# test_that("permutation_test detects incorrect parameters correctly",{ # # skip_if_not_installed("TDA") # skip_if_not_installed("TDAstats") # circle = TDA::ripsDiag(X = TDA::circleUnif(n = 20,r = 1),maxdimension = 2,maxscale = 2) # sphere = TDA::ripsDiag(X = TDA::sphereUnif(n = 20,d = 2,r = 1),maxdimension = 2,maxscale = 2) # expect_error(permutation_test(list(circle,2,circle),list(sphere,sphere,sphere),iterations = 5,p = 2,q = 2,dims = c(0,1),paired = F,distance = "wasserstein",sigma = NULL,verbose = F,num_workers = 2),"Diagrams must") # expect_error(permutation_test(list(circle,circle,circle),list(sphere,"2",sphere),iterations = 5,p = 2,q = 2,dims = c(0,1),paired = F,distance = "wasserstein",sigma = NULL,verbose = F,num_workers = 2),"Diagrams must") # expect_error(permutation_test(list(circle,circle,circle),list(sphere,sphere,sphere),iterations = NA,p = 2,q = 2,dims = c(0,1),paired = F,distance = "wasserstein",sigma = NULL,verbose = F,num_workers = 2),"NA") # expect_error(permutation_test(list(circle,circle,circle),list(sphere,sphere,sphere),iterations = 5,p = NULL,q = 2,dims = c(0,1),paired = F,distance = "wasserstein",sigma = NULL,verbose = F,num_workers = 2),"NULL") # expect_error(permutation_test(list(circle,circle,circle),list(sphere,sphere,sphere),iterations = 5,p = 2,q = NA,dims = c(0,1),paired = F,distance = "wasserstein",sigma = NULL,verbose = F,num_workers = 2),"NA") # expect_error(permutation_test(list(circle,circle,circle),list(sphere,sphere,sphere),iterations = 5,p = 2,q = 2,dims = c(-1,1),paired = F,distance = "wasserstein",sigma = NULL,verbose = F,num_workers = 2),"non-negative") # expect_error(permutation_test(list(circle,circle),list(sphere,sphere,sphere),iterations = 5,p = 2,q = 2,dims = c(0,1),paired = T,distance = "wasserstein",sigma = NULL,verbose = F,num_workers = 2),"same number") # expect_error(permutation_test(list(circle,circle,circle),list(sphere,sphere,sphere),iterations = 5,p = 2,q = 2,dims = c(0,1),paired = F,distance = "Wasserstein",sigma = NULL,verbose = F,num_workers = 2),"wasserstein") # expect_error(permutation_test(list(circle,circle,circle),list(sphere,sphere,sphere),iterations = 5,p = 2,q = 2,dims = c(0,1),paired = F,distance = "fisher",sigma = NULL,verbose = F,num_workers = 2),"sigma") # expect_error(permutation_test(list(circle,circle,circle),list(sphere,sphere),iterations = 5,p = 2,q = 2,dims = c(0,1),paired = T,distance = "fisher",sigma = 1,verbose = F,num_workers = 2),"paired") # expect_error(permutation_test(list(circle,circle,circle),list(sphere,sphere),num_workers = NA),"num_workers") # expect_error(permutation_test(list(circle,circle,circle),list(sphere,sphere),num_workers = NULL),"num_workers") # expect_error(permutation_test(list(circle,circle,circle),list(sphere),num_workers = 2),"2") # expect_error(permutation_test(list(circle,circle,circle),list(sphere,sphere),num_workers = 2,dims = c(1),distance = "fisher",sigma = 1,rho = NaN),"rho") # # }) # test_that("permutation_test can accept inputs from TDA, TDAstats and diagram_to_df",{ # # skip_if_not_installed("TDA") # skip_if_not_installed("TDAstats") # circle = TDA::ripsDiag(X = TDA::circleUnif(n = 20,r = 1),maxdimension = 1,maxscale = 2) # sphere = TDAstats::calculate_homology(TDA::sphereUnif(n = 20,d = 2,r = 1),threshold = 2) # expect_length(permutation_test(list(circle,circle,diagram_to_df(circle)),list(sphere,sphere,sphere),iterations = 1,dims = c(1),num_workers = 2)$permvals[[1]],1) # # }) # test_that("permutation_test can accept precomputed distance matrices",{ # # skip_if_not_installed("TDA") # skip_if_not_installed("TDAstats") # # circle = TDA::ripsDiag(X = TDA::circleUnif(n = 20,r = 1),maxdimension = 1,maxscale = 2) # sphere = TDAstats::calculate_homology(TDA::sphereUnif(n = 20,d = 2,r = 1),threshold = 2) # D0 = distance_matrix(diagrams = list(circle,sphere),dim = 0,num_workers = 2) # D1 = distance_matrix(diagrams = list(circle,sphere),dim = 1,num_workers = 2) # D2 = distance_matrix(diagrams = list(circle,sphere,circle,sphere),dim = 0,num_workers = 2) # D3 = distance_matrix(diagrams = list(circle,sphere,circle,sphere),dim = 1,num_workers = 2) # expect_error(permutation_test(dist_mats = list(D0,D1),iterations = 1,dims = c(1),num_workers = 2,group_sizes = NULL),"group_sizes") # expect_error(permutation_test(dist_mats = list(D0,D1),iterations = 1,dims = c(1),num_workers = 2,group_sizes = c(1,1)),"dims") # expect_error(permutation_test(dist_mats = list(D0,D1),iterations = 1,dims = c(0,1),num_workers = 2,group_sizes = c(1,2)),"sum") # expect_error(permutation_test(dist_mats = NULL,iterations = 1,dims = c(1),num_workers = 2,group_sizes = c(1,1)),"list") # expect_error(permutation_test(dist_mats = list(D0,matrix(data = c(0),nrow = 1)),iterations = 1,dims = c(0,1),num_workers = 2,group_sizes = c(1,1)),"size") # expect_error(permutation_test(dist_mats = list(D2,D3),iterations = 1,dims = c(0,1),paired = T,num_workers = 2,group_sizes = c(3,1)),"paired") # # D0 = distance_matrix(diagrams = list(circle,circle,sphere,sphere),dim = 0,num_workers = 2) # D1 = distance_matrix(diagrams = list(circle,circle,sphere,sphere),dim = 1,num_workers = 2) # expect_length(permutation_test(dist_mats = list(D0,D1),group_sizes = c(2,2),iterations = 1,dims = c(0,1),paired = T,num_workers = 2)$test_statistics,2) # expect_length(permutation_test(dist_mats = list(D0,D1),group_sizes = c(2,2),iterations = 3,dims = c(0,1),paired = T,num_workers = 2)$permvals[[1]],3) # expect_length(permutation_test(dist_mats = list(D0,D1),group_sizes = c(2,2),iterations = 1,dims = c(0,1),paired = F,num_workers = 2)$test_statistics,2) # expect_length(permutation_test(dist_mats = list(D0,D1),group_sizes = c(2,2),iterations = 3,dims = c(0,1),paired = F,num_workers = 2)$permvals[[1]],3) # # circle2 <- TDA::ripsDiag(X = TDA::circleUnif(n = 50,r = 1),maxdimension = 2,maxscale = 2,library = "dionysus",location = T) # sphere2 <- TDA::ripsDiag(X = TDA::sphereUnif(n = 50,d = 2,r = 1),maxdimension = 2,maxscale = 2,library = "dionysus",location = T) # d <- diagram_distance(circle2,sphere2,dim = 1) # wasserstein distance in dimension 1 # D1 <- distance_matrix(diagrams = list(circle2,circle2,circle2,circle2,circle2,sphere2),dim = 1,num_workers = 2) # D2 <- distance_matrix(diagrams = list(circle2,circle2,circle2,sphere2,sphere2,sphere2),dim = 2,num_workers = 2) # expect_length(permutation_test(dist_mats = list(D1),iterations = 1,dims = c(1),num_workers = 2,group_sizes = c(3,3))$permvals[[1]],1) # expect_length(permutation_test(dist_mats = list(D2),iterations = 1,dims = c(2),num_workers = 2,group_sizes = c(3,3))$permvals[[1]],1) # expect_length(permutation_test(dist_mats = list(D1,D2),iterations = 1,dims = c(1,2),num_workers = 2,group_sizes = c(3,3))$permvals,2) # expect_lte(abs(permutation_test(dist_mats = list(D1),iterations = 1,dims = c(1),num_workers = 2,group_sizes = c(3,3))$test_statistics[[1]]-d^2/3),0.003) # expect_equal(permutation_test(dist_mats = list(D2),iterations = 1,dims = c(2),num_workers = 2,group_sizes = c(3,3))$test_statistics[[1]],0) # # expect_lte(abs(permutation_test(dist_mats = list(D1),iterations = 1,dims = c(1),num_workers = 2,group_sizes = c(3,3))$permvals[[1]][[1]]-d^2/3),0.003) # v <- permutation_test(dist_mats = list(distance_matrix(diagrams = list(sphere2,sphere2,circle2,circle2,circle2,sphere2),dim = 1,num_workers = 2)),iterations = 1,dims = c(1),num_workers = 2,group_sizes = c(3,3))$permvals[[1]][[1]] # expect_lte(abs(v - 2*d^2/3)*v,0.002) # # }) # test_that("permutation_test is working",{ # # skip_if_not_installed("TDA") # skip_if_not_installed("TDAstats") # # circle <- TDA::ripsDiag(X = TDA::circleUnif(n = 50,r = 1),maxdimension = 2,maxscale = 2) # sphere <- TDA::ripsDiag(X = TDA::sphereUnif(n = 50,d = 2,r = 1),maxdimension = 2,maxscale = 2) # circle2 <- TDA::ripsDiag(X = TDA::circleUnif(n = 50,r = 1),maxdimension = 2,maxscale = 2,library = "dionysus",location = T) # sphere2 <- TDA::ripsDiag(X = TDA::sphereUnif(n = 50,d = 2,r = 1),maxdimension = 2,maxscale = 2,library = "dionysus",location = T) # d <- diagram_distance(circle,sphere,dim = 1) # wasserstein distance in dimension 1 # # one check to make sure when cycle locations are calculated there are no errors # expect_length(permutation_test(list(circle2,circle2,circle2),list(sphere2,sphere2,sphere2),iterations = 1,dims = c(1),num_workers = 2)$permvals[[1]],1) # expect_length(permutation_test(list(circle,circle,circle),list(sphere,sphere,sphere),iterations = 3,dims = c(1),num_workers = 2)$permvals[[1]],3) # expect_length(permutation_test(list(circle,circle,circle),list(sphere,sphere,sphere),iterations = 5,dims = c(1),num_workers = 2)$permvals[[1]],5) # expect_equal(permutation_test(list(circle,circle,circle),list(sphere,sphere,sphere),iterations = 1,dims = c(1),num_workers = 2)$test_statistics[[1]],0) # expect_equal(permutation_test(list(circle,circle,circle),list(sphere,sphere,sphere),iterations = 1,dims = c(2),num_workers = 2)$test_statistics[[1]],0) # expect_lte(abs(permutation_test(list(circle,circle,circle),list(sphere,circle,circle),iterations = 1,dims = c(1),num_workers = 2)$permvals[[1]][[1]] - d^2/3),0.01) # v <- permutation_test(list(circle,sphere,circle),list(sphere,circle,sphere),iterations = 1,dims = c(1),num_workers = 2)$permvals[[1]][[1]] # expect_lte(abs(v - 2*d^2/3)*v,0.02) # expect_length(unique(permutation_test(list(circle,sphere,circle),list(circle,sphere,circle),paired = T,iterations = 3,dims = c(1),num_workers = 2)$permvals[[1]]),1) # expect_length(unique(permutation_test(list(sphere,sphere,circle),list(sphere,sphere,circle),paired = T,iterations = 3,dims = c(1),num_workers = 2)$permvals[[1]]),1) # # expect_length(permutation_test(list(sphere,sphere,circle),list(sphere,sphere,circle),paired = T,iterations = 3,dims = c(1),num_workers = 2,distance = "fisher",sigma = 1,rho = 0.001)$permvals[[1]],3) # # }) # test_that("independence_test detects incorrect parameters correctly",{ # # skip_if_not_installed("TDA") # skip_if_not_installed("TDAstats") # g1 <- lapply(X = 1:6,FUN = function(X){return(TDA::ripsDiag(X = TDA::circleUnif(n = 50,r = 1),maxdimension = 1,maxscale = 2))}) # g2 <- lapply(X = 1:6,FUN = function(X){return(TDA::ripsDiag(X = TDA::sphereUnif(n = 50,d = 2,r = 1),maxdimension = 1,maxscale = 2))}) # expect_error(independence_test(g1,g2,dims = c(0,1),sigma = 1,t = NA,num_workers = 2),"NA") # expect_error(independence_test(g1,g2,dims = c(0,1),sigma = NaN,t = 1,num_workers = 2),"NaN") # expect_error(independence_test(g1,g2,dims = c(0,1),sigma = c(1,2),t = 1,num_workers = 2),"single") # expect_error(independence_test(g1,g2,dims = c(0,1.1),sigma = 1,t = 1,num_workers = 2),"whole") # expect_error(independence_test(g1,g2[1:5],dims = c(0,1),sigma = 1,t = 1,num_workers = 2),"same length") # expect_error(independence_test(g1[1:5],g2[1:5],dims = c(0,1),sigma = 1,t = 1,num_workers = 