CCM-package: Correlation classification method (CCM)

Description Details Author(s) See Also Examples

Description

Classification method that classifies an observation based on its correlation with observations having known class labels. There are two main functions. The function create.CCM creates a correlation matrix of correlations between training and test samples. Both Pearson's and Spearman's rank-based correlations are supported. The function predict.CCM assigns class labels to test observations according to the class that has the highest mean correlation by default. However, any (user-defined) function in addition to the mean (e.g., median, max) can be specified.

For a complete list of functions, use 'library(help="CCM")'

Details

Package: CCM
Type: Package
Version: 1.1
Date: 2013-11-09
License: GPL(>=2)
LazyLoad: yes

Author(s)

Garrett M. Dancik and Yuanbin Ru
Maintainer: Garrett M. Dancik <dancikg@easternct.edu>

See Also

create.CCM; predict.CCM; plot.CCM

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
     ## load data ##
     data(data.expr)
     data(data.gender)

     ## check within class correlations ##
     ## outliers may be caused by poor quality ##
     ## observations or may indicate CCM is not appropriate ##
     K = cor.by.class(data.expr, data.gender)
     ## visualize the results ##
     boxplot(K, xlab = "gender")
     
     ## split dataset into training / testing ##
     train.expr = data.expr[,1:20]
     test.expr = data.expr[,21:40]
     train.gender = data.gender[1:20]
     test.gender = data.gender[21:40]
     
     ## CCM using spearman correlation ##
     K = create.CCM(test.expr, train.expr, method = "spearman")

     ## predict based on the class with the highest mean correlation (the default) ##
     p = predict(K, train.gender)
     table(pred = p, true = test.gender) # check accuracy
    
     ## plot correlations for the 3rd observation ##
     plot(K, train.gender, index = 3, main = "correlations for obs #3", 
	       xlab = "gender", ylab = "correlation") 

CCM documentation built on May 29, 2017, 12:19 p.m.

Search within the CCM package
Search all R packages, documentation and source code