vegdata (version 0.9.8)

syntab: 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 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 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

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')
# }