## IGNORE_RDIFF_BEGIN .libPaths() # show full library tree {also as check of R CMD check!} ## IGNORE_RDIFF_END library(cluster) ####---------- Tests for FANNY i.e., fanny() -------------------------- #### ### -- thanks to ../.Rbuildignore , the output of this is ### -- only compared to saved values for the maintainer ###--- An extension of example(fanny) : ------------------- set.seed(21) ## generate 10+15 objects in two clusters, plus 3 objects lying ## between those clusters. x <- rbind(cbind(rnorm(10, 0, 0.5), rnorm(10, 0, 0.5)), cbind(rnorm(15, 5, 0.5), rnorm(15, 5, 0.5)), cbind(rnorm( 3,3.2,0.5), rnorm( 3,3.2,0.5))) .proctime00 <- proc.time() (fannyx <- fanny(x, 2)) summary(fannyx) str(fannyx) ## Different platforms differ (even gcc 3.0.1 vs 3.2 on same platform)! ## {70 or 71 iterations} ## ==> No "fanny-ex.Rout.save" is distributed ! ## -------------------------------------------- summary(fanny(x,3))# one extra cluster (fanny(x,2, memb.exp = 1.5)) (fanny(x,2, memb.exp = 1.2)) (fanny(x,2, memb.exp = 1.1)) (fanny(x,2, memb.exp = 3)) ## for subsetting, when compairing: not.conv <- setdiff(names(fannyx), c("convergence", "call")) notMconv <- setdiff(names(fannyx), c("membership", "convergence", "call")) data(ruspini) # < to run under R 1.9.1 summary(fanny(ruspini, 3), digits = 9) summary(fanny(ruspini, 4), digits = 9)# 'correct' #{clusters} summary(fanny(ruspini, 5), digits = 9) cat('Time elapsed: ', proc.time() - .proctime00,'\n') data(chorSub) p4cl <- pam(chorSub, k = 4, cluster.only = TRUE) ## The first two are "completely fuzzy" -- and now give a warnings f4.20 <- fanny(chorSub, k = 4, trace.lev = 1) ## IGNORE_RDIFF_BEGIN f4.20$coef ## IGNORE_RDIFF_END stopifnot(all.equal(f4.20$coef, c(dunn_coeff = 0.25, normalized = 3.330669e-15))) f4.18 <- fanny(chorSub, k = 4, memb.exp = 1.8) # same problem f4.18. <- fanny(chorSub, k = 4, memb.exp = 1.8, iniMem.p = f4.20$membership) # very quick convergence stopifnot(all.equal(f4.18[not.conv], f4.18.[not.conv], tol = 5e-7)) f4.16 <- fanny(chorSub, k = 4, memb.exp = 1.6) # now gives 4 crisp clusters ## IGNORE_RDIFF_BEGIN f4.16. <- fanny(chorSub, k = 4, memb.exp = 1.6, iniMem.p = f4.18$membership, trace.lev = 2)# wrongly "converged" immediately; no longer! f4.16.2<- fanny(chorSub, k = 4, memb.exp = 1.6, iniMem.p = cluster:::as.membership(p4cl), tol = 1e-10, trace.lev = 2) all.equal((m1 <- f4.16 $membership), (m2 <- f4.16.2$membership)) ## IGNORE_RDIFF_END stopifnot(identical(dimnames(m1), dimnames(m2)), 0 < m1,m1 < 1, 0 < m2,m2 < 1, ## the memberships are quite close but have only converged to precision 0.000228 all.equal(m1, m2, tol = 0.001)) stopifnot(exprs = { f4.16$clustering == f4.16.2$clustering all.equal(f4.16[notMconv], f4.16.2[notMconv], tol = 1e-7) }) f4.14 <- fanny(chorSub, k = 4, memb.exp = 1.4) f4.12 <- fanny(chorSub, k = 4, memb.exp = 1.2) table(f4.12$clustering, f4.14$clustering)# close but different table(f4.16$clustering, f4.14$clustering)# ditto table(f4.12$clustering, f4.16$clustering)# hence differ even more symnum(cbind(f4.16$membership, 1, f4.12$membership), cutpoints= c(0., 0.2, 0.6, 0.8, 0.9, 0.95, 1 -1e-7, 1 +1e-7), symbols = c(" ", ".", ",", "+", "*", "B","1")) ## Last Line: cat('Time elapsed: ', proc.time() - .proctime00,'\n')