distconnected {vegan}  R Documentation 
Function distconnected
finds groups that are connected
disregarding dissimilarities that are at or above a threshold or
NA
. The function can be used to find groups that can be
ordinated together or transformed by
stepacross
. Function no.shared
returns a logical
dissimilarity object, where TRUE
means that sites have no
species in common. This is a minimal structure for
distconnected
or can be used to set missing values to
dissimilarities.
distconnected(dis, toolong = 1, trace = TRUE) no.shared(x)
dis 
Dissimilarity data inheriting from class dist or
a an object, such as a matrix, that can be converted to a
dissimilarity matrix. Functions vegdist and
dist are some functions producing suitable
dissimilarity data. 
toolong 
Shortest dissimilarity regarded as NA .
The function uses a fuzz factor, so
that dissimilarities close to the limit will be made NA , too.
If toolong = 0 (or negative), no dissimilarity is regarded
as too long.

trace 
Summarize results of distconnected 
x 
Community data. 
Data sets are disconnected if they have sample plots or groups of
sample plots which share no species with other sites or groups of
sites. Such data sets cannot be sensibly ordinated by any
unconstrained method because these subsets cannot be related to each
other. For instance, correspondence analysis will polarize these
subsets with eigenvalue 1. Neither can such dissimilarities be
transformed with stepacross
, because there is no path
between all points, and result will contain NA
s. Function
distconnected
will find such subsets in dissimilarity
matrices. The function will return a grouping vector that can be used
for subsetting the data. If data are connected, the result vector will
be all 1s. The connectedness between two points can be defined
either by a threshold toolong
or using input dissimilarities
with NA
s.
Function no.shared
returns a dist
structure having value
TRUE
when two sites have nothing in common, and value
FALSE
when they have at least one shared species. This is a
minimal structure that can be analysed with distconnected
. The
function can be used to select dissimilarities with no shared species
in indices which do not have a fixed upper limit.
Function distconnected
uses depthfirst search
(Sedgewick 1990).
Function distconnected
returns a vector for
observations using integers to identify connected groups. If the data
are connected, values will be all 1
. Function no.shared
returns an object of class dist
.
Jari Oksanen
Sedgewick, R. (1990). Algorithms in C. Addison Wesley.
vegdist
or dist
for getting
dissimilarities, stepacross
for a case where you may need
distconnected
, and for connecting points spantree
.
## There are no disconnected data in vegan, and the following uses an ## extremely low threshold limit for connectedness. This is for ## illustration only, and not a recommended practice. data(dune) dis < vegdist(dune) gr < distconnected(dis, toolong=0.4) # Make sites with no shared species as NA in Manhattan dissimilarities dis < vegdist(dune, "manhattan") is.na(dis) < no.shared(dune)