test_that("Constructor", { x <- ltd$D$x y <- ltd$D$y m <- length(unique(x)) n <- length(y) w <- rep(1, n) max_iter <- 10000 stats <- ltd$stats_1 start <- c(0, 1, 1, 1, 1, 1) lower_bound <- c(0, -1, 0.5, 1, 0, 0.5) upper_bound <- c(3, 2, 2, 5, 2, 1) i <- c(1, 2, 4) s <- start s[-i] <- log(s[-i]) lb <- lower_bound lb[-i] <- log(lb[-i]) ub <- upper_bound ub[-i] <- log(ub[-i]) object <- logistic6_new(x, y, w, NULL, max_iter, NULL, NULL) expect_true(inherits(object, "logistic6")) expect_equal(object$x, x) expect_equal(object$y, y) expect_equal(object$w, w) expect_equal(object$n, n) expect_equal(object$m, m) expect_equal(object$stats, stats) expect_false(object$constrained) expect_equal(object$max_iter, max_iter) expect_null(object$start) expect_null(object$lower_bound) expect_null(object$upper_bound) object <- logistic6_new(x, y, w, start, max_iter, lower_bound, upper_bound) expect_true(inherits(object, "logistic6")) expect_equal(object$x, x) expect_equal(object$y, y) expect_equal(object$w, w) expect_equal(object$n, n) expect_equal(object$m, m) expect_equal(object$stats, stats) expect_true(object$constrained) expect_equal(object$max_iter, max_iter) expect_equal(object$start, s) expect_equal(object$lower_bound, lb) expect_equal(object$upper_bound, ub) w <- ltd$D$w stats <- ltd$stats_2 object <- logistic6_new(x, y, w, NULL, max_iter, NULL, NULL) expect_true(inherits(object, "logistic6")) expect_equal(object$x, x) expect_equal(object$y, y) expect_equal(object$w, w) expect_equal(object$n, n) expect_equal(object$m, m) expect_equal(object$stats, stats) expect_false(object$constrained) expect_equal(object$max_iter, max_iter) expect_null(object$start) expect_null(object$lower_bound) expect_null(object$upper_bound) object <- logistic6_new(x, y, w, start, max_iter, lower_bound, upper_bound) expect_true(inherits(object, "logistic6")) expect_equal(object$x, x) expect_equal(object$y, y) expect_equal(object$w, w) expect_equal(object$n, n) expect_equal(object$m, m) expect_equal(object$stats, stats) expect_true(object$constrained) expect_equal(object$max_iter, max_iter) expect_equal(object$start, s) expect_equal(object$lower_bound, lb) expect_equal(object$upper_bound, ub) }) test_that("Constructor: errors", { x <- ltd$D$x y <- ltd$D$y w <- ltd$D$w max_iter <- 10000 expect_error( logistic6_new(x, y, w, c(0, 1, 1, 1, 1), max_iter, NULL, NULL), "'start' must be of length 6" ) expect_error( logistic6_new(x, y, w, c(0, 1, 1, 1, 1, 1, 1), max_iter, NULL, NULL), "'start' must be of length 6" ) expect_error( logistic6_new(x, y, w, c(0, 1, 0, 1, 1, 1), max_iter, NULL, NULL), "parameter 'eta' cannot be negative nor zero" ) expect_error( logistic6_new(x, y, w, c(0, 1, -1, 1, 1, 1), max_iter, NULL, NULL), "parameter 'eta' cannot be negative nor zero" ) expect_error( logistic6_new(x, y, w, c(0, 1, 1, 1, 0, 1), max_iter, NULL, NULL), "parameter 'nu' cannot be negative nor zero" ) expect_error( logistic6_new(x, y, w, c(0, 1, 1, 1, -1, 1), max_iter, NULL, NULL), "parameter 'nu' cannot be negative nor zero" ) expect_error( logistic6_new(x, y, w, c(0, 1, 1, 1, 1, 0), max_iter, NULL, NULL), "parameter 'xi' cannot be negative nor zero" ) expect_error( logistic6_new(x, y, w, c(0, 1, 1, 1, 1, -1), max_iter, NULL, NULL), "parameter 'xi' cannot be negative nor zero" ) expect_error( logistic6_new(x, y, w, NULL, max_iter, rep(-Inf, 5), rep(Inf, 5)), "'lower_bound' must be of length 6" ) expect_error( logistic6_new(x, y, w, NULL, max_iter, rep(-Inf, 5), rep(Inf, 6)), "'lower_bound' must be of length 6" ) expect_error( logistic6_new(x, y, w, NULL, max_iter, rep(-Inf, 6), rep(Inf, 5)), "'upper_bound' must be of length 6" ) expect_error( logistic6_new( x, y, w, NULL, max_iter, rep(-Inf, 6), c(1, 1, 0, rep(Inf, 3)) ), "'upper_bound[3]' cannot be negative nor zero", fixed = TRUE ) expect_error( logistic6_new( x, y, w, NULL, max_iter, rep(-Inf, 6), c(1, 1, -1, rep(Inf, 3)) ), "'upper_bound[3]' cannot be negative nor zero", fixed = TRUE ) expect_error( logistic6_new( x, y, w, NULL, max_iter, rep(-Inf, 6), c(1, Inf, Inf, Inf, 0, Inf) ), "'upper_bound[5]' cannot be negative nor zero", fixed = TRUE ) expect_error( logistic6_new( x, y, w, NULL, max_iter, rep(-Inf, 6), c(1, Inf, Inf, Inf, -1, Inf) ), "'upper_bound[5]' cannot be negative nor zero", fixed = TRUE ) expect_error( logistic6_new( x, y, w, NULL, max_iter, rep(-Inf, 6), c(1, rep(Inf, 4), 0) ), "'upper_bound[6]' cannot be negative nor zero", fixed = TRUE ) expect_error( logistic6_new( x, y, w, NULL, max_iter, rep(-Inf, 