2),"6") # # expect_error(independence_test(list(g1[[1]],g1[[2]],g1[[3]],g1[[4]],g1[[5]],data.frame(dimension = numeric(),birth = numeric(),death = numeric())),g2,dims = c(0,1),sigma = 1,t = 1,num_workers = 2),"empty") # expect_error(independence_test(g1,g2,dims = c(0,1),num_workers = 2.3),"num_workers") # expect_error(independence_test(g1,g2,dims = c(0,1),num_workers = -2),"num_workers") # # }) # test_that("independence_test can accept inputs from TDA, TDAstats and diagram_to_df",{ # # skip_if_not_installed("TDA") # skip_if_not_installed("TDAstats") # circle = TDA::ripsDiag(X = TDA::circleUnif(n = 20,r = 1),maxdimension = 1,maxscale = 2) # sphere = TDAstats::calculate_homology(TDA::sphereUnif(n = 20,d = 2,r = 1),threshold = 2) # expect_length(independence_test(list(circle,circle,diagram_to_df(circle),circle,circle,circle),list(sphere,sphere,sphere,sphere,sphere,circle),dims = c(1),num_workers = 2)$p_values,1) # # }) # test_that("independence_test can accept precomputed Gram matrices",{ # # skip_if_not_installed("TDA") # skip_if_not_installed("TDAstats") # circle = TDA::ripsDiag(X = TDA::circleUnif(n = 20,r = 1),maxdimension = 1,maxscale = 2) # sphere = TDAstats::calculate_homology(TDA::sphereUnif(n = 20,d = 2,r = 1),threshold = 2) # K0 = gram_matrix(list(circle,circle,circle,circle,circle,circle),dim = 0,num_workers = 2) # K1 = gram_matrix(list(circle,circle,circle,circle,circle,circle),dim = 1,num_workers = 2) # L0 = gram_matrix(list(sphere,sphere,sphere,sphere,sphere,sphere),dim = 0,num_workers = 2) # L1 = gram_matrix(list(sphere,sphere,sphere,sphere,sphere,sphere),dim = 1,num_workers = 2) # expect_length(independence_test(Ks = list(K0,K1),Ls = list(L0,L1),dims = c(0,1),num_workers = 2)$p_values,2) # expect_length(independence_test(g1 = list(circle,circle,circle,circle,circle,circle),g2 = list(sphere,sphere,sphere,sphere,sphere,sphere),dims = c(0,1),num_workers = 2)$p_values,2) # expect_identical(independence_test(Ks = list(K0),Ls = list(L0),dims = c(0),num_workers = 2)$p_values,independence_test(g1 = list(circle,circle,circle,circle,circle,circle),g2 = list(sphere,sphere,sphere,sphere,sphere,sphere),dims = c(0),num_workers = 2)$p_values) # # expect_error(independence_test(Ks = list(K0,K1),Ls = 2,dims = c(0,1),num_workers = 2),"list") # expect_error(independence_test(Ks = list(K0,K1),Ls = list(L0),dims = c(0,1),num_workers = 2),"length") # K2 = gram_matrix(list(circle,circle,circle,circle,circle,circle,circle),dim = 1,num_workers = 2) # K3 = gram_matrix(list(circle,circle,circle,circle,circle),dim = 1,num_workers = 2) # expect_error(independence_test(Ks = list(K0,K2),Ls = list(L0,L1),dims = c(0,1),num_workers = 2),"dim") # expect_error(independence_test(Ks = list(K0,K1),Ls = list(L0,K3),dims = c(0,1),num_workers = 2),"6") # # }) test_that("independence_test is working",{ D1 <- data.frame(dimension = 0,birth = 2,death = 3) D2 <- data.frame(dimension = 0,birth = 2,death = 3.1) D3 <- data.frame(dimension = 0,birth = c(2,5),death = c(3.1,6)) k12 <- diagram_kernel(D1,D2,dim = 0) # sigma = 1,t = 1 k13 <- diagram_kernel(D1,D3,dim = 0) k23 <- diagram_kernel(D3,D2,dim = 0) HSIC <- 100*(1 - k13)*(1 - k23)/36^2 mu_x_sq <- (10 + 5*k13)/15 mu_y_sq <- (10 + 5*k23)/15 mu <- (1 + mu_x_sq*mu_y_sq - mu_x_sq - mu_y_sq)/6 v <- 209*((k13 - 1)^2)*((k23 - 1)^2)/314928 expect_equal(independence_test(g1 = list(D1,D1,D1,D1,D1,D3),g2 = list(D2,D2,D2,D2,D2,D3),dims = c(0),num_workers = 2)$test_statistics[[1]],HSIC) expect_equal(independence_test(g1 = list(D1,D1,D1,D1,D1,D3),g2 = list(D2,D2,D2,D2,D2,D3),dims = c(0),num_workers = 2)$p_values[[1]],stats::pgamma(q = HSIC,rate = mu/v,shape = mu^2/v,lower.tail = F)) })