overly: Overly of multivariate time series

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

Description

This function attempts to superimpose (overlay) multivariate time series that typically stem from different locations to form one single series. Series are combined pairwise following the arrangement in a minimum spanning tree, spantree. The result is a time series which may be longer than the contributing series, but shorter than their length total.

Usage

overly(veg, Plot.no, y, sint, ...)
overly2(veg, Plot.no, y, sint)

## Default S3 method:
overly(veg, Plot.no, y, sint, ...)
## S3 method for class 'overly'
plot(x,...,colors=NULL,l.widths=NULL)

Arguments

veg	This is a vegetation data frame, releves are rows, species columns. It is assumed that it constitutes two or more time series
Plot.no	Plot names. Rows with identical name are assumed to belong to the same time series.
y	Transformation of species scores: x'= x exp(y)
sint	Length of time interval. Affects display only.
...	Parameters colors=NULL, l.width=NULL, colors and line widths in plots.
colors	A vector of colors, such as c(1,2,3). The entries are recycled upon printing.
l.widths	A vector of line widths used for plotting, e.g., c=(0.5,1,1.5,2).The entries are recycled upon printing.
x	An object of class "overly"

Details

In plant ecology this procedure is also known as space-for-time substitution. See also pco,spantree.

Value

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

plot.labels	Names of plots, see Plot.no above
n.tseps	The resulting (synthetic) number of time steps
tseps	A vector of time steps in time units
tser.data	The resulting vegetation time steps
ord.scores	The pco scores of the ordination of time series
d.mat	Euclidean distance matrix of time series
vegraw	Input vegetation data frame veg (see above)
linex1	Starting address of the time series in the synthetic time frame
linex2	End address of the time series in the synthetic time frame
ltex	The plot names
sint	The time interval (see above)
vegtypes	The species names involved

Author(s)

Otto Wildi

References

Wildi, O. and Schuetz, M. 2000. Reconstruction of a long-term recovery process from pasture to forest. Community Ecology 1: 25–32. Wildi, O. 2017. Data Analysis in Vegetation Ecology. 3rd ed. CABI, Oxfordshire, Boston.

Examples

o.overly<- overly(sn59veg,sn59sit$Plot.no,y=0.5,sint=5)
# Plotting (i) minimum spanning tree, (ii) temporal arrangement of time series,
# (iii) synthetic multivariate time series
plot(o.overly,colors=NULL,l.width=NULL)

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