srank: Ranking species by IndVal or F-value

In dave: Functions for "Data Analysis in Vegetation Ecology"

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

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

Example output

Loading required package: cluster
Loading required package: labdsv
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-33. For overview type 'help("mgcv-package")'.
This is labdsv 2.0-1
convert existing ordinations with as.dsvord()

Attaching package: ‘labdsv’

The following object is masked from ‘package:stats’:

    density

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-7
Loading required package: nnet

Attaching package: ‘nnet’

The following object is masked from ‘package:mgcv’:

    multinom

Loading required package: tree
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
Call:
srank.default(veg = nveg, groups = groups, method = "jancey", 
    y = 0.5)
    Rank    No. Species                            F-value     error p 
     1      13  Veronica.officinalis                86.471   3.82e-06  
     2      19  Ranunculus.ficaria                  81.781   4.73e-06  
     3      12  Luzula.nemorosa                     60.853   1.45e-05  
     4      16  Primula.elatior                     54.090   2.25e-05  
     5       3  Acer.pseudoplatanus                 46.648   3.89e-05  
     6      17  Allium.ursinum                      30.979   0.000171  
     7      21  Polytrichum.formosum                27.777   0.000251  
     8       4  Fraxinus.excelsior                  22.093   0.000552  
     9       7  Sambucus.nigra                      14.018   0.00243   
    10       2  Quercus.petraea                      7.936   0.0126    
    11       6  Sambucus.racemosa                    6.427   0.0217    
    12       8  Vaccinium.myrtillus                  6.427   0.0217    
    13      15  Lamium.galeobdolon                   5.353   0.0334    
    14      18  Arum.maculatum                       5.346   0.0336    
    15       5  Lonicera.xylosteum                   4.069   0.0604    
    16       1  Fagus.silvatica                      2.007   0.197     
    17      14  Galium.odoratum                      0.460   0.647     
    18      10  Oxalis.acetosella                    0.371   0.701     
    19      20  Eurhynchium.striatum                 0.107   0.899     
    20      11  Viola.silvestris                     0.098   0.908     
    21       9  Carex.silvatica                      0.013   0.987     

dave documentation built on May 2, 2019, 1:30 p.m.