bestopt: Best Of Set Optimal Partitions From Random Starts

In optpart: Optimal Partitioning of Similarity Relations

Description

Produces a specified number of optpart solutions from random starts, keeping the best result of the set

Usage

bestopt(dist,numclu,numrep,maxitr=100)

Arguments

dist	an object of class ‘dist’ from dist, vegdist, or dsvdis, or a symmetric dissimilarity matrix
numclu	the number of clusters desired
numrep	the number of random starts requested
maxitr	the maximum number of iterations per replicate

Details

calls function optpart with an random initial assignment of items to clusters ‘numitr’ times, keeping the best result (highest within/among ratio observed). See optpart for more details.

Value

an object of class partana, with components:

ptc	the mean similarity of each item to each cluster
ctc	the mean similarity of each cluster to other clusters
musubx	the membership of each item in each cluster
clustering	the best ‘crisp’ partition from musubx
ratio	the within-cluster/among-cluster similarity ratio achieved at each iteration of the selected result.

Note

This is a simple wrapper function to automate independent random starts of function optpart.

Author(s)

David W. Roberts [e-mail]

See Also

optpart, partana, pam

Examples

data(shoshveg)
dis.bc <- dsvdis(shoshveg,'bray/curtis')
x <- bestopt(dis.bc,5,10)
summary(x)
## Not run: plot(x) 

Example output

Loading required package: cluster
Loading required package: labdsv
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-25. For overview type 'help("mgcv-package")'.
Loading required package: MASS

Attaching package: 'labdsv'

The following object is masked from 'package:stats':

    density

Loading required package: plotrix

Attaching package: 'optpart'

The following object is masked from 'package:labdsv':

    clustify

Ratios for respective optparts 
 [1] "4.123" "4.123" "2.993" "2.988" "2.988" "2.988" "2.993" "2.796" "2.993"
[10] "4.123"

Choosing #  2  ratio =  4.123 
Number of clusters =  5 

  1   2   3   4   5 
  7   1   3  28 111 

           [,1]        [,2]       [,3]        [,4]       [,5]
[1,] 0.12578378 0.035825098 0.02065326 0.035951111 0.04131058
[2,] 0.03582510 0.000000000 0.00000000 0.004538691 0.01827140
[3,] 0.02065326 0.000000000 0.35148290 0.098675901 0.01567215
[4,] 0.03595111 0.004538691 0.09867590 0.249659368 0.07002854
[5,] 0.04131058 0.018271397 0.01567215 0.070028536 0.24108138

Ratio of Within-cluster similarity/Among-cluster similarity =  4.123 in 59 iterations

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