Functions to access data from vegetation databases and evaluate taxon names

Description

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).

See Also

Useful links:

• https://germansl.infinitenature.org

Pipe operator

Description

Pipe operator

Usage

lhs %>% rhs

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

Description

Applies Taxonomic Concept Transfer Schema (TCS) to the different name list conventions of different sources

Usage

TCS.replace(x)

Arguments

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

References

Taxonomic Names and Concepts interest group. 2006. Taxonomic Concept Transfer Schema (TCS), version 1.01. Biodiversity Information Standards (TDWG) http://www.tdwg.org/standards/117

Rename data.frame columns to match Turboveg 2 conventions

Description

Rename data.frame columns to match Turboveg 2 conventions

Usage

TV.replace(x)

Arguments

Search taxonomic reference lists including concept synonomy and taxonomic hierarchy.

Description

Search all (accepted) children of a taxon down to gen generations

Usage

child(x, refl, gen = 3, syn = FALSE, include.parent = FALSE, quiet = FALSE, ...)

Arguments

Details

concept: GermanSL is a list with a single taxon view according to the standard lists of the different taxon groups (e.g Wisskirchen and Haeupler for higher plants, see). Nevertheless a huge number of synonyms is included which allows in many cases the transformation into different concepts. For illustration the concept of Armeria maritima from Korneck 1996 is included, which accepts e.g. Armeria maritima ssp. bottendorfensis. parse.taxa: parse genus and epitheta from name strings. taxname.removeAuthors Remove name authors from full scientific name strings.

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

References

Jansen, F. and Dengler, J. (2008) GermanSL - eine universelle taxonomische Referenzliste für Vegetationsdatenbanken. Tuexenia, 28, 239-253.

Combine species in vegetation matrix

Description

Combine species in vegetation matrix

Usage

comb.species(x, sel, newname, refl)

Arguments

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

Description

Calculates community weighted mean trait values, like mean Ellenberg indicator values. Alternatively (method = 'mode') environmental conditions can be calculated according to the concept of sums of amplitudes of species along ecological gradients.

Usage

cwm(veg, refl, trait.db = 'ecodbase.dbf', ivname, keyname = 'LETTERCODE',
      method, weight, db, ...)

Arguments

Details

Trait values of 0 will be handled as NA values because Turboveg dBase can not handle NA values properly.

Value

Vector with the ecological classification of sites. Either mean trait values or mode of gradient classes.

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

Examples

  ## Not run: 
    db <- 'elbaue'
    veg <- tv.veg(db, cover.transform='sqrt', check.critical = FALSE)
    site <- tv.site(db, verbose = FALSE)
    #' Exclude plots with very high water level fluctuation
    veg <- veg[site$SDGL < 60,]
    veg <- veg[,colSums(veg) > 0]
    site <- site[site$SDGL < 60,]
    #' Load species trait value database
    traits <- tv.traits(db)

    #' Mean indicator values of Ellenberg F values
    mEIV_F <- cwm(veg, trait.db = traits, ivname = 'OEK_F', method = 'mean')
    plot(site$MGL, mEIV_F, xlab = 'Mean groundwater level')

    #' Mode (most frequent level) of Ellenberg F values
    ilevel <- cwm(veg, trait.db = traitmat, ivname = as.character(1:11), method = 'mode')
    mode <- as.numeric(cwm(veg, trait.db = traits, ivname = 'OEK_F', method = 'mode'))
    boxplot(site$MGL ~ mode)
  
## End(Not run)

Download taxonomic databases

Description

Download taxonomic databases

Usage

db_download_eurosl(version = "latest", verbose = TRUE, overwrite = FALSE)

db_download_germansl(version = "latest", verbose = TRUE, overwrite = FALSE)

Arguments

Details

Downloads sql database, cleans up unneeded files, returns path to sql file

Value

(character) path to the downloaded SQL database

See Also

[tdb_cache]

Examples

## Not run: 
# EuroSL
# db_download_eurosl()
# src_eurosl()

# GermanSL
# db_download_germansl()
# db_download_germansl(overwrite=TRUE) # overwrite - download again
# src_germansl()


## End(Not run)

database path

Description

database path

Usage

db_path(db)

Arguments

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

Description

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

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

References

https://www.vegetweb.de

Layer combinations

Description

datasets with layer codes and how they should be combined in vegetation anlyses. lc.o: do not combine any layers

Usage

lc.0

Format

A data frame with rows and 2 variables:

LAYER

Layer code, i.e. 0:9 for Turboveg

COMB

Combinations. Same integer means, they will be combined

Layer combinations

Description

datasets with layer codes and how they should be combined in vegetation anlyses.

