X-Git-Url: https://git.auder.net/images/pieces/%22%20%20%20VariantRules.getPpath%28board%5Bi%5D%5Bj%5D%29%20%20%20%22.svg?a=blobdiff_plain;f=pkg%2Ftests%2Ftestthat%2Ftest.computeFilaments.R;h=e8f87521e13d14dcb3108e6197b99dfe8a040dd2;hb=6d97bfecf7310ed6682eecce1b7aa2f8185d4742;hp=9de6274a3162840a9b8ffa444b8c47c07dcb2de8;hpb=1e20780ee1505fac6c7ed68d340892c497524561;p=talweg.git diff --git a/pkg/tests/testthat/test.computeFilaments.R b/pkg/tests/testthat/test.computeFilaments.R index 9de6274..e8f8752 100644 --- a/pkg/tests/testthat/test.computeFilaments.R +++ b/pkg/tests/testthat/test.computeFilaments.R @@ -1,36 +1,103 @@ -#TODO: toy dataset, check that indices returned are correct + colors +context("Check that computeFilaments behaves as expected") -context("Check that getParamsDirs behaves as expected") +getDataTest = function(n, shift) +{ + x = seq(0,10,0.1) + L = length(x) + s1 = cos(x) + s2 = sin(x) + s3 = c( s1[1:(L%/%2)] , s2[(L%/%2+1):L] ) + #sum((s1-s2)^2) == 97.59381 + #sum((s1-s3)^2) == 57.03051 + #sum((s2-s3)^2) == 40.5633 + s = list( s1, s2, s3 ) + series = list() + for (i in seq_len(n)) + { + index = (i%%3) + 1 + level = mean(s[[index]]) + serie = s[[index]] - level + rnorm(L,sd=0.05) + # 10 series with NAs for index 2 + if (index == 2 && i >= 60 && i<= 90) + serie[sample(seq_len(L),1)] = NA + series[[i]] = list("level"=level,"serie"=serie) #no need for more + } + if (shift) + { + # Simulate shift at origin when predict_at > 0 + series[2:(n+1)] = series[1:n] + series[[1]] = list("level"=0, "serie"=s[[1]][1:(L%/%2)]) + } + new("Data", data=series) +} -test_that("on input of sufficient size, beta is estimated accurately enough", { - n = 100000 - d = 2 - K = 2 - Pr = c(0.5, 0.5) +test_that("output is as expected on simulated series", +{ + data = getDataTest(150, FALSE) - betas_ref = array( c(1,0,0,1 , 1,-2,3,1), dim=c(2,2,2) ) - for (i in 1:(dim(betas_ref)[3])) + # index 142 : serie type 2 + f = computeFilaments(data, 142, limit=60, plot=FALSE) + # Expected output: 22 series of type 3 (closer), then 50-2-10 series of type 2 + expect_identical(length(f$indices), 60) + expect_identical(length(f$colors), 60) + for (i in 1:22) { - beta_ref = betas_ref[,,i] - #all parameters are supposed to be of norm 1: thus, normalize beta_ref - norm2 = sqrt(colSums(beta_ref^2)) - beta_ref = beta_ref / norm2[col(beta_ref)] + expect_identical((f$indices[i] %% 3) + 1, 3) + expect_match(f2$colors[i], f$colors[1]) + } + for (i in 23:60) + { + expect_identical((f$indices[i] %% 3) + 1, 2) + expect_match(f2$colors[i], f$colors[23]) + } + expect_match(colors[1], "...") + expect_match(colors[23], "...") +}) - io = generateSampleIO(n, d, K, Pr, beta_ref) - beta = getParamsDirs(io$X, io$Y, K) - betas = .labelSwitchingAlign( - array( c(beta_ref,beta), dim=c(d,K,2) ), compare_to="first", ls_mode="exact") +test_that("output is as expected on simulated series", +{ + data = getDataTest(150, TRUE) - #Some traces: 0 is not well estimated, but others are OK - cat("\n\nReference parameter matrix:\n") - print(beta_ref) - cat("Estimated parameter matrix:\n") - print(betas[,,2]) - cat("Difference norm (Matrix norm ||.||_1, max. abs. sum on a column)\n") - diff_norm = norm(beta_ref - betas[,,2]) - cat(diff_norm,"\n") + # index 143 : serie type 3 + f = computeFilaments(data, 143, limit=70, plot=FALSE) + # Expected output: 22 series of type 2 (closer) then 50-2 series of type 3 + expect_identical(length(f$indices), 70) + expect_identical(length(f$colors), 70) + for (i in 1:22) + { + # -1 because of the initial shift + expect_identical(( (f$indices[i]-1) %% 3 ) + 1, 2) + expect_match(f$colors[i], f$colors[1]) + } + for (i in 23:70) + { + expect_identical(( (f$indices[i]-1) %% 3 ) + 1, 3) + expect_match(f$colors[i], f$colors[23]) + } + expect_match(colors[1], "...") + expect_match(colors[23], "...") +}) - #NOTE: 0.5 is loose threshold, but values around 0.3 are expected... - expect_that( diff_norm, is_less_than(0.5) ) +test_that("output is as expected on simulated series", +{ + data = getDataTest(150, TRUE) + + # index 144 : serie type 1 + f = computeFilaments(data, 144, limit=50, plot=FALSE) + # Expected output: 2 series of type 3 (closer), then 50-2 series of type 1 + expect_identical(length(f$indices), 50) + expect_identical(length(f$colors), 50) + for (i in 1:2) + { + # -1 because of the initial shift + expect_identical(( (f$indices[i]-1) %% 3 ) + 1, 3) + expect_match(f$colors[i], f$colors[1]) + } + for (i in 3:50) + { + expect_identical(( (f$indices[i]-1) %% 3 ) + 1, 1) + expect_match(f$colors[i], f$colors[3]) } + expect_match(colors[1], "...") + expect_match(colors[3], "...") })