consensus {agricolae} | R Documentation |
consensus of clusters
Description
The criterion of the consensus is to produce many trees by means of boostrap and to such calculate the relative frequency with members of the clusters.
Usage
consensus(data,distance=c("binary","euclidean","maximum","manhattan",
"canberra", "minkowski", "gower","chisq"),method=c("complete","ward","single","average",
"mcquitty","median", "centroid"),nboot=500,duplicate=TRUE,cex.text=1,
col.text="red", ...)
Arguments
data |
data frame |
distance |
method distance, see dist() |
method |
method cluster, see hclust() |
nboot |
The number of bootstrap samples desired. |
duplicate |
control is TRUE other case is FALSE |
cex.text |
size text on percentage consensus |
col.text |
color text on percentage consensus |
... |
parameters of the plot dendrogram |
Details
distance: "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski", "gower", "chisq". Method: "ward", "single", "complete", "average", "mcquitty", "median", "centroid". see functions: dist(), hclust() and daisy() of cluster.
Value
table.dend |
The groups and consensus percentage |
dendrogram |
The class object is hclust, dendrogram plot |
duplicate |
Homonymous elements |
Author(s)
F. de Mendiburu
References
An Introduction to the Boostrap. Bradley Efron and Robert J. Tibshirani. 1993. Chapman and Hall/CRC
See Also
Examples
library(agricolae)
data(pamCIP)
# only code
rownames(pamCIP)<-substr(rownames(pamCIP),1,6)
output<-consensus( pamCIP,distance="binary", method="complete",nboot=5)
# Order consensus
Groups<-output$table.dend[,c(6,5)]
Groups<-Groups[order(Groups[,2],decreasing=TRUE),]
print(Groups)
## Identification of the codes with the numbers.
cbind(output$dendrogram$labels)
## To reproduce dendrogram
dend<-output$dendrogram
data<-output$table.dend
plot(dend)
text(data[,3],data[,4],data[,5])
# Other examples
# classical dendrogram
dend<-as.dendrogram(output$dendrogram)
plot(dend,type="r",edgePar = list(lty=1:2, col=2:1))
text(data[,3],data[,4],data[,5],col="blue",cex=1)
plot(dend,type="t",edgePar = list(lty=1:2, col=2:1))
text(data[,3],data[,4],data[,5],col="blue",cex=1)
## Without the control of duplicates
output<-consensus( pamCIP,duplicate=FALSE,nboot=5)
## using distance gower, require cluster package.
# output<-consensus( pamCIP,distance="gower", method="complete",nboot=5)