isopam (version 1.1.0)

isotab: 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)

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.

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.

Author

Sebastian Schmidtlein

Details

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

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)