pcaser {dave}

R Documentation

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)

## Default S3 method:
pcaser(veg, plotlabels, y, ...)
## S3 method for class '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)

Author(s)

Otto Wildi

References

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

Examples

o.pcaser<- pcaser(sn6veg,sn6sit$Plot.no,y=0.25)
plot(o.pcaser,lines=TRUE)                

---