Handling Taxonomic Lists

Documentation for package ‘taxlist’ version 0.3.0

Help Pages

-- 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 --

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
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