vegdist {vegsoup} | R Documentation |
Vegsoup*
Objects Compute a dissimilarity matrix as specified by vegdist(x)
by internal calls to vegdist
of vegan. Method distconnected
is a wrapper for function distconnected
also found in package vegan.
## S4 method for signature 'Vegsoup' as.dist(m, diag = FALSE, upper = FALSE) ## S4 method for signature 'Vegsoup' vegdist(x, method = "bray", binary = FALSE, diag = FALSE, upper = FALSE, na.rm = FALSE, ...) ## S4 replacement method for signature 'Vegsoup' vegdist(x) <- value ## S4 method for signature 'Vegsoup' distconnected(dis, toolong, trace)
x, m, dis |
|
value |
A single character valid as argument |
diag, upper, na.rm |
Compute diagonals or return only the upper diagonal. |
method, binary |
Not used. |
... |
For |
toolong |
Shortest dissimilarity regarded as NA. See |
trace |
Summarize results. |
Note, the method returned by decostand(obj)
will be applied before
calculation of the distance matrix. Use vegdist(obj)
to query which
method is active for an object. The print
, show
and
summary
methods will report this value for a Vegsoup*
object.
If vegdist
is rested using the replacement method vegdist<-
for
objects of classes 'VegsoupPartition'
and 'VegsoupPartitionFidelity'
the respective objects are recomputed as to honor the changed distance method.
Method distconnected
is a simple wrapper for function
distconnected
in package
vegan and checks for connectedness of dissimilarities.
as.dist
returns an object of class "dist"
with an additional attribute "mode"
.
vegdist
returns a "character"
, the distance index active for a Vegsoup*
object.
distconnected
returns an "integer"
vector to identify connected groups.
As vegan::vegdist
, as.dist
returns dissimilarities not distances.
If the resulting "dist"
object is not a dissimilarity matrix
(max(D) > 1
), it will be divided by max(D)
to obtain
dissimilarities.
Roland Kaiser
vegdist
and distconnected
are methods for functions in package vegan.
require(vegsoup) data(barmstein) x <- barmstein # query disssimlilarity measure set for the object vegdist(x) # change the default distance 'euclidean' vegdist(x) <- "bray" d <- as.dist(x, "numeric") class(d) attributes(d) attr(d, "mode") # replace vegdist method for VegsoupPartition object x <- VegsoupPartition(barmstein, k = 2) vegdist(x) p1 <- partitioning(x) # change vegdist vegdist(x) <- "bray" p2 <- partitioning(x) table(p1, p2) # R-mode analysis # currently disfunct due to missing ... argument in stats:as.dist # chi square distances can be obtained # by computing euclidean distances on standardized data # see ?vegan::vegdist ## Not run: # decostand(x) <- "chi.square" # d <- as.dist(dta, mode = "R") # class(d) # attr(d, "mode") ## End(Not run) # connectivity of distances distconnected(x)