connectedness {connectedness}R Documentation

Find disconnected subsets in a two-way classification

Description

connectedness finds disconnected subsets in a two-way classification without interaction. Its output can be used for plotting and subseting the data.

Usage

connectedness(x, y, sort=TRUE, subsetData=TRUE, drop=FALSE)

Arguments

x vector, factor1
y vector, factor2
sort logical, sort subsets by number of records
subsetData logical, fill the subsetData slot, see details
drop logical, drop unused levels, see details

Details

x and y must be vectors of the same length. Class of x and y need not be factor, however this is the most common usage.

Only complete cases (via complete.cases) of x and y are processed i.e. combinations with NA are removed.

List structure of returned value is:

If you work with big datasets, subsetData=FALSE might help you in returning smaller object. However, subset method can not be used on such "truncated" object; read also help page of subset.connectedness.

Argumnet drop can be used to drop unused levels before finding subsets. This will remove rows with either factor having missing values (NA).

In case of many levels print method truncates them to keep print within getOption("width"). Use levelsBySubset to get all levels by subset.

Value

A list of class "connectedness" and "list" returned with structure as described in details.

Author(s)

Gregor Gorjanc

References

Fernando, R. L. and Gianola, D. and Grossman, M. (1983) Identify all connected subsets in a two-way classification without interaction. Journal of Dairy Science, 66:1399-1402

Searle, S.R. (1987) Linear models for unbalanced models. John Wiley and Sons Inc.

See Also

plot.connectedness, levelsBySubset and subset.connectedness; similar functionality is available in pheno package: connectedSets and maxConnectedSet

Examples


data(connect)
table(connect$group, connect$season)
tmp <- connectedness(x=connect$group, y=connect$season)
tmpD <- connectedness(x=connect$group, y=connect$season, drop=TRUE)

## Print method
tmp
print(tmp)
print(tmpD)

## Plot method
par(mfrow=c(2, 2))
plot(tmp)

plot(tmp, matrix=FALSE, lines=TRUE, col=c("green", "blue"),
     pointsArg=list(pch=c(15, 19), cex=2), linesArg=list(lwd=2))

plot(tmp, scale=FALSE, lines=TRUE, linesSubset=1,
     linesArg=list(col="black", lwd=2))

plot(tmp, subset=1, col=c("gray"),
     plotArg=list(xlab="Group", ylab="Season"))

## Subset method
subset(x=tmp, data=connect, subset=1)
subset(x=tmpD, data=connect, subset=1)
subset(x=tmp, data=connect, subset=2)
subset(x=tmp, data=connect, subset=c(1, 2))
subset(x=tmp, data=connect)

## levelBySet method
levelsBySubset(x=tmp)
levelsBySubset(x=tmpD)
levelsBySubset(x=tmp, subset=1, factor="x")
levelsBySubset(x=tmp, subset=2, factor="xy")
levelsBySubset(x=tmp, subset=c(1, 2), factor="y")


[Package connectedness version 0.2.2 Index]