Description Usage Arguments Details Value Note Author(s) References See Also Examples
Calculates the number of indicator species/cluster across a range of partitions
1  optimclass(comm, stride, pval = 0.01, counts = 2)

comm 
a community matrix with sample units as rows and species as columns 
stride 
an object of class ‘stride’from function

pval 
the minimum probability for inclusion in the list of indicators 
counts 
the minimum number of clusters for inclusion in the list 
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.
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 
The concept and first implementation were by Tichy in software package ‘Juice’, and this is a simple port of the algorithm to R.
Lubomir Tichy wrote the original algorithm
David W. Roberts droberts@montana.edu
Tichy, L., M. Chytry, M. Hajek, S. Talbot, and Z. BottaDukat. 2010. OptimClass: Using speciestocluster fidelity to determine the optimal partition in classification of ecological communities. J. Veg. Sci. 21:287299.
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convert existing ordinations with as.dsvord()
Attaching package: ‘labdsv’
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