simper(comm, group, ...)
## S3 method for class 'simper':
summary(object, ordered = TRUE,
digits = max(3, getOption("digits") - 3), ...)simper."simper" with following items:cusum back to the original data order.simper (Clarke 1993) is based
on the decomposition of Bray-Curtis dissimilarity index (see
vegdist, designdist). The contribution
of individual species $i$ to the overall Bray-Curtis dissimilarity
$d_{jk}$ is given by $$d_{ijk} = \frac{|x_{ij}-x_{ik}|}{\sum_{i=1}^S (x_{ij}+x_{ik})}$$
where $x$ is the abundance of species $i$ in sampling units
$j$ and $k$. The overall index is the sum of the individual
contributions over all $S$ species
$d_{jk}=\sum_{i=1}^S d_{ijk}$.
The simper functions performs pairwise comparisons of groups
of sampling units and finds the average contributions
of each species to the average overall Bray-Curtis dissimilarity.
The function displays most important species for each pair of
groups. These species contribute at least to 70 % of the
differences between groups. The function returns much more
extensive results which can be accessed directly from the result
object (see section Value). Function summary transforms the
result to a list of data frames. With argument ordered = TRUE
the data frames also include the cumulative contributions and
are ordered by species contribution.
data(dune)
data(dune.env)
(sim <- with(dune.env, simper(dune, Management)))
summary(sim)Run the code above in your browser using DataLab