Description Usage Arguments Value Author(s) Examples
Project a set of points defined by a distance matrix
or a set of variables in an eucleadean space.
If the distance matrix is a metric, this is done using
the pcoa
function,
for other distance the nmds
is used.
When points are described by a set of variable the
nmds
is used.
1 2 3 4 5 6 7 8 9 10 11 12 13 |
data |
a numeric matrix describing the points |
... |
other parameters specific to some implementation |
tol |
a tolerance threshold : an eigenvalue is considered positive if it is larger than -tol*lambda1 where lambda1 is the largest eigenvalue. |
scale |
a |
a numeric matrix with at most n-1
dimensions, with
n
the number pf observations. This matrix defines the
coordinates of each point in the orthogonal space.
Eric Coissac
Christelle Gonindard-Melodelima
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | library(vegan)
data(bacteria)
data(eukaryotes)
data(soil)
dataset <- procmod_frame(euk = vegdist(decostand(eukaryotes,
method = "hellinger"),
method = "euclidean"),
bac = vegdist(decostand(bacteria,
method = "hellinger"),
method = "euclidean"),
soil = scale(soil,
center = TRUE,
scale = TRUE))
dp <- ortho(dataset)
bacteria_rel_freq <- sweep(bacteria,
1,
rowSums(bacteria),
"/")
bacteria_hellinger <- sqrt(bacteria_rel_freq)
bacteria_dist <- dist(bacteria_hellinger)
project <- ortho(bacteria_dist)
|
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