vegdata (version 0.6.2)

syntab: Frequency tables

Description

Make relative or absolute frequency tables.

Usage

syntab(veg, clust, type = c('rel','abs','mean.cover'), fullnames=FALSE, limit=0, mupa=NULL, alpha=0.05, minstat=0, dec=0, refl, ...)

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).

fullnames

Replace rownames (LETTERCODES) with full scientific names.

limit

Minimum value to display.

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.

alpha

Significance threshold.

minstat

Minimal indicator value

dec

Number of decimals in result.

refl

Name of Turboveg taxonomic reference list to use for fullnames.

...

additional arguments

See Also

package indicspecies from M. Cac'{e}res with function multipatt for indicator species analysis along multiple cluster combinations

Examples

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')
syntab(elbaue, clust, limit=30, mupa=TRUE, fullnames=TRUE)