6), c(1, rep(Inf, 4), -1) ), "'upper_bound[6]' cannot be negative nor zero", fixed = TRUE ) }) test_that("Function value", { x <- ltd$stats_1[, 1] theta <- ltd$theta_6 m <- length(x) true_value <- c( 0.8, 0.79999984704883975, 0.77510647298564850, 0.61621786196251596, 0.057664189665438460, 0.040170539009997540, 0.040164314348407453, 0.040164314348407453 ) value <- logistic6_fn(x, theta) expect_type(value, "double") expect_length(value, m) expect_equal(value, true_value) object <- structure(list(stats = ltd$stats_1), class = "logistic6") value <- fn(object, object$stats[, 1], theta) expect_type(value, "double") expect_length(value, m) expect_equal(value, true_value) object <- structure(list(stats = ltd$stats_1), class = "logistic6_fit") value <- fn(object, object$stats[, 1], theta) expect_type(value, "double") expect_length(value, m) expect_equal(value, true_value) }) test_that("Gradient (1)", { x <- ltd$stats_1[, 1] theta <- ltd$theta_6 m <- length(x) true_gradient <- matrix( c( # alpha rep(1, m), # delta 9.6437492398195889e-23, 1.5295116025091289e-07, 0.024893527014351497, 0.18378213803748404, 0.74233581033456154, 0.75982946099000246, 0.75983568565159255, 0.75983568565159255, # eta 2.4276486539439174e-21, 1.1736381182546699e-06, 0.041653962050552102, 0.12331460190108316, -0.021582949777827438, -0.000033032686382156039, -1.8583072261039617e-42, -1.3923270509654377e-85, # phi 4.8218746199097945e-23, 7.6475580125456447e-08, 0.012446749168025124, 0.091576578355026419, 0.033030421569699108, 0.000012449068216533443, 7.5377239464421580e-44, 2.8040905767036438e-87, # nu -1.2161526556915815e-21, -5.9051181979806446e-07, -0.021428022923202986, -0.066384858676451105, -0.051166597326927950, -0.052172373971476468, -0.052172801351587403, -0.052172801351587403, # xi 0, 2.0926851264125609e-35, 2.3898584374049245e-09, 0.000052415110619266708, 0.056356247266263610, 0.063317046904464116, 0.063319640470966046, 0.063319640470966046 ), nrow = m, ncol = 6 ) G <- logistic6_gradient(x, theta) expect_type(G, "double") expect_length(G, m * 6) expect_equal(G, true_gradient) }) test_that("Hessian (1)", { x <- ltd$stats_1[, 1] theta <- ltd$theta_6 m <- length(x) true_hessian <- array( c( # (alpha, alpha) rep(0, m), # (alpha, delta) rep(0, m), # (alpha, eta) rep(0, m), # (alpha, phi) rep(0, m), # (alpha, nu) rep(0, m), # (alpha, xi) rep(0, m), # (delta, alpha) rep(0, m), # (delta, delta) rep(0, m), # (delta, eta) -2.4276486539439174e-21, -1.1736381182546699e-06, -0.041653962050552102, -0.12331460190108316, 0.021582949777827438, 0.000033032686382156039, 1.8583072261039617e-42, 1.3923270509654377e-85, # (delta, phi) -4.8218746199097945e-23, -7.6475580125456447e-08, -0.012446749168025124, -0.091576578355026419, -0.033030421569699108, -0.000012449068216533443, -7.5377239464421580e-44, -2.8040905767036438e-87, # (delta, nu) 1.2161526556915815e-21, 5.9051181979806446e-07, 0.021428022923202986, 0.066384858676451105, 0.051166597326927950, 0.052172373971476468, 0.052172801351587403, 0.052172801351587403, # (delta, xi) -2.0853048558916222e-111, -2.0926851264125609e-35, -2.3898584374049245e-09, -0.000052415110619266708, -0.056356247266263610, -0.063317046904464116, -0.063319640470966046, -0.063319640470966046, # (eta, alpha) rep(0, m), # (eta, delta) -2.4276486539439174e-21, -1.1736381182546699e-06, -0.041653962050552102, -0.12331460190108316, 0.021582949777827438, 0.000033032686382156039, 1.8583072261039617e-42, 1.3923270509654377e-85, # (eta, eta) -6.1111895803565778e-20, -9.0056618750765000e-06, -0.069698623184655625, -0.081605338544629843, 0.025068184884160287, 0.00017529242457613078, 9.1627280890809950e-41, 1.3826761752674973e-83, # (eta, phi) -1.1897149538724097e-21, -5.4858126906460671e-07, -0.014603486473844729, -0.014813923084545845, -0.021848994443557445, -0.000059838132613523584, -3.6789258324757125e-42, -2.7706336490473572e-85, # (eta, nu) 3.0007647424909336e-20, 4.2377570196669037e-06, 0.025441707980853873, 0.013819938082184523, -0.0010074674090324482, -2.2678615960535156e-06, -1.2759744716990998e-43, -9.5601725502228708e-87, # (eta, xi) -2.6246988596328932e-109, -8.0288865734436783e-34, -1.9994569793277198e-08, -0.00017584811474708742, 0.0081926133528867864, 0.000013763168318811387, 7.7429467754331736e-43, 