# Syntaxonomic frequency tables Calculate and display relative or absolute frequency tables with or without use of function multipatt from package indicspecies ```r 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 - `veg`: Vegetation dataframe - `clust`: Vector with cluster information with length equal to number of rows of veg - `type`: Relative (species or type) or absolute frequency, mean species response values or strength of association. - `mupa`: Either logical for (not) using multipatt from package indicspecies to detect significance of cluster association strength or supply output from previous use of multipatt. - `dec`: Number of decimals in result. - `refl`: Name of Turboveg taxonomic reference list to use for fullnames. - `...`: additional arguments - `x`: Object from function syntab - `zero.print`: Replacement for zero values. - `trait`: Optional vector of trait values to be plotted behind the species. - `limit`: Minimum value to display. - `minstat`: Minimal indicator value - `alpha`: Significance threshold. ## Examples ```r ## 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') st <- syntab(elbaue, clust, mupa=TRUE) traits <- tv.traits() m <- match(rownames(st$syntab), traits$LETTERCODE, nomatch = 0) trait <- traits[m, c("OEK_F","OEK_N")] rownames(trait) <- traits$LETTERCODE[m] print(st, limit=30, trait=trait) #' Configure the syntaxonomic table sttable <- st$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) ``` ## See Also Package indicspecies with function multipatt for indicator species analysis along multiple cluster combinations ## Author(s) Florian Jansen florian.jansen@uni-rostock.de

syntab function