isotab: Ordered frequency table for Isopam clusters

In isopam: Clustering of Sites with Species Data

Ordered frequency table for Isopam clusters

Description

Computes an ordered frequency table based on Isopam clustering results. The upper part of the table lists typical descriptors (usually species) with a significant binding to single clusters (according to customisable thresholds). The lower part of the table is ordered by descending overall frequency.

Usage

isotab(ip, level = 1, phi.min = 'auto', p.max = .05, wordy = FALSE)

Arguments

ip	object of class isopam.
level	level in cluster hierarchy starting with 1 = first division.
phi.min	threshold of phi determining which descriptors (species) are listed in the upper part of the table. Applies only to descriptors passing the criterion defined by p.max. If phi.min = 'auto' (the default) isotab suggests a suitable value based on the numbers of clusters, observations, and descriptors.
p.max	threshold of Fisher's p determining which descriptors (species) are listed in the upper part of the table. Applies only to descriptors passing the criterion defined by phi.min.
wordy	logical. If TRUE status messages and output tables are shown.

Details

phi.min is based on the standardized phi value according to Chitrý et al. 2002.

Value

tab	dataframe with ordered frequencies and their significance. The latter is derived from Fisher's exact test (p <= 0.05: *, p <= 0.01: **, p <= 0.001: ***).
n	matrix with cluster sizes.
thresholds	phi.min and p.max used.
typical	text with items (often species) typically found in clusters (according to thresholds).
typical_vector	typical as a single character vector.
isopam_indicators	items (species) used as indicators in the original isopam clustering process.

Author(s)

Sebastian Schmidtlein

References

Chitrý, M., Tichý, L., Holt, J., Botta-Dukát, Z. (2002): Determination of diagnostic species with statistical fidelity measures. Journal of Vegetation Science 13, 79–90.

Schmidtlein, S., Tichý, L., Feilhauer, H., Faude, U. (2010): A brute force approach to vegetation classification. Journal of Vegetation Science (in press).

See Also

isopam

Examples

   ## load data to the current environment
   data(andechs)
     
   ## call isopam with the standard options
   ip<-isopam(andechs)
    
   ## build table (uppermost hierarchy level)
   isotab(ip)

   ## build table (lower hierarchy level)
   isotab(ip,2)

isopam documentation built on Sept. 8, 2023, 5:06 p.m.