5.8013627123559905e-86, # (phi, alpha) rep(0, m), # (phi, delta) -4.8218746199097945e-23, -7.6475580125456447e-08, -0.012446749168025124, -0.091576578355026419, -0.033030421569699108, -0.000012449068216533443, -7.5377239464421580e-44, -2.8040905767036438e-87, # (phi, eta) -1.1897149538724097e-21, -5.4858126906460671e-07, -0.014603486473844729, -0.014813923084545845, -0.021848994443557445, -0.000059838132613523584, -3.6789258324757125e-42, -2.7706336490473572e-85, # (phi, phi) -2.4109373099548972e-23, -3.8237790062728224e-08, -0.0062233387361772991, -0.045004753323180023, 0.058712357899407301, 0.000024897116603569502, 1.5075447892884316e-43, 5.6081811534072877e-87, # (phi, nu) 5.9602164129601628e-22, 2.7613701486766812e-07, 0.0076023154114251624, 0.010263039600614143, 0.0015418222986489271, 8.5469172528994537e-07, 5.1756475975932719e-45, 1.9253802288156686e-88, # (phi, xi) -5.2132621397290555e-111, -5.2317128160314022e-35, -5.9746392104900531e-09, -0.00013058930905553107, -0.012537928114042809, -5.1869417853060373e-06, -3.1407183110175658e-44, -1.1683710736265183e-87, # (nu, alpha) rep(0, m), # (nu, delta) 1.2161526556915815e-21, 5.9051181979806446e-07, 0.021428022923202986, 0.066384858676451105, 0.051166597326927950, 0.052172373971476468, 0.052172801351587403, 0.052172801351587403, # (nu, eta) 3.0007647424909336e-20, 4.2377570196669037e-06, 0.025441707980853873, 0.013819938082184523, -0.0010074674090324482, -2.2678615960535156e-06, -1.2759744716990998e-43, -9.5601725502228708e-87, # (nu, phi) 5.9602164129601628e-22, 2.7613701486766812e-07, 0.0076023154114251624, 0.010263039600614143, 0.0015418222986489271, 8.5469172528994537e-07, 5.1756475975932719e-45, 1.9253802288156686e-88, # (nu, nu) -1.4730072359242754e-20, -1.9869741882303387e-06, -0.0081199112657906938, 0.0063612510169811997, 0.021964708947817155, 0.022503861272861439, 0.022504045632100321, 0.022504045632100321, # (nu, xi) 2.5254682512573550e-110, 7.0330685392331877e-35, 8.6223039892301619e-10, -7.2295861790158238e-06, -0.011458416654500857, -0.011482225054956227, -0.011482176671775895, -0.011482176671775895, # (xi, alpha) rep(0, m), # (xi, delta) -2.0853048558916222e-111, -2.0926851264125609e-35, -2.3898584374049245e-09, -0.000052415110619266708, -0.056356247266263610, -0.063317046904464116, -0.063319640470966046, -0.063319640470966046, # (xi, eta) -2.6246988596328932e-109, -8.0288865734436783e-34, -1.9994569793277198e-08, -0.00017584811474708742, 0.0081926133528867864, 0.000013763168318811387, 7.7429467754331736e-43, 5.8013627123559905e-86, # (xi, phi) -5.2132621397290555e-111, -5.2317128160314022e-35, -5.9746392104900531e-09, -0.00013058930905553107, -0.012537928114042809, -5.1869417853060373e-06, -3.1407183110175658e-44, -1.1683710736265183e-87, # (xi, nu) 2.5254682512573550e-110, 7.0330685392331877e-35, 8.6223039892301619e-10, -7.2295861790158238e-06, -0.011458416654500857, -0.011482225054956227, -0.011482176671775895, -0.011482176671775895, # (xi, xi) -2.2545673025434913e-199, -1.4316109244036342e-62, -1.1471703763678777e-15, -7.4744582105950359e-08, -0.021392115008602703, -0.026381238386562497, -0.026383183529569186, -0.026383183529569186 ), dim = c(m, 6, 6) ) H <- logistic6_hessian(x, theta) expect_type(H, "double") expect_length(H, m * 6 * 6) expect_equal(H, true_hessian) }) test_that("Gradient and Hessian (1)", { x <- ltd$stats_1[, 1] theta <- ltd$theta_6 m <- length(x) true_gradient <- matrix( c( # alpha rep(1, m), # delta 9.6437492398195889e-23, 1.5295116025091289e-07, 0.024893527014351497, 0.18378213803748404, 0.74233581033456154, 0.75982946099000246, 0.75983568565159255, 0.75983568565159255, # eta 2.4276486539439174e-21, 1.1736381182546699e-06, 0.041653962050552102, 0.12331460190108316, -0.021582949777827438, -0.000033032686382156039, -1.8583072261039617e-42, -1.3923270509654377e-85, # phi 4.8218746199097945e-23, 7.6475580125456447e-08, 0.012446749168025124, 0.091576578355026419, 0.033030421569699108, 0.000012449068216533443, 7.5377239464421580e-44, 2.8040905767036438e-87, # nu -1.2161526556915815e-21, -5.9051181979806446e-07, -0.021428022923202986, -0.066384858676451105, -0.051166597326927950, -0.052172373971476468, -0.052172801351587403, -0.052172801351587403, # xi 0, 2.0926851264125609e-35, 2.3898584374049245e-09, 0.000052415110619266708, 0.056356247266263610, 0.063317046904464116, 0.063319640470966046, 0.063319640470966046 ), nrow = m, ncol = 6 ) true_hessian <- array( c( # (alpha, alpha) rep(0, m), # (alpha, delta) rep(0, m), # (alpha, eta) rep(0, m), # (alpha, phi) rep(0, m), # (alpha, nu) rep(0, m), # (alpha, xi) rep(0, m), # (delta, alpha) rep(0, m), # (delta, delta) rep(0, m), # (delta, eta) -2.4276486539439174e-21, -1.1736381182546699e-06, -0.041653962050552102, -0.12331460190108316, 