dave (version 2.0)

pcaser: Connecting time series in ordinations

Description

Given a vegetation data frame containing various time series this plots a pca-ordination (pca) and connects points belonging to the same series with lines. The plots where the releves come from are identified by plotlabels (see below).

Usage

pcaser(veg, plotlabels, y, ...)
pcaser2(veg, plotlabels, y=1)
# S3 method for default
pcaser(veg, plotlabels, y, ...)
# S3 method for pcaser
plot(x,lines=TRUE,arrows=TRUE,...)

Arguments

veg

This is a vegetation data frame, releves are rows, species columns

plotlabels

Plot names. Rows with identical name are assumed to belong to the same time series.

y

Transformation of species scores: x'= x exp(y)

…

Parameter lines=TRUE will connect the series. Otherwise they are distinguished by symbols used in plot only.

x

An object of class "pcaser".

lines

A logical variable. When TRUE then points of the same time series are connected.

arrows

A logical variable. When TRUE then the first and the last points of the same time series are connected.

Value

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

comp1

Description of 'comp1'

nrel

Total number of releves involved (i.e., row number)

nser

Total number of time series (i.e., locations where the data stem from

scores

The pca-ordination scores

plotlab

Plot labels used for plotting

plotlabels

Plot names

Eigv

Eigenvalues (percentage)

References

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

Examples

# NOT RUN {
o.pcaser<- pcaser(sn6veg,sn6sit$Plot.no,y=0.25)
plot(o.pcaser,lines=TRUE)                
# }