search for: sil_width

...07 [206] 0.7848961 0.7943846 0.8437946 0.7817344 0.8867006 [211] 0.7575857 0.8390473 0.7382348 0.6789859 0.7129010 [216] 0.6938173 0.7384170 0.6747648 0.7203337 0.7278963 > silhouette(cl1, dist(x1)^2) ##### CRASHED! ###### >silhouette(ifelse(cl1==3,2,1), dist(x1)^2) cluster neighbor sil_width [1,] 2 1 1.0000000 [2,] 2 1 1.0000000 [3,] 2 1 1.0000000 [4,] 2 1 1.0000000 [5,] 2 1 1.0000000 [6,] 2 1 1.0000000 [7,] 2 1 1.0000000 [8,] 2 1 1.0000000 [9,] 2 1 1.0...

...l, I am trying (without much success) to use the fuction 'silhouette'. Would anyone encountered that before (or would know where I am wrong ?) Please find below the R ouput. Thanks in advance, L. > s <- silhouette(ct, as.dist(metric)) Error in "[<-"(*tmp*, iC, "sil_width", value = s.i) : number of items to replace is not a multiple of replacement length In addition: Warning messages: 1: longer object length is not a multiple of shorter object length in: b.i - a.i 2: number of rows of result is not a multiple of vector length (arg 2) in: cbind(mmm, as.vec...

hello, i'm pete ,how can i order rows of matrix by max to min value? I have a matrix of membership degrees, with 82 (i) rows and K coloumns, K are clusters. I need first and second largest elements of the i-th row. for example 1 0.66 0.04 0.01 0.30 2 0.02 0.89 0.09 0.00 3 0.06 0.92 0.01 0.01 4 0.07 0.71 0.21 0.01 5 0.10 0.85 0.04 0.01 6 0.91 0.04 0.02 0.02 7 0.00 0.01 0.98 0.00 8 0.02

...0.04 0.02 0.02 > H.Asort=head(t(A.sort)) > H.Asort[,1]-H.Asort[,2] 1 2 3 4 5 6 0.36 0.80 0.86 0.50 0.75 0.87 > H.Asort=t(H.Asort[,1]-H.Asort[,2]) This is the differences vector by multiplying trasformed table ris$silinfo. > ris$silinfo $widths cluster neighbor sil_width 72 1 3 0.43820207 54 1 3 0.43427773 29 1 6 0.41729079 62 1 6 0.40550562 64 1 6 0.32686757 32 1 3 0.30544722 45 1 3 0.30428723 79 1 3 0.30192624 12 1 3 0.30034472 60 1...

...y writing out sorted results to a file, then plotting from the file si3.sorted<-sortSilhouette(si3) write.table(si3.sorted,"/...myPath.../si3.sorted.txt",sep="\t") Inspecting the si3.sorted.txt file, cluster numbers are ordered as expected (1's then 2's then...), and sil_width's within each cluster appear correctly sorted (descending). Given this, if I load the file into say Mathematica, and plot it with colours, I easily generate a graphic that is like the one from R, but in which all cluster colours are as expected, i.e. there are no black bars in the yellow region...

...if (n != attr(dist, "Size")) stop("clustering `x' and dissimilarity `dist' are incompatible") dmatrix <- as.matrix(dist) } wds <- matrix(NA, n, 3, dimnames = list(names(x), c("cluster", "neighbor", "sil_width"))) for (j in 1:k) { Nj <- sum(iC <- x == clid[j]) # # the following line changed from wds[iC, "cluster"] <- j # wds[iC, "cluster"] <- clid[j] a.i <- if (Nj > 1) colSums(dmatrix[iC, iC])/(Nj - 1) else 0 # #...

...s from 58 to 60 and, finally, group 5 by units from 61 to 75. However, this seems to be in contrast with the output of silhouette where the fourth group is composed by units from 46 to 48 instead of units from 58 to 60 (belonging to the third cluster), see > si3 cluster neighbor sil_width [1,] 1 5 0.679838078 [2,] 1 5 0.745615002 [3,] 1 5 0.758796123 [4,] 1 4 0.715554768 [5,] 1 5 0.664657114 [6,] 1 4 0.783993831 [7,] 1 2 0.590057470 [8,] 1 4 0.747969458 [9,]...

...#largest si value I met the following problems: > for(k in 2:maxk) + { + hc<-diana(mdist,diss =TRUE, stand = FALSE) + si<-silhouette.default(cutree(as.hclust(hc),k=k),mdist) + myindex<-summary(si)$avg.width + } Error in "[<-"(*tmp*, iC, "sil_width", value = s.i) : number of items to replace is not a multiple of replacement length In addition: Warning messages: 1: longer object length is not a multiple of shorter object length in: b.i - a.i 2: number of rows of result is not a multiple of vector length (arg 2)...

...ectors are clustered. for example, after running pam you can see vector 3,6,9 ..., 8 are forms cluster 1 and rest of the data forms cluster 2. Now instead of just getting index 3,4,...9 etx how can I actually get this data in the same order as below Silhouette plot information: cluster neighbor sil_width 3 1 2 0.8845423 6 1 2 0.8828709 9 1 2 0.8778533 1 1 2 0.8697712 10 1 2 0.8641114 2 1 2 0.8530604 5 1 2 0.8109133 7 1 2 0.8107987 4 1 2 0.8064146 8 1 2 0.7863462...