0.021582949777827438, 0.000033032686382156039, 1.8583072261039617e-42, 1.3923270509654377e-85, # (delta, phi) -4.8218746199097945e-23, -7.6475580125456447e-08, -0.012446749168025124, -0.091576578355026419, -0.033030421569699108, -0.000012449068216533443, -7.5377239464421580e-44, -2.8040905767036438e-87, # (delta, nu) 1.2161526556915815e-21, 5.9051181979806446e-07, 0.021428022923202986, 0.066384858676451105, 0.051166597326927950, 0.052172373971476468, 0.052172801351587403, 0.052172801351587403, # (delta, xi) -2.0853048558916222e-111, -2.0926851264125609e-35, -2.3898584374049245e-09, -0.000052415110619266708, -0.056356247266263610, -0.063317046904464116, -0.063319640470966046, -0.063319640470966046, # (eta, alpha) rep(0, m), # (eta, delta) -2.4276486539439174e-21, -1.1736381182546699e-06, -0.041653962050552102, -0.12331460190108316, 0.021582949777827438, 0.000033032686382156039, 1.8583072261039617e-42, 1.3923270509654377e-85, # (eta, eta) -6.1111895803565778e-20, -9.0056618750765000e-06, -0.069698623184655625, -0.081605338544629843, 0.025068184884160287, 0.00017529242457613078, 9.1627280890809950e-41, 1.3826761752674973e-83, # (eta, phi) -1.1897149538724097e-21, -5.4858126906460671e-07, -0.014603486473844729, -0.014813923084545845, -0.021848994443557445, -0.000059838132613523584, -3.6789258324757125e-42, -2.7706336490473572e-85, # (eta, nu) 3.0007647424909336e-20, 4.2377570196669037e-06, 0.025441707980853873, 0.013819938082184523, -0.0010074674090324482, -2.2678615960535156e-06, -1.2759744716990998e-43, -9.5601725502228708e-87, # (eta, xi) -2.6246988596328932e-109, -8.0288865734436783e-34, -1.9994569793277198e-08, -0.00017584811474708742, 0.0081926133528867864, 0.000013763168318811387, 7.7429467754331736e-43, 5.8013627123559905e-86, # (phi, alpha) rep(0, m), # (phi, delta) -4.8218746199097945e-23, -7.6475580125456447e-08, -0.012446749168025124, -0.091576578355026419, -0.033030421569699108, -0.000012449068216533443, -7.5377239464421580e-44, -2.8040905767036438e-87, # (phi, eta) -1.1897149538724097e-21, -5.4858126906460671e-07, -0.014603486473844729, -0.014813923084545845, -0.021848994443557445, -0.000059838132613523584, -3.6789258324757125e-42, -2.7706336490473572e-85, # (phi, phi) -2.4109373099548972e-23, -3.8237790062728224e-08, -0.0062233387361772991, -0.045004753323180023, 0.058712357899407301, 0.000024897116603569502, 1.5075447892884316e-43, 5.6081811534072877e-87, # (phi, nu) 5.9602164129601628e-22, 2.7613701486766812e-07, 0.0076023154114251624, 0.010263039600614143, 0.0015418222986489271, 8.5469172528994537e-07, 5.1756475975932719e-45, 1.9253802288156686e-88, # (phi, xi) -5.2132621397290555e-111, -5.2317128160314022e-35, -5.9746392104900531e-09, -0.00013058930905553107, -0.012537928114042809, -5.1869417853060373e-06, -3.1407183110175658e-44, -1.1683710736265183e-87, # (nu, alpha) rep(0, m), # (nu, delta) 1.2161526556915815e-21, 5.9051181979806446e-07, 0.021428022923202986, 0.066384858676451105, 0.051166597326927950, 0.052172373971476468, 0.052172801351587403, 0.052172801351587403, # (nu, eta) 3.0007647424909336e-20, 4.2377570196669037e-06, 0.025441707980853873, 0.013819938082184523, -0.0010074674090324482, -2.2678615960535156e-06, -1.2759744716990998e-43, -9.5601725502228708e-87, # (nu, phi) 5.9602164129601628e-22, 2.7613701486766812e-07, 0.0076023154114251624, 0.010263039600614143, 0.0015418222986489271, 8.5469172528994537e-07, 5.1756475975932719e-45, 1.9253802288156686e-88, # (nu, nu) -1.4730072359242754e-20, -1.9869741882303387e-06, -0.0081199112657906938, 0.0063612510169811997, 0.021964708947817155, 0.022503861272861439, 0.022504045632100321, 0.022504045632100321, # (nu, xi) 2.5254682512573550e-110, 7.0330685392331877e-35, 8.6223039892301619e-10, -7.2295861790158238e-06, -0.011458416654500857, -0.011482225054956227, -0.011482176671775895, -0.011482176671775895, # (xi, alpha) rep(0, m), # (xi, delta) -2.0853048558916222e-111, -2.0926851264125609e-35, -2.3898584374049245e-09, -0.000052415110619266708, -0.056356247266263610, -0.063317046904464116, -0.063319640470966046, -0.063319640470966046, # (xi, eta) -2.6246988596328932e-109, -8.0288865734436783e-34, -1.9994569793277198e-08, -0.00017584811474708742, 0.0081926133528867864, 0.000013763168318811387, 7.7429467754331736e-43, 5.8013627123559905e-86, # (xi, phi) -5.2132621397290555e-111, -5.2317128160314022e-35, -5.9746392104900531e-09, -0.00013058930905553107, -0.012537928114042809, -5.1869417853060373e-06, -3.1407183110175658e-44, -1.1683710736265183e-87, # (xi, nu) 