Last data update: 2014.03.03
R: Flexible shortest path adjustment
Flexible shortest path adjustment
Description
Flexible shortest path adjustment is a heuristic ordination method attempting to adjust pattern to ecological situations. It erases long distances in the resemblance matrix and replaces these by the sum of intermediate steps. Subsequent ordination uses function pco
.
Usage
fspa(veg, method, d.rev, n.groups, ...)
fspa2(veg,method,d.rev=0.5,n.groups=3)
## Default S3 method:
fspa(veg, method, d.rev, n.groups, ...)
## S3 method for class 'fspa'
plot(x,...,axes=c(1,2))
Arguments
veg
A data frame of vegetation releves (rows) by species (columns)
method
The method used for calculating distance as available in function vegdist of package
vegan, for instance method = "bray".
d.rev
The percentage of distances revised, for instance 0.5 (50 percent, the default).
n.groups
This classifies the data points for illustrative purposes (uses Ward's method).
...
Variable axes=c(1,2) (default), the axes to be plotted
x
An object of class "fspa".
axes
A vector of length two, assessing the axes used for plotting. Default is c(1,2).
Value
An output list of class "fspa" with at least the following intems:
oldpoints
Ordination scores before adjustment
newpoints
Ordination scores after adjustment
symbols
The symbols used for classified plot
nline
The number of lines to be drawn in the graph
startline
Coordinates where the lines start
endline
Coordinates where the lines end
dmat.before
Distance matrix before analysis
dmat.after
Distance matrix after analysis
endline
Coordinates where the lines end
d.rev
proportion of distances revised
Author(s)
Otto Wildi
References
Bradfield, G.E. & Kenkel, N.C. 1987. Nonlinear ordination using flexible shortest path adjustment of ecological distances. Ecology 68: 750–753.
Wildi, O. 2013. Data Analysis in Vegetation Ecology. 2nd ed. Wiley-Blackwell, Chichester.
Examples
o.fspa<- fspa(sveg,method="euclid",d.rev=0.75,n.groups=6) # sveg is vegetation data
plot(o.fspa,axes=c(1,2)) # plots axis 1, 2
Results