R Under development (unstable) (2024-10-21 r87258 ucrt) -- "Unsuffered Consequences"
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> library("Mercator")
Loading required package: Thresher
Loading required package: ClassDiscovery
Loading required package: cluster
Loading required package: oompaBase
Loading required package: PCDimension
> data("CML500")
> temp <- removeDuplicateFeatures(CML500)
> ### need a plain old binary matrix
> working <- temp@binmat
> dim(working)
[1] 770 470
> N <- dim(working)[2]
> 
> jacc <- binaryDistance(working, "jaccard")
> all(dim(as.matrix(jacc)) == c(N, N))
[1] TRUE
> plot(hclust(jacc, "ward.D2"))
> 
> canb <- binaryDistance(working, "canberra")
> all(dim(as.matrix(canb)) == c(N, N))
[1] TRUE
> plot(hclust(canb, "ward.D2"))
> 
> X <- binaryDistance(working, "sokal")
> all(dim(as.matrix(X)) == c(N, N))
[1] TRUE
> plot(hclust(X, "ward.D2"))
> 
> X <- binaryDistance(working, "hamming")
> all(dim(as.matrix(X)) == c(N, N))
[1] TRUE
> plot(hclust(X, "ward.D2"))
> 
> X <- binaryDistance(working, "russell")
> all(dim(as.matrix(X)) == c(N, N))
[1] TRUE
> plot(hclust(X, "ward.D2"))
> 
> X <- binaryDistance(working, "goodman")
> all(dim(as.matrix(X)) == c(N, N))
[1] TRUE
> plot(hclust(X, "ward.D2"))
> 
> X <- binaryDistance(working, "manhattan")
> all(dim(as.matrix(X)) == c(N, N))
[1] TRUE
> plot(hclust(X, "ward.D2"))
> 
> X <- binaryDistance(working, "binary")
> all(dim(as.matrix(X)) == c(N, N))
[1] TRUE
> plot(hclust(X, "ward.D2"))
> 
> X <- binaryDistance(working, "euclid")
> all(dim(as.matrix(X)) == c(N, N))
[1] TRUE
> plot(hclust(X, "ward.D2"))
> 
> 
> proc.time()
   user  system elapsed 
   5.56    0.32    5.87