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Last data update: 2014.03.03

R: Syntaxonomic frequency tables

syntab

R Documentation

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=NULL, 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 or absolute frequency, mean species response values or strength of association (see function multipatt in package indicspecis).
`mupa`	Either logical for (not) using multipatt from package indispecies to detect significance of cluster association strength or supply output from previous use of multipatt.
`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.
`dec`	Number of decimals in result.
`refl`	Name of Turboveg taxonomic reference list to use for fullnames.
`...`	additional arguments

Author(s)

Florian Jansen jansen@uni-greifswald.de

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) 
taxa <- tax(rownames(sttable))
rownames(sttable) <- taxa[match(rownames(sttable), taxa$LETTERCODE, nomatch = 0),'TaxonName']
write.csv(sttable, 'sttable.csv')

## End(Not run)