Usage

lc.1

Format

A data frame with rows and 3 variables:

LAYER

Layer code, i.e. 0:9 for Turboveg

COMB

Combinations. Same integer means, they will be combined

Layer combinations

Description

combine all layers

Usage

lc.all

Format

A data frame with rows and 2 variables:

LAYER

Layer code, i.e. 0:9 for Turboveg

COMB

Combinations. Same integer means, they will be combined

#' Parents of a taxon

Description

#' Parents of a taxon

Usage

parent(x, refl = tv.refl(), rank, quiet = FALSE, ...)

Arguments

Details

concept: GermanSL is a list with a single taxon view according to the standard lists of the different taxon groups (e.g Wisskirchen and Haeupler for higher plants, see). Nevertheless a huge number of synonyms is included which allows in many cases the transformation into different concepts. For illustration the concept of Armeria maritima from Korneck 1996 is included, which accepts e.g. Armeria maritima ssp. bottendorfensis. parse.taxa: parse genus and epitheta from name strings. taxname.removeAuthors Remove name authors from full scientific name strings.

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

References

Jansen, F. and Dengler, J. (2008) GermanSL - eine universelle taxonomische Referenzliste für Vegetationsdatenbanken. Tuexenia, 28, 239-253.

Parse taxon strings into genus part and epitheta

Description

Parse taxon strings into genus part and epitheta

Usage

parse.taxa(x, epis)

Arguments

Recode species names, lettercodes or ID's

Description

Recode species names, lettercodes or ID's

Usage

recode.species(
  x,
  names = c("shortletters", "Numbers", "ScientificNames"),
  refl
)

Arguments

Query and get data back into a data.frame

Description

Query and get data back into a data.frame

Usage

sql_collect(src, query, ...)

Arguments

Details

we run [dplyr::tbl()], then [dplyr::collect()]

Examples

## Not run: 
src <- src_germansl()
sql_collect(src, "select * from GermanSL limit 5")
## or pipe the src to sql_collect
src %>% sql_collect("select * from GermanSL limit 5")

## End(Not run)

src - dplyr src objects

Description

src - dplyr src objects

Usage

src_eurosl(path = db_path("eurosl"), ...)

src_germansl(path = db_path("germansl"), ...)

Arguments

Value

an src object

Examples

## Not run: 
# src_eurosl()
# src_germansl()

## End(Not run)

Search synonyms of a taxon

Description

Search synonyms of a taxon

Usage

syn(x, refl = tv.refl(), quiet = FALSE, ...)

Arguments

Details

concept: GermanSL is a list with a single taxon view according to the standard lists of the different taxon groups (e.g Wisskirchen and Haeupler for higher plants, see). Nevertheless a huge number of synonyms is included which allows in many cases the transformation into different concepts. For illustration the concept of Armeria maritima from Korneck 1996 is included, which accepts e.g. Armeria maritima ssp. bottendorfensis. parse.taxa: parse genus and epitheta from name strings. taxname.removeAuthors Remove name authors from full scientific name strings.

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

References

Jansen, F. and Dengler, J. (2008) GermanSL - eine universelle taxonomische Referenzliste für Vegetationsdatenbanken. Tuexenia, 28, 239-253.

Syntaxonomic frequency tables

Description

Calculate and display relative or absolute frequency tables with or without use of function multipatt from package indicspecies

Usage

syntab(veg, clust, type = c('rel','abs','mean.cover'), mupa, dec=0, refl, ...)

## S3 method for class 'syntab'
print(x, zero.print = ".", trait, limit = 1, minstat = 0, alpha = 0.05, ...)

Arguments

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

See Also

Package indicspecies with function multipatt for indicator species analysis along multiple cluster combinations

Examples

## Not run: 
 elbaue <- tv.veg('elbaue')
 elbaue.env <- tv.site('elbaue')
 clust <- vector('integer', nrow(elbaue.env))
 clust[elbaue.env$MGL < -50 & elbaue.env$SDGL < 50] <- 1
 clust[elbaue.env$MGL < -50 & elbaue.env$SDGL >= 50] <- 2
 clust[elbaue.env$MGL >= -50 & elbaue.env$SDGL >= 50] <- 3
 clust[elbaue.env$MGL >= -50 & elbaue.env$SDGL < 50] <- 4
 levels(clust) <- c('dry.ld','dry.hd', 'wet.hd','wet.ld')
 traits <- tv.traits()
 m <- match(rownames(st$syntab), traits$LETTERCODE, nomatch = 0)
 trait <- traits[m, c("OEK_F","OEK_N")]
 rownames(trait) <- traits$LETTERCODE[m]
 st <- syntab(elbaue, clust, mupa=TRUE)
 print(st, limit=30, trait=trait)
 #'  Manipulation of the syntaxonomic table
 sttable <- st$syntab
 sttable <- sttable[sttable$p.value < 0.05 & !is.na(sttable$p.value),
 !names(sttable) %in% c('stat')]
 taxa <- tax(rownames(sttable))
 rownames(sttable) <- taxa[match(rownames(sttable), taxa$LETTERCODE, nomatch = 0),'TaxonName']
 write.csv(sttable, 'sttable.csv')

