Calculates the fidelity of species to clusters. Returns equalized phi coefficients of association, an ordered frequency table and Fisher`s exact test for the probability of obtaining the observed frequencies. Isopam objects as well as other combinations of tables and cluster vectors are accepted as input data. An associated plotting method visualises how closely individual species are associated with clusters.
isotab(x, level = NULL, clusters = NULL, phi.min = "isotab", p.max = .05)
# S3 method for isotab
print(x, n = NA, ...)
generating call
Number of levels in the cluster hierarchy from the original clustering procedure.
Level chosen for isotab.
Ordered species by cluster table with frequencies and their
significance. The latter is derived from Fisher's exact test (see
fisher_p and details, p <= 0.05: *, p <= 0.01: **,
p <= 0.001: ***).
Dataframe with equalized phi values (see details).
Numerical results from Fisher's exact test (see details)
Matrix with cluster sizes.
phi.min and p.max used for table sorting.
Text with items (often species) typically
found in clusters (according to thresholds).
typical as a single character vector.
Ordered species by plot table.
Object either of class isopam or a dataframe or matrix with rownames
(plot names) and column names (species names) that is accompanied by a
cluster vector (clusters) with named elements corresponding to the
rows in x. Tibbles need a column with plot names (<chr>), while the
other columns are of class <dbl> or <int>. In method print, x
is an object of class isotab.
Vector with assignments of clusters to plots, only
needed if x is not an isopam object. The names of the elements need
to be identical to the rownames of x.
Level in cluster hierarchy starting with 1 = first division.
Threshold of equalized phi determining which species are listed
in the upper part of the table. Applies only to species passing the
criterion defined by p.max. If phi.min = "isopam" (the
default) isotab suggests a value based on the numbers of observations.
Threshold of Fisher's p determining which species are listed in the
upper part of the table. Applies only to species passing the criterion
defined by phi.min.
number of lines used by print. If NA (the default),
n is oriented on the number of diagnosic species. Use n = Inf to print
all rows.
other arguments used by print.
Sebastian Schmidtlein
phi.min is based on the 'equalized phi' value according to
Tichý & Chitrý 2006. The threshold proposed if
phi.min is set to "isotab" should be adjusted to local conditions.
The significance (Fisher's p) refers to the probability that the
observed frequency is reached. The test is two-tailed, which means that
exceptionally low frequencies can result as highly significant as well as
exceptionally high frequencies. This allows positive and negative
characterisation of a cluster by species.
Tichý, L., Chytrý, M. (2006): Statistical determination of diagnostic species for site groups of unequal size. Journal of Vegetation Science 17: 809-–818.
Schmidtlein, S., Tichý, L., Feilhauer, H., Faude, U. (2010): A brute force approach to vegetation classification. Journal of Vegetation Science 21: 1162--1171.
isopam, plot.isotab
## load data to the current environment
data(andechs)
## call isopam with the standard options
ip <-isopam(andechs)
## build table
it <- isotab(ip)
it
## change phi threshold
it <- isotab(ip, phi.min = 0.8)
## switch cluster level
it <- isotab(ip, level = 1)
it
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