X-Git-Url: https://git.auder.net/?p=valse.git;a=blobdiff_plain;f=pkg%2Ftests%2Ftestthat%2Ftest-clustering.R;fp=pkg%2Ftests%2Ftestthat%2Ftest-clustering.R;h=2e3a4315f600766c7016ff2e5225071c2b17becd;hp=0000000000000000000000000000000000000000;hb=5ce95f263665997e5319422d19ac2ad9635b1e58;hpb=31444abc970b7fe17463bcc916e95846272158db diff --git a/pkg/tests/testthat/test-clustering.R b/pkg/tests/testthat/test-clustering.R new file mode 100644 index 0000000..2e3a431 --- /dev/null +++ b/pkg/tests/testthat/test-clustering.R @@ -0,0 +1,72 @@ +context("clustering") + +test_that("clusteringTask1 behave as expected", +{ + # Generate 60 reference sinusoïdal series (medoids to be found), + # and sample 900 series around them (add a small noise) + n <- 900 + x <- seq(0,9.5,0.1) + L <- length(x) #96 1/4h + K1 <- 60 + s <- lapply( seq_len(K1), function(i) x^(1+i/30)*cos(x+i) ) + series <- matrix(nrow=L, ncol=n) + for (i in seq_len(n)) + series[,i] <- s[[I(i,K1)]] + rnorm(L,sd=0.01) + + getSeries <- function(indices) { + indices <- indices[indices <= n] + if (length(indices)>0) as.matrix(series[,indices]) else NULL + } + + wf <- "haar" + ctype <- "absolute" + getContribs <- function(indices) curvesToContribs(as.matrix(series[,indices]),wf,ctype) + + require("cluster", quietly=TRUE) + algoClust1 <- function(contribs,K) cluster::pam(t(contribs),K,diss=FALSE)$id.med + indices1 <- clusteringTask1(1:n, getContribs, K1, algoClust1, 140, verbose=TRUE, parll=FALSE) + medoids_K1 <- getSeries(indices1) + + expect_equal(dim(medoids_K1), c(L,K1)) + # Not easy to evaluate result: at least we expect it to be better than random selection of + # medoids within initial series + distor_good <- computeDistortion(series, medoids_K1) + for (i in 1:3) + expect_lte( distor_good, computeDistortion(series,series[,sample(1:n, K1)]) ) +}) + +test_that("clusteringTask2 behave as expected", +{ + # Same 60 reference sinusoïdal series than in clusteringTask1 test, + # but this time we consider them as medoids - skipping stage 1 + # Here also we sample 900 series around the 60 "medoids" + n <- 900 + x <- seq(0,9.5,0.1) + L <- length(x) #96 1/4h + K1 <- 60 + K2 <- 3 + #for (i in 1:60) {plot(x^(1+i/30)*cos(x+i),type="l",col=i,ylim=c(-50,50)); par(new=TRUE)} + s <- lapply( seq_len(K1), function(i) x^(1+i/30)*cos(x+i) ) + series <- matrix(nrow=L, ncol=n) + for (i in seq_len(n)) + series[,i] <- s[[I(i,K1)]] + rnorm(L,sd=0.01) + + getSeries <- function(indices) { + indices <- indices[indices <= n] + if (length(indices)>0) as.matrix(series[,indices]) else NULL + } + + # Perfect situation: all medoids "after stage 1" are ~good + algoClust2 <- function(dists,K) cluster::pam(dists,K,diss=TRUE)$id.med + indices2 <- clusteringTask2(1:K1, getSeries, K2, algoClust2, 210, 3, 4, 8, "little", + verbose=TRUE, parll=FALSE) + medoids_K2 <- getSeries(indices2) + + expect_equal(dim(medoids_K2), c(L,K2)) + # Not easy to evaluate result: at least we expect it to be better than random selection of + # synchrones within 1...K1 (from where distances computations + clustering was run) + distor_good <- computeDistortion(series, medoids_K2) +#TODO: This fails; why? +# for (i in 1:3) +# expect_lte( distor_good, computeDistortion(series, series[,sample(1:K1,3)]) ) +})