## End(Not run)

Search taxonomic reference lists including concept synonomy and taxonomic hierarchy.

Description

Input is either species number (integer), shortletter (7 characters) or full (exact!) species name.

Usage

tax(x, refl, detailed = TRUE, syn = TRUE, concept = NULL, strict = FALSE,
                        simplify = FALSE, quiet = FALSE, ...)

Arguments

Details

concept: GermanSL is a list with a single taxon view according to the standard lists of the different taxon groups (e.g Wisskirchen and Haeupler for higher plants, see). Nevertheless a huge number of synonyms is included which allows in many cases the transformation into different concepts. For illustration the concept of Armeria maritima from Korneck 1996 is included, which accepts e.g. Armeria maritima ssp. bottendorfensis. parse.taxa: parse genus and epitheta from name strings. taxname.removeAuthors Remove name authors from full scientific name strings.

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

References

Jansen, F. and Dengler, J. (2008) GermanSL - eine universelle taxonomische Referenzliste für Vegetationsdatenbanken. Tuexenia, 28, 239-253.

Taxonomic hierarchy levels

Description

hierarchy of taxon levels

Usage

taxlevels

Format

A data frame with rows and 3 variables:

rank

Layer code, i.e. 0:9 for Turboveg

level

Combinations. Same integer means, they will be combined

Euro.Med

taxon level name in http://www.europlusmed.org/ database

description

Explanation of level codes

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

Description

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

Usage

taxname.abbr(x, hybrid = TRUE, concept = FALSE, species = TRUE, cf = TRUE, ...)

Arguments

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

Remove name authors from taxon names

Description

Remove name authors from taxon names

Usage

taxname.removeAuthors(x, sep)

Arguments

Simplify name parts for better string matching

Description

Simplify name parts for better string matching

Usage

taxname.simplify(
  x,
  genus = TRUE,
  epithet = TRUE,
  concept = TRUE,
  rank = TRUE,
  tax.status = TRUE,
  ...
)

Arguments

Details

taxname.abbr will be applied beforehand automatically. The function simplifies name parts which are empirically unstable, i.e. sylvatica might also written as silvatica, or majus vs. maius. Sex of latin genus or epithet name parts often change and are therefore deleted (us vs. a, ea vs. eos, etc.). Hybrid signs are removed. taxname.simpl works well for plant names, but be careful with very long name lists or if combined with animal taxa which are sometimes very short and can be confused after applying taxname.simpl

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

Handling of taxonomy in vegetation data.

Description

Performs taxonomic valuation of species names according to synonomy, taxonomic level, unambiguous biotic content etc. Necessary prerequisite is information about taxonomic status (synonomy) and hierarchy (next higher aggregate). Until now only applicable for reference list 'GermanSL' (>= version 1.1, see References Section), which is valid in Germany and adjacent countries.

Usage

taxval(obs, refl, db, ag = c('conflict', 'adapt', 'preserve'), rank,
mono = c('species', 'higher', 'lower', 'preserve'), monolist = "monotypic-D",
maxtaxlevel = 'AGG', check.critical = TRUE, interactive = FALSE, ...)

Arguments

Details

Working with vegetation datasets, especially from different sources needs taxonomic valuation. The function tries to automate this process. Therefore the German taxonomic reference list (GermanSL, https://germansl.infinitenature.org ) contains additional taxon attributes (tax.dbf) and monotypic taxa of Germany (monotypic.dbf). Without an appropriate species list (see tax) the function will not work.

The taxonomic reference list needs Taxonrank corresponding to values given in taxlevels Possible values for adapting the taxonomic hierarchy within the dataset (child/parent taxa) are: preserve: Leave everything untouched. conflict: Dissolve only in case of conflicts, e.g. if a subspecies occurs also at the species level within the same dataset. In this case the subspecies will be aggregated to the higher level. adapt: Dissolve all nested taxa to e.g. species level for option ag. For this option also option rank, specifying the rank to which the taxa shall be adapted, must be given.

