isotab {isopam}

Fidelity and frequency of species in clusters

Description

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.

Usage

isotab(x, level = NULL, clusters = NULL, phi.min = "isotab", p.max = .05)
## S3 method for class 'isotab'
print(x, n = NA, ...)

Arguments

x

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 sites 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.

clusters

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

Level in cluster hierarchy starting with 1 = first division.

phi.min

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.

p.max

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.

n

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.

Details

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.

Value

call

generating call

depth

Number of levels in the cluster hierarchy from the original clustering procedure.

level

Level chosen for isotab.

tab

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: ***).

phi

Dataframe with equalized phi values (see details).

fisher_p

Numerical results from Fisher's exact test (see details)

n

Matrix with cluster sizes.

thresholds

phi.min and p.max used for table sorting.

typical

Text with items (often species) typically found in clusters (according to thresholds).

typical_vector

typical as a single character vector.

sorted_table

Ordered species by plot table.

Author(s)

Sebastian Schmidtlein

References

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.

See Also

isopam, plot.isotab

Examples

   ## 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