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(root)/trunk/cluster/tests/pam.R – Rev 7920
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library(cluster)## Compare on these:nms <- c("clustering", "objective", "isolation", "clusinfo", "silinfo")nm2 <- c("medoids", "id.med", nms)nm3 <- nm2[- pmatch("obj", nm2)](x <- x0 <- cbind(V1 = (-3:4)^2, V2 = c(0:6,NA), V3 = c(1,2,NA,7,NA,8:9,8)))(px <- pam(x,2, metric="manhattan"))stopifnot(identical(x,x0))# DUP=FALSE ..pd <- pam(dist(x,"manhattan"), 2)px2 <- pam(x,2, metric="manhattan", keep.diss=FALSE, keep.data=FALSE)pdC <- pam(x,2, metric="manhattan", cluster.only = TRUE)p1 <- pam(x,1, metric="manhattan")stopifnot(identical(px[nms], pd[nms]),identical(px[nms], px2[nms]),identical(pdC, px2$clustering),## and for default dist "euclidean":identical(pam(x, 2)[nms],pam(dist(x),2)[nms]),identical(p1[c("id.med", "objective", "clusinfo")],list(id.med = 6L, objective = c(build=9.25, swap=9.25),clusinfo = array(c(8, 18, 9.25, 45, 0), dim = c(1, 5),dimnames=list(NULL, c("size", "max_diss", "av_diss","diameter", "separation"))))),p1$clustering == 1, is.null(p1$silinfo))set.seed(253)## generate 250 objects, divided into 2 clusters.x <- rbind(cbind(rnorm(120, 0,8), rnorm(120, 0,8)),cbind(rnorm(130,50,8), rnorm(130,10,8))).proctime00 <- proc.time()summary(px2 <- pam(x, 2))pdx <- pam(dist(x), 2)all.equal(px2[nms], pdx[nms], tol = 1e-12) ## TRUEpdxK <- pam(dist(x), 2, keep.diss = TRUE)stopifnot(identical(pdx[nm2], pdxK[nm2]))spdx <- silhouette(pdx)summary(spdx)spdxpostscript("pam-tst.ps")if(FALSE)plot(spdx)# the silhouette## is now identical :plot(pdx)# failed in 1.7.0 -- now only does silhouettepar(mfrow = 2:1)## new 'dist' argument for clusplot():plot(pdx, dist=dist(x))## but this should work automagically (via eval()) as well:plot(pdx)## or thisclusplot(pdx)data(ruspini)summary(pr4 <- pam(ruspini, 4))(pr3 <- pam(ruspini, 3))(pr5 <- pam(ruspini, 5))data(votes.repub)summary(pv3 <- pam(votes.repub, 3))(pv4 <- pam(votes.repub, 4))(pv6 <- pam(votes.repub, 6, trace = 3))cat('Time elapsed: ', proc.time() - .proctime00,'\n')## re-starting with medoids from pv6 shouldn't change:pv6. <- pam(votes.repub, 6, medoids = pv6$id.med, trace = 3)identical(pv6[nm3], pv6.[nm3])## This example seg.faulted at some point:d.st <- data.frame(V1= c(9, 12, 12, 15, 9, 9, 13, 11, 15, 10, 13, 13,13, 15, 8, 13, 13, 10, 7, 9, 6, 11, 3),V2= c(5, 9, 3, 5, 1, 1, 2, NA, 10, 1, 4, 7,4, NA, NA, 5, 2, 4, 3, 3, 6, 1, 1),V3 = c(63, 41, 59, 50, 290, 226, 60, 36, 32, 121, 70, 51,79, 32, 42, 39, 76, 60, 56, 88, 57, 309, 254),V4 = c(146, 43, 78, 88, 314, 149, 78, NA, 238, 153, 159, 222,203, NA, NA, 74, 100, 111, 9, 180, 50, 256, 107))dd <- daisy(d.st, stand = TRUE)(r0 <- pam(dd, 5))# cluster 5 = { 23 } -- on single observation## pam doing the "daisy" computation internally:r0s <- pam(d.st, 5, stand=TRUE, keep.diss=FALSE, keep.data=FALSE)(ii <- which(names(r0) %in% c("call","medoids")))stopifnot(all.equal(r0[-ii], r0s[-ii], tol=1e-14),identical(r0s$medoids, data.matrix(d.st)[r0$medoids, ]))## This