2.5254682512573550e-110, 7.0330685392331877e-35, 8.6223039892301619e-10, -7.2295861790158238e-06, -0.011458416654500857, -0.011482225054956227, -0.011482176671775895, -0.011482176671775895, # (xi, xi) -2.2545673025434913e-199, -1.4316109244036342e-62, -1.1471703763678777e-15, -7.4744582105950359e-08, -0.021392115008602703, -0.026381238386562497, -0.026383183529569186, -0.026383183529569186 ), dim = c(m, 6, 6) ) gh <- logistic6_gradient_hessian(x, theta) expect_type(gh, "list") expect_type(gh$G, "double") expect_type(gh$H, "double") expect_length(gh$G, m * 6) expect_length(gh$H, m * 6 * 6) expect_equal(gh$G, true_gradient) expect_equal(gh$H, true_hessian) }) test_that("Gradient (2)", { x <- ltd$stats_1[, 1] theta <- ltd$theta_6 m <- length(x) true_gradient <- matrix( c( # alpha rep(1, m), # delta 9.6437492398195889e-23, 1.5295116025091289e-07, 0.024893527014351497, 0.18378213803748404, 0.74233581033456154, 0.75982946099000246, 0.75983568565159255, 0.75983568565159255, # log_eta 4.8552973078878348e-21, 2.3472762365093397e-06, 0.083307924101104204, 0.24662920380216631, -0.043165899555654876, -0.000066065372764312077, -3.7166144522079233e-42, -2.7846541019308754e-85, # phi 4.8218746199097945e-23, 7.6475580125456447e-08, 0.012446749168025124, 0.091576578355026419, 0.033030421569699108, 0.000012449068216533443, 7.5377239464421580e-44, 2.8040905767036438e-87, # log_nu -4.8646106227663261e-21, -2.3620472791922578e-06, -0.085712091692811944, -0.26553943470580442, -0.20466638930771180, -0.20868949588590587, -0.20869120540634961, -0.20869120540634961, # log_xi 0, 6.2780553792376827e-35, 7.1695753122147735e-09, 0.00015724533185780012, 0.16906874179879083, 0.18995114071339235, 0.18995892141289814, 0.18995892141289814 ), nrow = m, ncol = 6 ) G <- logistic6_gradient_2(x, theta) expect_type(G, "double") expect_length(G, m * 6) expect_equal(G, true_gradient) }) test_that("Hessian (2)", { x <- ltd$stats_1[, 1] theta <- ltd$theta_6 m <- length(x) true_hessian <- array( c( # (alpha, alpha) rep(0, m), # (alpha, delta) rep(0, m), # (alpha, log_eta) rep(0, m), # (alpha, phi) rep(0, m), # (alpha, log_nu) rep(0, m), # (alpha, log_xi) rep(0, m), # (delta, alpha) rep(0, m), # (delta, delta) rep(0, m), # (delta, log_eta) -4.8552973078878348e-21, -2.3472762365093397e-06, -0.083307924101104204, -0.24662920380216631, 0.043165899555654876, 0.000066065372764312077, 3.7166144522079233e-42, 2.7846541019308754e-85, # (delta, phi) -4.8218746199097945e-23, -7.6475580125456447e-08, -0.012446749168025124, -0.091576578355026419, -0.033030421569699108, -0.000012449068216533443, -7.5377239464421580e-44, -2.8040905767036438e-87, # (delta, log_nu) 4.8646106227663261e-21, 2.3620472791922578e-06, 0.085712091692811944, 0.26553943470580442, 0.20466638930771180, 0.20868949588590587, 0.20869120540634961, 0.20869120540634961, # (delta, log_xi) 0, -6.2780553792376827e-35, -7.1695753122147735e-09, -0.00015724533185780012, -0.16906874179879083, -0.18995114071339235, -0.18995892141289814, -0.18995892141289814, # (log_eta, alpha) rep(0, m), # (log_eta, delta) -4.8552973078878348e-21, -2.3472762365093397e-06, -0.083307924101104204, -0.24662920380216631, 0.043165899555654876, 0.000066065372764312077, 3.7166144522079233e-42, 2.7846541019308754e-85, # (log_eta, log_eta) -2.3959228590637528e-19, -0.000033675371263796660, -0.19548656863751830, -0.079792150376353060, 0.057106839980986273, 0.00063510432554021104, 3.6279250911103188e-40, 5.5028581600506806e-83, # (log_eta, phi) -2.3794299077448194e-21, -1.0971625381292134e-06, -0.029206972947689459, -0.029627846169091689, -0.043697988887114891, -0.00011967626522704717, -7.3578516649514251e-42, -5.5412672980947144e-85, # (log_eta, log_nu) 2.4006117939927469e-19, 0.000033902056157335230, 0.20353366384683098, 0.11055950465747618, -0.0080597392722595856, -0.000018142892768428125, -1.0207795773592799e-42, -7.6481380401782966e-86, # (log_eta, log_xi) 0, -4.8173319440662070e-33, -1.1996741875966319e-07, -0.0010550886884825245, 0.049155680117320718, 0.000082579009912868325, 4.6457680652599042e-42, 3.4808176274135943e-85, # (phi, alpha) rep(0, m), # (phi, delta) -4.8218746199097945e-23, -7.6475580125456447e-08, -0.012446749168025124, -0.091576578355026419, -0.033030421569699108, -0.000012449068216533443, -7.5377239464421580e-44, -2.8040905767036438e-87, # (phi, log_eta) -2.3794299077448194e-21, -1.0971625381292134e-06, -0.029206972947689459, -0.029627846169091689, -0.043697988887114891, -0.00011967626522704717, -7.3578516649514251e-42, -5.5412672980947144e-85, # (phi, phi) -2.4109373099548972e-23, -3.8237790062728224e-08, -0.0062233387361772991, -0.045004753323180023, 