Monotypic taxa, e.g. a species which occur only with 1 subspecies in the survey area. They have to be combined, since otherwise two different (valid) taxa would denominate the same entity. If lower the higher taxon (e.g. species rank) is replaced by the lower level (subspecies rank). If neither lower nor higher monotypic species are preserved. Since the list of monotypic species strongly depends on the considered area you have to choose, which area is covered by your database and create an appropriate list of monotypic taxa. Within the package "monotypic-D.csv" is provided as a compilation of monotypic species within the GermanSL list.

Option maxtaxlevel determines the maximum taxonomic level within the given names, which should be used. All higher taxon observations are deleted. If you have a single field observation determined as Asteraceae spec. all your obervations of taxa from that family will be aggregated to the family level, if you choose ag=conflict.

Interactive If you want to manually adapt the taxonomic harmonization interactive=TRUE will create a table with all original names and NewTaxonID's according to the chosen rules. The table will be saved as taxvalDecisionTable.csv in your actual working directory. You can manipulate the column NewTaxonID. If you run taxval again (e.g. through function tv.veg) and a file with this name exist in your working directory, it will be used.

Value

Functions return the input dataframe of observations with harmonised taxon numbers.

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

References

Jansen, F. and Dengler, J. (2008) GermanSL - eine universelle taxonomische Referenzliste f\"ur Vegetationsdatenbanken. Tuexenia, 28, 239-253. Jansen, F. and Dengler, J. (2010) Plant names in vegetation databases - a neglected source of bias. Journal of Vegetation Science, 21, 1179-1186.

See Also

tv.veg, tv.obs

Examples

## Not run: 
# Turboveg installation needed
 obs <- taxval(db='taxatest')
# For explanations see vignette('vegdata').

 veg <- tv.veg('taxatest')
 veg <- comb.species(veg, c('ARMEM-E','ARMEM-H'))

## End(Not run)

Caching

Description

Manage cached vegdata files with hoardr

Details

'cache_delete' only accepts 1 file name, while ‘cache_delete_all' doesn’t accept any names, but deletes all files. For deleting many specific files, use 'cache_delete' in a [lapply()] type call

Useful user functions

- 'tdb_cache$cache_path_get()' get cache path - 'tdb_cache$cache_path_set()' set cache path - 'tdb_cache$list()' returns a character vector of full path file names - 'tdb_cache$files()' returns file objects with metadata - 'tdb_cache$details()' returns files with details - 'tdb_cache$delete()' delete specific files - 'tdb_cache$delete_all()' delete all files, returns nothing

Examples

## Not run: 
tdb_cache

# list files in cache
tdb_cache$list()

# delete certain database files
# tdb_cache$delete("file path")
# tdb_cache$list()

# delete all files in cache
# tdb_cache$delete_all()
# tdb_cache$list()

## End(Not run)

Check bibliographic references from Turboveg codes

Description

Check bibliographic references from Turboveg codes

Usage

tv.bib(x = "all", db, dict = tv.dict(db), quiet = FALSE, tv_home, ...)

Arguments

Value

Dataframe of (selected) bibliographic references (when assigned to an object).

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

Cover code translation

Description

Translate cover code into percentage cover values for Turboveg database observations.

Usage

tv.coverperc(db, obs, RelScale, tv_home, tvscale, quiet = FALSE,  ...)

Arguments

Value

data.frame of observations with additional column COVER_PERC

keywords Turboveg

Read list of available Turboveg2 databases in given Turboveg directory

Description

Read list of available Turboveg2 databases in given Turboveg directory

Read list of available Turboveg2 databases in given Turboveg directory

Usage

tv.db(path)

tv.dict(db, tv_home)

Arguments

Value

List of databases below specified path

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

Where is your Turboveg 2 installation path?

Description

Reads and sets invisbly option('tv_home')

Usage

tv.home(check = FALSE)

Arguments

Value

Reads and sets invisbly option('tv_home')

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

Show metainfo of vegetation database or ecodbase

Description

Showing "metadata.txt" when specified and saved in Turboveg database directory. When db = 'eco' and refl specified, metainfo of species attribute table is displayed.

Usage

tv.metadata(db, refl, tv_home, filename = 'metadata.txt', ...)

Arguments

Details

Because Turboveg provides no formalised method to store information about database fields, I suggest to save a simple text file, named for example "metadata.txt" into the directory of your Turboveg database.

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

Dataframe of plot-species observations directly from Turboveg

Description

Dataframe of plot-species observations directly from Turboveg.

Usage

tv.obs(db, tv_home, ...)

