speedprof: Plotting velocity profiles of multivariate time series

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

Description

From a multivariate time series of vegetation data this first computes a distance matrix (vegdist, euclidean). The first plot is a graphical representation of the full distance matrix, the second a profile of change per time step of different length (velocity).

Usage

speedprof(veg, timescale, orders, y = 1, adjust,...)
speedprof2(veg, timescale, orders, y = 1, adjust)

## Default S3 method:
speedprof(veg, timescale, orders, y = 1, adjust,...)
## S3 method for class 'speedprof'
plot(x,...)

Arguments

veg	This is a vegetation data frame, releves are rows, species columns. Releves are considered a time series.
timescale	A vector of points in time of releves (rows)
orders	Orders used for printing the velocity profile, i.e., the number of time steps used for calculating speed (rate of change per time unit).
y	Transformation of species scores: x'= x exp(y)
adjust	Parameter adjust=TRUE re-scales releves to vector sum=100 percent (assuming cover
x	An object of class "speedprof".
...	Parameter out.seq, the plotting interval

Value

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

nrel	The number of releves
dmatrix	The distance matrix
timescale	The time scale
orders	Time step lengths considered for plotting the profile

Author(s)

Otto Wildi

References

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

Examples

orders<- c(1,2,3,4)
o.spp<- speedprof(tveg,tsit$Year,orders,y=1.0,adjust=TRUE)
plot(o.spp)

Example output

Loading required package: labdsv
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-25. For overview type 'help("mgcv-package")'.
Loading required package: MASS
Loading required package: cluster

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 2.5-3
Call:
speedprof.default(veg = tveg, timescale = tsit$Year, orders = orders, 
    y = 1, adjust = TRUE)

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