0.058712357899407301, 0.000024897116603569502, 1.5075447892884316e-43, 5.6081811534072877e-87, # (phi, log_nu) 2.3840865651840651e-21, 1.1045480594706725e-06, 0.030409261645700650, 0.041052158402456571, 0.0061672891945957084, 3.4187669011597815e-06, 2.0702590390373088e-44, 7.7015209152626744e-88, # (phi, log_xi) 0, -1.5695138448094207e-34, -1.7923917631470159e-08, -0.00039176792716659321, -0.037613784342128428, -0.000015560825355918112, -9.4221549330526975e-44, -3.5051132208795548e-87, # (log_nu, alpha) rep(0, m), # (log_nu, delta) 4.8646106227663261e-21, 2.3620472791922578e-06, 0.085712091692811944, 0.26553943470580442, 0.20466638930771180, 0.20868949588590587, 0.20869120540634961, 0.20869120540634961, # (log_nu, log_eta) 2.4006117939927469e-19, 0.000033902056157335230, 0.20353366384683098, 0.11055950465747618, -0.0080597392722595856, -0.000018142892768428125, -1.0207795773592799e-42, -7.6481380401782966e-86, # (log_nu, phi) 2.3840865651840651e-21, 1.1045480594706725e-06, 0.030409261645700650, 0.041052158402456571, 0.0061672891945957084, 3.4187669011597815e-06, 2.0702590390373088e-44, 7.7015209152626744e-88, # (log_nu, log_nu) -2.4054576837065039e-19, -0.000034153634290877677, -0.21563067194546304, -0.16375941843410523, 0.14676895385736267, 0.15137228447987715, 0.15137352470725553, 0.15137352470725553, # (log_nu, log_xi) 0, 8.4396822470798252e-34, 1.0346764787076194e-08, -0.000086755034148189886, -0.13750099985401029, -0.13778670065947473, -0.13778612006131073, -0.13778612006131073, # (log_xi, alpha) rep(0, m), # (log_xi, delta) 0, -6.2780553792376827e-35, -7.1695753122147735e-09, -0.00015724533185780012, -0.16906874179879083, -0.18995114071339235, -0.18995892141289814, -0.18995892141289814, # (log_xi, log_eta) 0, -4.8173319440662070e-33, -1.1996741875966319e-07, -0.0010550886884825245, 0.049155680117320718, 0.000082579009912868325, 4.6457680652599042e-42, 3.4808176274135943e-85, # (log_xi, phi) 0, -1.5695138448094207e-34, -1.7923917631470159e-08, -0.00039176792716659321, -0.037613784342128428, -0.000015560825355918112, -9.4221549330526975e-44, -3.5051132208795548e-87, # (log_xi, log_nu) 0, 8.4396822470798252e-34, 1.0346764787076194e-08, -0.000086755034148189886, -0.13750099985401029, -0.13778670065947473, -0.13778612006131073, -0.13778612006131073, # (log_xi, log_xi) 0, 6.2780553792376827e-35, 7.1695649876813862e-09, 0.00015657263061884657, -0.023460293278633494, -0.047480004765670128, -0.047489730353224534, -0.047489730353224534 ), dim = c(m, 6, 6) ) H <- logistic6_hessian_2(x, theta) expect_type(H, "double") expect_length(H, m * 6 * 6) expect_equal(H, true_hessian) }) test_that("Gradient and Hessian (2)", { x <- ltd$stats_1[, 1] theta <- ltd$theta_6 m <- length(x) true_gradient <- matrix( c( # alpha rep(1, m), # delta 9.6437492398195889e-23, 1.5295116025091289e-07, 0.024893527014351497, 0.18378213803748404, 0.74233581033456154, 0.75982946099000246, 0.75983568565159255, 0.75983568565159255, # log_eta 4.8552973078878348e-21, 2.3472762365093397e-06, 0.083307924101104204, 0.24662920380216631, -0.043165899555654876, -0.000066065372764312077, -3.7166144522079233e-42, -2.7846541019308754e-85, # phi 4.8218746199097945e-23, 7.6475580125456447e-08, 0.012446749168025124, 0.091576578355026419, 0.033030421569699108, 0.000012449068216533443, 7.5377239464421580e-44, 2.8040905767036438e-87, # log_nu -4.8646106227663261e-21, -2.3620472791922578e-06, -0.085712091692811944, -0.26553943470580442, -0.20466638930771180, -0.20868949588590587, -0.20869120540634961, -0.20869120540634961, # log_xi 0, 6.2780553792376827e-35, 7.1695753122147735e-09, 0.00015724533185780012, 0.16906874179879083, 0.18995114071339235, 0.18995892141289814, 0.18995892141289814 ), nrow = m, ncol = 6 ) true_hessian <- array( c( # (alpha, alpha) rep(0, m), # (alpha, delta) rep(0, m), # (alpha, log_eta) rep(0, m), # (alpha, phi) rep(0, m), # (alpha, log_nu) rep(0, m), # (alpha, log_xi) rep(0, m), # (delta, alpha) rep(0, m), # (delta, delta) rep(0, m), # (delta, log_eta) -4.8552973078878348e-21, -2.3472762365093397e-06, -0.083307924101104204, -0.24662920380216631, 0.043165899555654876, 0.000066065372764312077, 3.7166144522079233e-42, 