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vegdata (version 0.9.11.4)

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

317

Version

0.9.11.4

License

GPL (>= 2)

Maintainer

Florian Jansen

Last Published

December 17th, 2022

Functions in vegdata (0.9.11.4)

tax

Search taxonomic reference lists including concept synonomy and taxonomic hierarchy.
taxname.abbr

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

Taxonomic hierarchy levels
syntab

Syntaxonomic frequency tables
recode.species

Recode species names, lettercodes or ID's
parse.taxa

Parse taxon strings into genus part and epitheta
parent

#' Parents of a taxon
tdb_cache

Caching
tv.traits

Load species traits from Turboveg reference list
taxval

Handling of taxonomy in vegetation data.
lc.all

Layer combinations
%>%

Pipe operator
tv.bib

Check bibliographic references from Turboveg codes
sql_collect

Query and get data back into a data.frame
tv.db

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

Cover code translation
tv.metadata

Show metainfo of vegetation database or ecodbase
tv.site

Load site data from Turboveg Database
tv.home

Where is your Turboveg 2 installation path?
tv.readXML

Reads a Turboveg XML file
tv.refl

Taxon reference list to be used
taxname.removeAuthors

Remove name authors from taxon names
taxname.simpl

Simplify name parts for better string matching
vegdata-internal

Internal vegdata functions
tv.write

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

Tabulates vegetation tables from Turboveg database
vegdata-package

vegdata
tv.obs

Dataframe of plot-species observations directly from Turboveg
lc.1

Layer combinations
child

Search taxonomic reference lists including concept synonomy and taxonomic hierarchy.
TCS.replace

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

Download taxonomic databases
db_path

database path
comb.species

Combine species in vegetation matrix
TV.replace

Rename data.frame columns to match Turboveg 2 conventions
cwm

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

This is an example vegetation dataset to be included in package vegdata
lc.0

Layer combinations
syn

Search synonyms of a taxon
src_vegdata

src - dplyr src objects