California Soil Resource Lab

Cluster Analysis 1: finding groups in a randomly generated 2-dimensional dataset

Submitted by dylan on Thu, 2006-03-09 19:00.

Figure 1. Two class example

Figure 2: Four class example

Cluster Analysis 1: 2 class example with 2-way fuzzy membership

Figure 3: 2-way fuzzy membership

Examples based on a random data set (see example code below), illustrating some of the differences between the K-means and C-means clustering methods as implemented in R. Next time an example with soil profile data collected from the Pinnacles National Monument soil survey efforts. An online version of the PINN soil survey will be available soon here.

Articles:

Example in R:

## load required packages:

 require(cluster)

 require(e1071)

## make a dateset with 5 populations

x <- matrix( c(

rnorm(50, mean=.3, sd=.5),

rnorm(50, mean=.16, sd=.1),

rnorm(50, mean=.4, sd=.3),

rnorm(50, mean=.6, sd=.2),

rnorm(50, mean=.2, sd=.2)

), ncol=2)

## load function membership() : see attached file at bottom of page

source('cluster_demo_function.R')

## run an example with 2, then 4 classes: See Figures 1 and 2

membership(x,2)

membership(x,4)

## two-way fuzzy membership illustrated with color: See Figure 3

## display 2-way fuzzy membership

plot(x, main="C-means: 2-way Fuzzy Membership", type="n", xlab="Variable 1", ylab="Variable 2")

points(cc$centers, col = c("red", "blue"), pch = 8, cex=2)

points(x, col = rgb(cc$membership[,1], 0 ,cc$membership[,2]) , cex=0.5, pch=16)

Attachment	Size
cluster_demo_function.R	2.13 KB

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Cluster Analysis 1: finding groups in a randomly generated 2-dimensional dataset

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