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vegdata (version 0.9.12)

Access Vegetation Databases and Treat Taxonomy

Description

Handling of vegetation data from different sources ( Turboveg 2.0 ; the German national repository and others. Taxonomic harmonization (given appropriate taxonomic lists, e.g. the German taxonomic standard list "GermanSL", ).

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Version

Install

install.packages('vegdata')

Monthly Downloads

711

Version

0.9.12

License

GPL (>= 2)

Maintainer

Florian Jansen

Last Published

January 29th, 2024

Functions in vegdata (0.9.12)

syn

Search synonyms of a taxon
parent

#' Parents of a taxon
taxname.removeAuthors

Remove name authors from taxon names
tv.bib

Check bibliographic references from Turboveg codes
tv.coverperc

Cover code translation
taxname.abbr

Standardisation of taxonomic names, especially taxon rank indicators and hybrid signs name taxname.abbr
taxlevels

Taxonomic hierarchy levels
tv.traits

Load species traits from Turboveg reference list
tv.metadata

Show metainfo of vegetation database or ecodbase
tv.site

Load site data from Turboveg Database
taxval

Handling of taxonomy in vegetation data.
taxname.simpl

Simplify name parts for better string matching
tdb_cache

Caching
vegdata-package

Functions to access data from vegetation databases and evaluate taxon names
tv.write

Write species-plot observations and site information to Turboveg database.
tv.obs

Dataframe of plot-species observations directly from Turboveg
tv.refl

Taxon reference list to be used
tv.veg

Tabulates vegetation tables from Turboveg database
tv.db

Read list of available Turboveg2 databases in given Turboveg directory
tv.home

Where is your Turboveg 2 installation path?
tv.readXML

Reads a Turboveg XML file
lc.0

Layer combinations
comb.species

Combine species in vegetation matrix
cwm

Indicate site conditions with community weighted mean values of traits or with mode of gradient classes (sum of species amplitudes).
TV.replace

Rename data.frame columns to match Turboveg 2 conventions
TCS.replace

Standardise taxon list field names to match the Taxonomic Concept Transfer Schema (TCS)
db_path

database path
child

Search taxonomic reference lists including concept synonomy and taxonomic hierarchy.
db_download

Download taxonomic databases
recode.species

Recode species names, lettercodes or ID's
sql_collect

Query and get data back into a data.frame
syntab

Syntaxonomic frequency tables
src_vegdata

src - dplyr src objects
parse.taxa

Parse taxon strings into genus part and epitheta
tax

Search taxonomic reference lists including concept synonomy and taxonomic hierarchy.
elbaue

This is an example vegetation dataset to be included in package vegdata
%>%

Pipe operator
lc.all

Layer combinations
lc.1

Layer combinations