syntab: Syntaxonomic frequency tables

In vegdata: Access Vegetation Databases and Treat Taxonomy

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

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.
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.

Author(s)

Florian Jansen [e-mail]

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)

vegdata documentation built on May 29, 2024, 4:19 a.m.