlist objects to data frames
taxlist2df.taxlist | Coerce taxlist objects to data frames
taxlist2taxmap | Deprecated functions
taxmap2taxlist | Deprecated functions
taxon_names | Handle information on taxon usage names.
taxon_names-method | Handle information on taxon usage names.
taxon_names.taxlist | Handle information on taxon usage names.
taxon_names<- | Handle information on taxon usage names.
taxon_names<--method | Handle information on taxon usage names.
taxon_names<-.taxlist | Handle information on taxon usage names.
taxon_relations | Retrieve or replace slot taxonRelations in taxlist objects
taxon_relations-method | Retrieve or replace slot taxonRelations in taxlist objects
taxon_relations.taxlist | Retrieve or replace slot taxonRelations in taxlist objects
taxon_relations<- | Retrieve or replace slot taxonRelations in taxlist objects
taxon_relations<--method | Retrieve or replace slot taxonRelations in taxlist objects
taxon_relations<-.taxlist | Retrieve or replace slot taxonRelations in taxlist objects
taxon_traits | Manipulation of taxon traits in taxlist objects.
taxon_traits-method | Manipulation of taxon traits in taxlist objects.
taxon_traits.taxlist | Manipulation of taxon traits in taxlist objects.
taxon_traits<- | Manipulation of taxon traits in taxlist objects.
taxon_traits<--method | Manipulation of taxon traits in taxlist objects.
taxon_traits<-.taxlist | Manipulation of taxon traits in taxlist objects.
taxon_views | Management of concept views in taxonomic lists.
taxon_views-method | Management of concept views in taxonomic lists.
taxon_views.taxlist | Management of concept views in taxonomic lists.
taxon_views<- | Management of concept views in taxonomic lists.
taxon_views<--method | Management of concept views in taxonomic lists.
taxon_views<-.taxlist | Management of concept views in taxonomic lists.
tnrs | Deprecated functions
tv2taxlist | Import species lists from Turboveg databases

## -- U --

update_concept | Add new taxonomic concepts into taxlist objects
update_concept-method | Retrieve or replace slot taxonRelations in taxlist objects
update_name | Handle information on taxon usage names.
update_name-method | Handle information on taxon usage names.
update_name.taxlist | Handle information on taxon usage names.
update_trait | Manipulation of taxon traits in taxlist objects.
update_trait-method | Manipulation of taxon traits in taxlist objects.
update_trait.taxlist | Manipulation of taxon traits in taxlist objects.

## -- misc --

$ | Extract or Replace Parts of taxlist Objects
$-method | Extract or Replace Parts of taxlist Objects
[ | Extract or Replace Parts of taxlist Objects
[-method | Extract or Replace Parts of taxlist Objects