dave (version 2.0)

srank: 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)
# S3 method for default
srank(veg, groups, method, y,...)
# S3 method for 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

References

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

Wildi, O. 2017. Data Analysis in Vegetation Ecology. 3rd ed. CABI, Oxfordshire, Boston.

Examples

# NOT RUN {
# 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
# }