Clusters a presence-absence matrix object by taking the
'h-cut'-partition of a hierarchical clustering and
declaring all members of too small clusters as 'noise' (this gives a
distance-based clustering method, which estimates the number of
clusters and allows for noise/non-clustered points). Note that this
is experimental. Often, the prabclust-solutions
is more convincing due to higher flexibility of that method. However,
hprabclust may be more stable sometimes.
Note: Data formats are described
on the prabinit help page. You may also consider the example datasets
kykladspecreg.dat and nb.dat. Take care of the
parameter rows.are.species of prabinit.
hprabclust(prabobj, cutdist=0.4, cutout=1,
method="average", nnout=2, mdsplot=TRUE, mdsmethod="classical")# S3 method for comprabclust
print(x, ...)
hprabclust generates an object of class comprabclust. This is a
list with components
vector of integers indicating the cluster memberships of
the species (cutout-outliers are noise, but small clusters
are allowed). Noise is coded as 0.
vector of integers indicating the cluster memberships of
the species, noise as described under nnout.
Noise is coded as 0.
see above.
see above.
see above.
see above.
number of points minus cutout-outliers.
vector of characters corresponding to rclustering, but
estimated noise by "N".
numerical matrix. MDS configuration (if mdsplot=TRUE).
function call.
object of class prab as
generated by prabinit. Presence-absence data to be analyzed.
non-negative integer. Cutoff distance to determine the
partition, see cutree.
non-negative integer. Points that have at most
nnout distances smaller or equal than cutout are
treated as noise.
string. Clustering method, see hclust.
non-negative integer. Members of clusters with less or
equal than nnout points or that have less or equal than
nnout neighbors closer than cutout are treated as noise.
logical. If TRUE, the cluster solution is
plotted on the first two MDS dimensions, see mdsmethod.
"classical", "kruskal", or
"sammon". The MDS method
to transform the distances to data points. "classical" indicates
metric MDS by function cmdscale, "kruskal" is
non-metric MDS. Note that if mdsmethod!="classical" zero
distances between different objects are replaced by the minimum of
the nonzero distances divided by 10 (otherwise the MDS method would
produce an error). Note that mdsmethod is ignored if
mdsplot=FALSE.
comprabclust-object as generated by hprabclus.
necessary for print method.
Christian Hennig christian.hennig@unibo.it https://www.unibo.it/sitoweb/christian.hennig/en
data(kykladspecreg)
data(nb)
data(waterdist)
x <- prabinit(prabmatrix=kykladspecreg, neighborhood=nb,
geodist=waterdist, distance="geco")
hprabclust(x,mdsplot=FALSE)
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