optimclass: Optimum Classification by Counts of Indicator Species

In optpart: Optimal Partitioning of Similarity Relations

Description

Calculates the number of indicator species/cluster across a range of partitions

Usage

optimclass(comm, stride, pval = 0.01, counts = 2)

Arguments

comm	a community matrix with sample units as rows and species as columns
stride	an object of class ‘stride’from function stride
pval	the minimum probability for inclusion in the list of indicators
counts	the minimum number of clusters for inclusion in the list

Details

Calculates the number of indicator species/cluster and the number of clusters with at least ‘counts’ indicators, using the φ index to identify indicators with probabilities less than or equal to ‘pval’. Arguably the optimal partition is the one with the most indicator species and the most clusters with adequate indicators.

Value

A data.frame of

clusters	number of clusters
sig.spc	the number of species with significant indicator value
sig.clust	the number of clusters with at least ‘counts’ indicator species

Note

The concept and first implementation were by Tichy in software package ‘Juice’, and this is a simple port of the algorithm to R.

Author(s)

Lubomir Tichy wrote the original algorithm

David W. Roberts [e-mail]

References

Tichy, L., M. Chytry, M. Hajek, S. Talbot, and Z. Botta-Dukat. 2010. OptimClass: Using species-to-cluster fidelity to determine the optimal partition in classification of ecological communities. J. Veg. Sci. 21:287-299.

See Also

indval

Examples

data(shoshveg)
dis.bc <- dsvdis(shoshveg,'bray')
opt.2.10 <- stride(2:20,dis.bc)
## Not run: optimclass(shoshveg,opt.2.10)

Example output

Loading required package: cluster
Loading required package: labdsv
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-33. For overview type 'help("mgcv-package")'.
This is labdsv 2.0-1
convert existing ordinations with as.dsvord()

Attaching package: ‘labdsv’

The following object is masked from ‘package:stats’:

    density

Loading required package: MASS
Loading required package: plotrix

optpart documentation built on March 26, 2020, 6:18 p.m.