2.7846541019308754e-85, # (delta, phi) -4.8218746199097945e-23, -7.6475580125456447e-08, -0.012446749168025124, -0.091576578355026419, -0.033030421569699108, -0.000012449068216533443, -7.5377239464421580e-44, -2.8040905767036438e-87, # (delta, log_nu) 4.8646106227663261e-21, 2.3620472791922578e-06, 0.085712091692811944, 0.26553943470580442, 0.20466638930771180, 0.20868949588590587, 0.20869120540634961, 0.20869120540634961, # (delta, log_xi) 0, -6.2780553792376827e-35, -7.1695753122147735e-09, -0.00015724533185780012, -0.16906874179879083, -0.18995114071339235, -0.18995892141289814, -0.18995892141289814, # (log_eta, alpha) rep(0, m), # (log_eta, delta) -4.8552973078878348e-21, -2.3472762365093397e-06, -0.083307924101104204, -0.24662920380216631, 0.043165899555654876, 0.000066065372764312077, 3.7166144522079233e-42, 2.7846541019308754e-85, # (log_eta, log_eta) -2.3959228590637528e-19, -0.000033675371263796660, -0.19548656863751830, -0.079792150376353060, 0.057106839980986273, 0.00063510432554021104, 3.6279250911103188e-40, 5.5028581600506806e-83, # (log_eta, phi) -2.3794299077448194e-21, -1.0971625381292134e-06, -0.029206972947689459, -0.029627846169091689, -0.043697988887114891, -0.00011967626522704717, -7.3578516649514251e-42, -5.5412672980947144e-85, # (log_eta, log_nu) 2.4006117939927469e-19, 0.000033902056157335230, 0.20353366384683098, 0.11055950465747618, -0.0080597392722595856, -0.000018142892768428125, -1.0207795773592799e-42, -7.6481380401782966e-86, # (log_eta, log_xi) 0, -4.8173319440662070e-33, -1.1996741875966319e-07, -0.0010550886884825245, 0.049155680117320718, 0.000082579009912868325, 4.6457680652599042e-42, 3.4808176274135943e-85, # (phi, alpha) rep(0, m), # (phi, delta) -4.8218746199097945e-23, -7.6475580125456447e-08, -0.012446749168025124, -0.091576578355026419, -0.033030421569699108, -0.000012449068216533443, -7.5377239464421580e-44, -2.8040905767036438e-87, # (phi, log_eta) -2.3794299077448194e-21, -1.0971625381292134e-06, -0.029206972947689459, -0.029627846169091689, -0.043697988887114891, -0.00011967626522704717, -7.3578516649514251e-42, -5.5412672980947144e-85, # (phi, phi) -2.4109373099548972e-23, -3.8237790062728224e-08, -0.0062233387361772991, -0.045004753323180023, 0.058712357899407301, 0.000024897116603569502, 1.5075447892884316e-43, 5.6081811534072877e-87, # (phi, log_nu) 2.3840865651840651e-21, 1.1045480594706725e-06, 0.030409261645700650, 0.041052158402456571, 0.0061672891945957084, 3.4187669011597815e-06, 2.0702590390373088e-44, 7.7015209152626744e-88, # (phi, log_xi) 0, -1.5695138448094207e-34, -1.7923917631470159e-08, -0.00039176792716659321, -0.037613784342128428, -0.000015560825355918112, -9.4221549330526975e-44, -3.5051132208795548e-87, # (log_nu, alpha) rep(0, m), # (log_nu, delta) 4.8646106227663261e-21, 2.3620472791922578e-06, 0.085712091692811944, 0.26553943470580442, 0.20466638930771180, 0.20868949588590587, 0.20869120540634961, 0.20869120540634961, # (log_nu, log_eta) 2.4006117939927469e-19, 0.000033902056157335230, 0.20353366384683098, 0.11055950465747618, -0.0080597392722595856, -0.000018142892768428125, -1.0207795773592799e-42, -7.6481380401782966e-86, # (log_nu, phi) 2.3840865651840651e-21, 1.1045480594706725e-06, 0.030409261645700650, 0.041052158402456571, 0.0061672891945957084, 3.4187669011597815e-06, 2.0702590390373088e-44, 7.7015209152626744e-88, # (log_nu, log_nu) -2.4054576837065039e-19, -0.000034153634290877677, -0.21563067194546304, -0.16375941843410523, 0.14676895385736267, 0.15137228447987715, 0.15137352470725553, 0.15137352470725553, # (log_nu, log_xi) 0, 8.4396822470798252e-34, 1.0346764787076194e-08, -0.000086755034148189886, -0.13750099985401029, -0.13778670065947473, -0.13778612006131073, -0.13778612006131073, # (log_xi, alpha) rep(0, m), # (log_xi, delta) 0, -6.2780553792376827e-35, -7.1695753122147735e-09, -0.00015724533185780012, -0.16906874179879083, -0.18995114071339235, -0.18995892141289814, -0.18995892141289814, # (log_xi, log_eta) 0, -4.8173319440662070e-33, -1.1996741875966319e-07, -0.0010550886884825245, 0.049155680117320718, 0.000082579009912868325, 4.6457680652599042e-42, 3.4808176274135943e-85, # (log_xi, phi) 0, -1.5695138448094207e-34, -1.7923917631470159e-08, -0.00039176792716659321, -0.037613784342128428, -0.000015560825355918112, -9.4221549330526975e-44, -3.5051132208795548e-87, # (log_xi, log_nu) 0, 8.4396822470798252e-34, 1.0346764787076194e-08, -0.000086755034148189886, -0.13750099985401029, -0.13778670065947473, -0.13778612006131073, -0.13778612006131073, # (log_xi, log_xi) 0, 6.2780553792376827e-35, 7.1695649876813862e-09, 