Package: vegdata 0.9.12

Florian Jansen

vegdata: Access Vegetation Databases and Treat Taxonomy

Handling of vegetation data from different sources ( Turboveg 2.0 <https://www.synbiosys.alterra.nl/turboveg/>; the German national repository <https://www.vegetweb.de> and others. Taxonomic harmonization (given appropriate taxonomic lists, e.g. the German taxonomic standard list "GermanSL", <https://germansl.infinitenature.org>).

Authors:Florian Jansen <[email protected]>

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vegdata.pdf |vegdata.html✨
vegdata/json (API)

# Install 'vegdata' in R:
install.packages('vegdata', repos = c('https://florianjansen.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • lc.0 - Layer combinations
  • lc.1 - Layer combinations
  • lc.all - Layer combinations
  • taxlevels - Taxonomic hierarchy levels

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.80 score 2 stars 3 packages 35 scripts 762 downloads 1 mentions 39 exports 47 dependencies

Last updated 10 months agofrom:472078459f. Checks:OK: 7. Indexed: yes.

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Doc / VignettesOKOct 26 2024
R-4.5-winOKOct 26 2024
R-4.5-linuxOKOct 26 2024
R-4.4-winOKOct 26 2024
R-4.4-macOKOct 26 2024
R-4.3-winOKOct 26 2024
R-4.3-macOKOct 26 2024

Exports:%>%childcomb.speciescwmdb_download_eurosldb_download_germansldb_pathlc.0lc.1lc.allparentparse.taxarecode.speciessql_collectsrc_euroslsrc_germanslsynsyntabtaxtaxlevelstaxname.abbrtaxname.removeAuthorstaxname.simplifytaxvalTCS.replacetdb_cachetv.bibtv.coverperctv.dbtv.dicttv.hometv.obstv.readXMLtv.reflTV.replacetv.sitetv.traitstv.vegtv.write

Dependencies:askpassbitbit64blobcachemclicpp11curlDBIdbplyrdigestdplyrfansifastmapforeigngenericsgluehoardrhttrindicspeciesjsonlitelifecyclemagrittrmemoisemimeopensslpermutepillarpkgconfigplogrplyrpurrrR6rappdirsRcpprlangRSQLitestringistringrsystibbletidyrtidyselectutf8vctrswithrxml2

An R package for vegetation data access, formatting and taxonomic unification

Rendered fromvegdata.Rnwusingknitr::knitron Oct 26 2024.

Last update: 2024-01-30
Started: 2012-01-16

Readme and manuals

Help Manual

Help pageTopics
Functions to access data from vegetation databases and evaluate taxon namesvegdata-package vegdata
Search taxonomic reference lists including concept synonomy and taxonomic hierarchy.child
Combine species in vegetation matrixcomb.species
Indicate site conditions with community weighted mean values of traits or with mode of gradient classes (sum of species amplitudes).cwm
Download taxonomic databasesdb_download db_download_eurosl db_download_germansl
database pathdb_path
This is an example vegetation dataset to be included in package vegdataelbaue
Layer combinationslc.0
Layer combinationslc.1
Layer combinationslc.all
#' Parents of a taxonparent
Parse taxon strings into genus part and epithetaparse.taxa
Recode species names, lettercodes or ID'srecode.species
Query and get data back into a data.framesql_collect
src - dplyr src objectssrc_eurosl src_germansl src_vegdata
Search synonyms of a taxonsyn
Syntaxonomic frequency tablesprint.syntab syntab
Search taxonomic reference lists including concept synonomy and taxonomic hierarchy.tax
Taxonomic hierarchy levelstaxlevels
Standardisation of taxonomic names, especially taxon rank indicators and hybrid signs name taxname.abbrtaxname.abbr
Remove name authors from taxon namestaxname.removeAuthors
Simplify name parts for better string matchingtaxname.simpl taxname.simplify
Handling of taxonomy in vegetation data.taxval
Standardise taxon list field names to match the Taxonomic Concept Transfer Schema (TCS)TCS.replace
Cachingtdb_cache
Check bibliographic references from Turboveg codestv.bib
Cover code translationtv.coverperc
Read list of available Turboveg2 databases in given Turboveg directorytv.db tv.dict
Where is your Turboveg 2 installation path?tv.home
Show metainfo of vegetation database or ecodbasetv.metadata
Dataframe of plot-species observations directly from Turbovegtv.obs
Reads a Turboveg XML filetv.readXML
Taxon reference list to be usedtv.refl
Rename data.frame columns to match Turboveg 2 conventionsTV.replace
Load site data from Turboveg Databasetv.site
Load species traits from Turboveg reference listtv.eco tv.traits
Tabulates vegetation tables from Turboveg databasetv.veg
Write species-plot observations and site information to Turboveg database.tv.write