Arguments

Value

Data.frame of species occurrences in Turboveg format, that is every occurrence is a row with releve number, species number, layer, cover code and optional additional species-plot information.

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

See Also

tv.veg

Examples

  ## Not run: 
    # Turboveg installation needed
    obs <- tv.obs('taxatest')
    head(obs)
  
## End(Not run)

Reads a Turboveg XML file

Description

Reads Turboveg XML formatted files species-plot observations and site information into a list

Usage

tv.readXML(file)

Arguments

Value

S3 list with elements tvwin, tvadmin, site, and obs

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

See Also

tv.veg, tv.site

Taxon reference list to be used

Description

Taxon reference list to be used

Usage

tv.refl(refl, db, tv_home)

Arguments

Load site data from Turboveg Database

Description

Loading Turboveg header data and do basic data evaluation. Empty columns are eliminated and warnings about possibly wrong '0' values are performed

Usage

tv.site(db, tv_home, drop=TRUE, common.only = FALSE, verbose = TRUE, replace.names, ...)

Arguments

Details

Please specify pathnames below but not above Turbowin/Data. Can be a single database or a character vector of multiple databases. In the latter case you have to assure, that all databases use the same taxonomic reference list.

You can use the example in the final output line to make a summary statistic for attributes with potentially misleading '0' values. Just delete the \" at beginning and end.

Value

data.frame of site variables.

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

Load species traits from Turboveg reference list

Description

Loading Turboveg ecodbase or any other specified dBase file in this directory and do basic data evaluation. Empty columns are eliminated.

Usage

tv.traits(db, trait.db = 'ecodbase.dbf', refl, ...)

Arguments

Details

You can use the final output line to make a summary statistic for attributes with potentially misleading '0' values.

Value

data.frame of ecological traits, see metainfo(refl, eco=TRUE)

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

Tabulates vegetation tables from Turboveg database

Description

Tabulates vegetation tables from Turboveg resp. VegetWeb database, including taxonomic emendation and layer combination. Using various default parameters for the included functions. It is a wrapper for *tv.obs*, *taxval*, *tv.coverperc* and creating a vegetation matrix

Usage

tv.veg(db, taxval=TRUE,tv_home,convcode=TRUE,
lc = c("layer","mean","max","sum","first"),
pseudo, values='COVER_PERC', spcnames=c('shortletters','ScientificNames','Numbers'),
dec = 0, cover.transform = c('no', 'pa', 'sqrt'), obs, site, refl, RelScale, ...)

Arguments

Details

layer means, the different layers are combined assuming there independence (a species occurring in two layers with a cover of 50% will result in a overall cover of 75%. sum will sum up cover values of all layers With option pseudo you can decide, which layers should be combined. Give a list with a combination data.frame and second the name of the column for combination. The default is pseudo = list(lc.1, c('LAYER')), where lc.1 is a data.frame data(lc.1), which will combine all tree layers, all shrub layers and all layers below shrubs. An alternative would be data(lc.all), combining all layers. With option pseudo=NULL there will be no layer aggregation.

Value

an object of class matrix with (combined) cover values.

Author(s)

Florian Jansen florian.jansen@uni-rostock.de

See Also

taxval, tv.coverperc, tv.obs, tv.site

Examples

  ## Not run: 
    vignette("vegdata")
    #' If you have Turboveg installed on your computer try for a beginning
    #' tv.veg('databasename', tax=FALSE).
    args(tv.veg)
    help('taxval')

    veg <- tv.veg('taxatest')
    names(veg)
    tv.veg('taxatest', uncertain=list('DET_CERT', data.frame(0:2,c('pres','agg','agg'))),
           pseudo=list(lc.0,'LAYER'), genus = 'delete')
  
## End(Not run)

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

Description

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

Usage

tv.write(x, site, name, tvadmin, remarks, dict = "", cover = c("code", "perc"),
drop = FALSE, obl = TRUE, overwrite = FALSE, ...)

Arguments

Details

By default Covercode is written to Turboveg. This is only meaningful, if correct CoverScales are given in the site dataframe. Unique plot ID's are stored in *TvAdmin.dbf*. If you want to preserve already given UUID's you have to prepare an appropriate data.frame. Look for existing *TvAdmin.dbf* files for necessary columns.

Value

Five files will be created in "tv_home/Data/databasename" directory. *tvabund.dbf* with occurrence information n long format, *tvhabita.dbf* with plot information, remarks.dbf with comments longer then 255 characters, *TvAdmin.dbf* with plot UUID's and tvwin.dbf with information about taxonomic reference list, and dictionary used.

Author(s)

Florian Jansen @email florian.jansen@uni-rostock.de

See Also

tv.veg