R: Coefficients Comparing Classification Agreement

classAgreement {e1071} | R Documentation

## Coefficients Comparing Classification Agreement

### Description

`classAgreement()` computes several coefficients of agreement between the columns and rows of a 2-way contingency table.

### Usage

    classAgreement(tab, match.names=FALSE)

### Arguments

`tab` | A 2-dimensional contingency table.
`match.names` | Flag whether row and columns should be matched by name.

### Details

Suppose we want to compare two classifications summarized by the contingency table T=[t_{ij}] where i,j=1,…,K and t_{ij} denotes the number of data points which are in class i in the first partition and in class j in the second partition. If both classifications use the same labels, then obviously the two classification agree completely if only elements in the main diagonal of the table are non-zero. On the other hand, large off-diagonal elements correspond to smaller agreement between the two classifications. If `match.names` is `TRUE`, the class labels as given by the row and column names are matched, i.e. only columns and rows with the same dimnames are used for the computation.

If the two classification do not use the same set of labels, or if identical labels can have different meaning (e.g., two outcomes of cluster analysis on the same data set), then the situation is a little bit more complicated. Let A denote the number of all pairs of data points which are either put into the same cluster by both partitions or put into different clusters by both partitions. Conversely, let D denote the number of all pairs of data points that are put into one cluster in one partition, but into different clusters by the other partition. Hence, the partitions disagree for all pairs D and agree for all pairs A. We can measure the agreement by the Rand index A/(A+D) which is invariant with respect to permutations of the columns or rows of T.

Both indices have to be corrected for agreement by chance if the sizes of the classes are not uniform.

### Value

A list with components

`diag` | Percentage of data points in the main diagonal of `tab`.
`kappa` | `diag` corrected for agreement by chance.
`rand` | Rand index.
`crand` | Rand index corrected for agreement by chance.

### Author(s)

Friedrich Leisch

### References

J.~Cohen. A coefficient of agreement for nominal scales. Educational and Psychological Measurement, 20, 37–46, 1960.

Lawrence Hubert and Phipps Arabie. Comparing partitions. Journal of Classification, 2, 193–218, 1985.

### See Also

`matchClasses`

### Examples

    ## no class correlations: both kappa and crand almost zero
    g1 <- sample(1:5, size=1000, replace=TRUE)
    g2 <- sample(1:5, size=1000, replace=TRUE)
    tab <- table(g1, g2)
    classAgreement(tab)

    ## let pairs (g1=1,g2=1) and (g1=3,g2=3) agree better
    k <- sample(1:1000, size=200)
    g1[k] <- 1
    g2[k] <- 1

    k <- sample(1:1000, size=200)
    g1[k] <- 3
    g2[k] <- 3

    tab <- table(g1, g2)
    ## both kappa and crand should be significantly larger than before
    classAgreement(tab)

[Package e1071 version 1.7-6 Index]