gave only 3 different medoids -> and seg.fault:(r5 <- pam(dd, 5, medoids = c(1,3,20,2,5), trace = 2)) # now "fine"dev.off()##------------------------ Testing pam() with new "pamonce" argument:## This is from "next version of Matrix" test-tools-1.R:showSys.time <- function(expr) {## prepend 'Time' for R CMD Rdiffst <- system.time(expr)writeLines(paste("Time", capture.output(print(st))))invisible(st)}show6Ratios <- function(...) {stopifnot(length(rgs <- list(...)) == 6,nchar(ns <- names(rgs)) > 0)r <- round(cbind(..1, ..2, ..3, ..4, ..5, ..6)[c(1,5),], 5)dimnames(r) <- list(paste("Time ", rownames(r)), ns)r}n <- 1000## If not enough cases, all CPU times equals 0.n <- 500 # for now, and automatic testingsd <- 0.5set.seed(13)n2 <- as.integer(round(n * 1.5))x <- rbind(cbind(rnorm( n,0,sd), rnorm( n,0,sd)),cbind(rnorm(n2,5,sd), rnorm(n2,5,sd)),cbind(rnorm(n2,7,sd), rnorm(n2,7,sd)),cbind(rnorm(n2,9,sd), rnorm(n2,9,sd)))## original algorithmst0 <- showSys.time(pamx <- pam(x, 4, trace.lev=2))# 8.157 0.024 8.233## bswapPamOnce algorithmst1 <- showSys.time(pamxonce <- pam(x, 4, pamonce=TRUE, trace.lev=2))# 6.122 0.024 6.181## bswapPamOnceDistIndicest2 <- showSys.time(pamxonce2 <- pam(x, 4, pamonce = 2, trace.lev=2))# 4.101 0.024 4.151## bswapPamSchubert FastPAM1st3 <- showSys.time(pamxonce3 <- pam(x, 4, pamonce = 3, trace.lev=2))### bswapPamSchubert FastPAM2st4 <- showSys.time(pamxonce4 <- pam(x, 4, pamonce = 4, trace.lev=2))### bswapPamSchubert FastPAM2 with linearized memory accessst5 <- showSys.time(pamxonce5 <- pam(x, 4, pamonce = 5, trace.lev=2))### bswapPamSchubert FasterPAMst6 <- showSys.time(pamxonce6 <- pam(x, 4, pamonce = 6, trace.lev=2))#show6Ratios('6:orig' = st6/st0, '5:orig' = st5/st0, '4:orig' = st4/st0, '3:orig' = st3/st0, '2:orig' = st2/st0, '1:orig' = st1/st0)## only call element is not equal(icall <- which(names(pamx) == "call"))pamx[[icall]]stopifnot(all.equal(pamx [-icall], pamxonce [-icall]),all.equal(pamxonce[-icall], pamxonce2[-icall]),all.equal(pamxonce[-icall], pamxonce3[-icall]),all.equal(pamxonce[-icall], pamxonce4[-icall]),all.equal(pamxonce[-icall], pamxonce5[-icall]),all.equal(pamxonce[-icall], pamxonce6[-icall]))## Same using specified medoids(med0 <- 1 + round(n* c(0,1, 2.5, 4)))# lynne (~ 2010, AMD Phenom II X4 925)st0 <- showSys.time(pamxst <- pam(x, 4, medoids = med0, trace.lev=2))# 13.071 0.024 13.177st1 <- showSys.time(pamxoncest <- pam(x, 4, medoids = med0, pamonce=TRUE, trace.lev=2))# 8.503 0.024 8.578st2 <- showSys.time(pamxonce2st <- pam(x, 4, medoids = med0, pamonce=2, trace.lev=2))# 5.587 0.025 5.647st3 <- showSys.time(pamxonce3st <- pam(x, 4, medoids = med0, pamonce=3, trace.lev=2))#st4 <- showSys.time(pamxonce4st <- pam(x, 4, medoids = med0, pamonce=4, trace.lev=2))#st5 <- showSys.time(pamxonce5st <- pam(x, 4, medoids = med0, pamonce=5, trace.lev=2))#st6 <- showSys.time(pamxonce6st <- pam(x, 4, medoids = med0, pamonce=6, trace.lev=2))#show6Ratios('6:orig' = st6/st0, '5:orig' = st5/st0, '4:orig' = st4/st0, '3:orig' = st3/st0, '2:orig' = st2/st0, '1:orig' = st1/st0)## only call element is not equalstopifnot(all.equal(pamxst [-icall], pamxoncest [-icall]),all.equal(pamxoncest[-icall], pamxonce2st[-icall]),all.equal(pamxoncest[-icall], pamxonce3st[-icall]),all.equal(pamxoncest[-icall], pamxonce4st[-icall]),all.equal(pamxoncest[-icall], pamxonce5st[-icall]),all.equal(pamxoncest[-icall], pamxonce6st[-icall]))## Different starting valuesmed0 <- 1:4 # lynne (~ 2010, AMD Phenom II X4 925)st0 <- showSys.time(pamxst <- pam(x, 4, medoids = med0, trace.lev=2))# 13.416 0.023 13.529st1 <- showSys.time(pamxoncest <- pam(x, 4, medoids = med0, pamonce=TRUE, trace.lev=2))# 8.384 0.024 8.459st2 <- showSys.time(pamxonce2st <- pam(x, 4, medoids = med0, pamonce=2, trace.lev=2))# 5.455 0.030 5.520st3 <- showSys.time(pamxonce3st <- pam(x, 4, medoids = med0, pamonce=3, trace.lev=2))#st4 <- showSys.time(pamxonce4st <- pam(x, 4, medoids = med0, pamonce=4, trace.lev=2))#st5 <- showSys.time(pamxonce5st <- pam(x, 4, medoids = med0, pamonce=5, trace.lev=2))#st6 <- showSys.time(pamxonce6st <- pam(x, 4, medoids = med0, pamonce=6, trace.lev=2))#show6Ratios('6:orig' = st6/st0, '5:orig' = st5/st0, '4:orig' = st4/st0, '3:orig' = st3/st0, '2:orig' = st2/st0, '1:orig' = st1/st0)## only call element is not equalstopifnot(all.equal(pamxst [-icall], pamxoncest [-icall]),all.equal(pamxoncest[-icall], pamxonce2st[-icall]),all.equal(pamxoncest[-icall], pamxonce3st[-icall]),all.equal(pamxoncest[-icall], pamxonce4st[-icall]),all.equal(pamxoncest[-icall], pamxonce5st[-icall]),all.equal(pamxoncest[-icall], pamxonce6st[-icall]))## Medoid bug --- MM: Fixed, well "0L+ hack", in my pam.q, on 2012-01-31## ----------med0 <- (1:6)st0 <- showSys.time(pamxst <- pam(x, 6, medoids = med0 , trace.lev=2))stopifnot(identical(med0, 1:6))med0 <- (1:6)st1 <- showSys.time(pamxst.1 <- pam(x, 6, medoids = med0 , pamonce=1, trace.lev=2))stopifnot(identical(med0, 1:6))med0 <- (1:6)st2 <- showSys.time(pamxst.2 <- pam(x, 6, medoids = med0 , pamonce=2, trace.lev=2))stopifnot(identical(med0, 1:6))med0 <- (1:6)st3 <- showSys.time(pamxst.3 <- pam(x, 6, medoids = med0 , pamonce=3, trace.lev=2))stopifnot(identical(med0, 1:6))med0 <- (1:6)st4 <- showSys.time(pamxst.4 <- pam(x, 6, medoids = med0 , pamonce=4, trace.lev=2))stopifnot(identical(med0, 1:6))med0 <- (1:6)st5 <- showSys.time(pamxst.5 <- pam(x, 6, medoids = med0 , pamonce=5, trace.lev=2))stopifnot(identical(med0, 1:6))med0 <- (1:6)st6 <- showSys.time(pamxst.6 <- pam(x, 6, medoids = med0 , pamonce=6, trace.lev=2))stopifnot(identical(med0, 1:6))stopifnot(all.equal(pamxst[-icall], pamxst.1 [-icall]),all.equal(pamxst[-icall], pamxst.2 [-icall]),all.equal(pamxst[-icall], pamxst.3 [-icall]),all.equal(pamxst[-icall], pamxst.4 [-icall]),all.equal(pamxst[-icall], pamxst.5 [-icall]))# FasterPAM finds a better solution here, by chancestopifnot(pamxst$objective >= pamxst.6$objective)## Last Line:cat('Time elapsed: ', proc.time() - .proctime00,'\n')