taxval(obs, refl, db, concept=NULL, syn = c('adapt','conflict','preserve'), ag = c('conflict', 'adapt', 'preserve'), rank, mono = c('higher','lower', 'preserve'), monolist = "monotypic-D", uncertain = NULL, maxtaxlevel = 'ROOT', quiet = FALSE, sysPath = FALSE, ...)tv.obstvabund.dbf, tvhabita.dbf and twin.set"monotypic-D" for the area of germany.tax) the function will not work.
Before we replace synonyms we can choose to evaluate the data under a different taxonomical concepts than the original GermanSL. In the moment only an outline of such an approach is realised, because complete lists of differing taxonyms and there taxonomical re-evaluation have to be provided which are not available. With the inbuild test-dataset and the interpretation of the Armeria maritima complex you can have a shot on applying different concepts using a dataset referenced with GermanSL and using Korneck1996.dbf. See package vignette.
The three possible values for synonyms and child/parent taxa are: preserve: Leave everything untouched; conflict: Dissolve only in case of conflicts, e.g. if a subspecies occurrs also at the species level within the same dataset. In this case the subspecies will be aggregated to the higher level. adapt: All respective taxa will be adapted, e.g. set to species level.
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.dbf" is provided as a compilation of monotypic species within the GermanSL list (see tv.mono.
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.
Only the above mentioned types are embraced in this function. Others like forms are always synonyms in Standard lists.tv.veg, tv.obs# Turboveg installation needed
obs <- tv.taxval('taxatest')
## For explanations see vignette('vegdata').Run the code above in your browser using DataLab