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taxlist (version 0.3.0)

Handling Taxonomic Lists

Description

Handling taxonomic lists through objects of class 'taxlist'. This package provides functions to import species lists from 'Turboveg' () and the possibility to create backups from resulting R-objects. Also quick displays are implemented as summary-methods.

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Install

install.packages('taxlist')

Monthly Downloads

461

Version

0.3.0

License

GPL (>= 2)

Issues

14

Pull Requests

0

Stars

12

Forks

4

Maintainer

Miguel Alvarez

Last Published

July 3rd, 2024

Functions in taxlist (0.3.0)

as

Coerce taxlist objects to lists.
insert_rows

Insert additional rows to a data frame.
dissect_name

Dissect Scientific Names into their Elements
clean_strings

Cleaning character strings.
get_children

Retrieve children or parents of taxon concepts
id_generator

Generate Identifiers
print_name

Format usage names for publications
matched_names-class

Names matched with a reference taxonomic list
merge_taxa

Merge concepts or move names
overview_taxon

Function producing the overview of single taxon concepts.
prune_levels

Prune not used taxonomic ranks
merge_to_parent

Merge taxa to their respective parents
overview_taxlist

Function producing the overview of whole object.
levels

Set and retrieves hierarchical levels
match_names

Search matchings between character and taxlist objects
parents

Retrieve parents for specific concepts
taxlist2df

Coerce taxlist objects to data frames
tax2traits

Set taxonomic information as taxon traits
summary

Print overviews for taxlist Objects and their content
taxon_names

Handle information on taxon usage names.
subset

Subset method for taxlist objects
replace_x

Data manipulation.
taxon_relations

Retrieve or replace slot taxonRelations in taxlist objects
taxon_traits

Manipulation of taxon traits in taxlist objects.
taxlist-class

An S4 class to represent taxonomic lists.
taxlist-package

taxlist: Handling Taxonomic Lists
tv2taxlist

Import species lists from Turboveg databases
taxon_views

Management of concept views in taxonomic lists.
two2one_df

Inserting new rows and columns by merging two data frames
Extract

Extract or Replace Parts of taxlist Objects
clean_once_taxlist

One run clean function
clean

Delete orphaned records
add_concept

Add new taxonomic concepts into taxlist objects
Deprecated-functions

Deprecated functions
accepted_name

Manage accepted names, synonyms and basionyms
backup_object

Make and load backups of R objects
df2taxlist

Convert data frames and strings into taxlist objects
indented_list

Print hierarchical structure in indented lists
count_taxa

Count taxa within a taxlist object.
Easplist-data

List of vascular plants from East Africa
add_suffix

Add a suffix when strings are identical
collapse_names

Collapse names
add_nacolumn

Filling missed columns with NAs