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Last data update: 2014.03.03

R: Ranking species by IndVal or F-value

srank

R Documentation

Ranking species by IndVal or F-value

Description

Given a vegetation data frame with grouped rows (releves) indicator value analysis (funcion indval) or analysis of variance (aoc) is performed on columns (species) and these are ordered by decreasing IndVal (function indval()) or F-value (aov()) accordingly.

Usage

srank(veg, groups, method, y,...)
srank2(veg,groups,method,y)

## Default S3 method:
srank(veg, groups, method, y,...)
## S3 method for class 'srank'
print(x,...)

Arguments

`veg`	This is a vegetation data frame, releves are rows, species columns
`groups`	Group membership of rows (releves)
`method`	Either "indval" or "jancey"
`y`	Transformation of species scores: x'= x exp(y)
`...`	Further variables used for printing
`x`	A list of class "srank" generated by centroid

Value

An object of class "srank" with at least the following items:

`rank`	A sequence of numbers, 1,2,3,...,p where p= number of species
`species.no`	The corresponding species no. (i.e. the column no.
`species`	The corresponding species names (taken from column names
`Indval`	The corresponding indicator values (method "indval")
`F_value`	The corresponding F-values (method "jancey")
`error.probability`	The corresponding error probabilities

Author(s)

Otto Wildi

References

Jancey, R.C. 1979. Species ordering on a variance criterion. Vegetatio 39: 59–63.

Wildi, O. 2013. Data Analysis in Vegetation Ecology. 2nd ed. Wiley-Blackwell, Chichester.

Examples

# Starts with classifying releves by cluster analysis
dd<- vegdist(nveg^0.5,method="euclid")         # dd is distance matrix
o.clust<- hclust(dd,method="ward")             # clustering
groups<- as.factor(cutree(o.clust,k=3))        # forming 3 groups

# Applies ranking and prints ordered table of species (the columns)
o.srank<- srank(nveg,groups,method="jancey",y=0.5)
o.srank