goodness.metaMDS {vegan} | R Documentation |
Function goodness.metaMDS
find goodness of fit measure for
points in nonmetric multidimensional scaling, and function
stressplot
makes a Shepard
diagram.
## S3 method for class 'metaMDS': goodness(object, dis, ...) stressplot(object, dis, pch, p.col = "blue", l.col = "red", lwd = 2, ...)
object |
A result object from metaMDS or
isoMDS . |
dis |
Dissimilarities. Normally this should not used with
metaMDS , but should be always used with
isoMDS . |
pch |
Plotting character for points. Default is dependent on the number of points. |
p.col, l.col |
Point and line colours. |
lwd |
Line width. |
... |
Other parameters to functions, e.g. graphical parameters. |
Function goodness.metaMDS
finds a goodness of fit statistic for
observations (points). This is defined so that sum of squared values
is equal to squared stress. Large values indicate poor fit.
Function stressplot
is a wrapper to Shepard
function in MASS package. It plots ordination distances
against original dissimilarities, and draws a step line of the
nonlinear fit. In addition, it adds to the graph two correlation-like
statistics on the goodness of fit. The nonmetric fit is based on stress S and
defined as sqrt(1-S^2). The “linear fit”
is the correlation between fitted values and ordination distances.
Both functions can be used both with metaMDS
and with
isoMDS
. With metaMDS
, the functions
try to reconstruct the dissimilarities using
metaMDSredist
, and dissimilarities should not be given.
With isoMDS
the dissimilarities must be given.
In either case, the functions inspect that dissimilarities are
consistent with current ordination, and refuse to analyse inconsistent
dissimilarities. Function goodness.metaMDS
is generic in
vegan
, but you must spell its name completely with
isoMDS
which has no class.
Function goodness
returns a vector of values. Function
stressplot
returns invisibly a Shepard
object.
Jari Oksanen.
data(varespec) mod <- metaMDS(varespec) stressplot(mod) gof <- goodness(mod) gof plot(mod, display = "sites", type = "n") points(mod, display = "sites", cex = gof/2)