0.00015657263061884657, -0.023460293278633494, -0.047480004765670128, -0.047489730353224534, -0.047489730353224534 ), dim = c(m, 6, 6) ) gh <- logistic6_gradient_hessian_2(x, theta) expect_type(gh, "list") expect_type(gh$G, "double") expect_type(gh$H, "double") expect_length(gh$G, m * 6) expect_length(gh$H, m * 6 * 6) expect_equal(gh$G, true_gradient) expect_equal(gh$H, true_hessian) object <- structure(list(stats = ltd$stats_1), class = "logistic6") gh <- gradient_hessian(object, theta) expect_type(gh, "list") expect_type(gh$G, "double") expect_type(gh$H, "double") expect_length(gh$G, m * 6) expect_length(gh$H, m * 6 * 6) expect_equal(gh$G, true_gradient) expect_equal(gh$H, true_hessian) }) test_that("Value of the RSS", { theta <- ltd$theta_6 theta[c(3, 5, 6)] <- log(theta[c(3, 5, 6)]) true_value <- 0.36255789619259319 object <- structure( list(stats = ltd$stats_1, m = nrow(ltd$stats_1)), class = "logistic6" ) rss_fn <- rss(object) expect_type(rss_fn, "closure") value <- rss_fn(theta) expect_type(value, "double") expect_length(value, 1) expect_equal(value, true_value) known_param <- c(theta[1], NA, NA, theta[4], theta[5], NA) rss_fn <- rss_fixed(object, known_param) expect_type(rss_fn, "closure") value <- rss_fn(theta[c(2, 3, 6)]) expect_type(value, "double") expect_length(value, 1) expect_equal(value, true_value) }) test_that("Gradient and Hessian of the RSS", { theta <- ltd$theta_6 theta[c(3, 5, 6)] <- log(theta[c(3, 5, 6)]) true_gradient <- c( -0.59376001498058462, -0.73330143767252627, 0.17369846729420963, 0.017669970115745026, 0.080623092690263486, -0.19216034447600408 ) true_hessian <- matrix( c( # alpha 19, 6.0512600139805846, 1.0235759411998543, 0.49030375496021016, -2.6823512883787693, 1.2676631260150411, # delta 6.0512600139805846, 4.0989218556934594, -0.084427619158893432, 0.12383872776827310, -1.3701711378917644, 1.1461364594573599, # log_eta 1.0235759411998543, -0.084427619158893432, 0.12128671379906373, 0.10305675773587517, -0.13332557577248706, -0.063800298599788432, # phi 0.49030375496021016, 0.12383872776827310, 0.10305675773587517, -0.034948837041012630, -0.097276873662293284, 0.048434100462574590, # log_nu -2.6823512883787693, -1.3701711378917644, -0.13332557577248706, -0.097276873662293284, 0.29576678334915398, -0.11057898822366290, # log_xi 1.2676631260150411, 1.1461364594573599, -0.063800298599788432, 0.048434100462574590, -0.11057898822366290, 0.26231706463305267 ), nrow = 6, ncol = 6 ) object <- structure( list(stats = ltd$stats_1, m = nrow(ltd$stats_1)), class = "logistic6" ) rss_gh <- rss_gradient_hessian(object) expect_type(rss_gh, "closure") gh <- rss_gh(theta) expect_type(gh$G, "double") expect_type(gh$H, "double") expect_length(gh$G, 6) expect_length(gh$H, 6 * 6) expect_equal(gh$G, true_gradient) expect_equal(gh$H, true_hessian) known_param <- c(theta[1], NA, NA, theta[4], theta[5], NA) rss_gh <- rss_gradient_hessian_fixed(object, known_param) expect_type(rss_gh, "closure") gh <- rss_gh(theta[c(2, 3, 6)]) expect_type(gh$G, "double") expect_type(gh$H, "double") expect_length(gh$G, 3) expect_length(gh$H, 3 * 3) expect_equal(gh$G, true_gradient[c(2, 3, 6)]) expect_equal(gh$H, true_hessian[c(2, 3, 6), c(2, 3, 6)]) }) test_that("mle_asy", { x <- ltd$D$x y <- ltd$D$y w <- rep(1, length(y)) max_iter <- 10000 theta <- c( 0, 1, -0.13948206931816815, 3.9201472292959156, 2.1396800314205292, 0.54368155924756683 ) true_value <- c( 0.84948649909664558, -0.80697277910347021, -0.13948206931816815, 3.9201472292959156, 2.1396800314205292, 0.54368155924756683 ) object <- logistic6_new(x, y, w, NULL, max_iter, NULL, NULL) result <- mle_asy(object, theta) expect_type(result, "double") expect_length(result, 6) expect_equal(result, true_value) }) test_that("fit", { x <- ltd$D$x y <- ltd$D$y n <- length(y) w <- rep(1, n) k <- as.numeric(table(x)) max_iter <- 10000 # logistic6 model is basically unidentifiable: many parameters are # associated with the same residual sum of squares # there is no point in testing the values of `result$coefficients` estimated <- c( alpha = TRUE, delta = TRUE, eta = TRUE, phi = TRUE, nu = TRUE, xi = TRUE ) rss_value <- 0.050168602337768019 fitted_values <- rep( c( 0.84947145597244308, 0.83001285437491464, 0.62226246927410375, 0.50732524066346644, 0.33637480874558723, 0.14349972605987800, 0.092532338486404620, 0.092532338486404619 ), k ) residuals <- c( 0.0032285440275569165, -0.092371455972443084, 0.087528544027556916, -0.0025128543749146426, -0.052212854374914643, 0.054587145625085357, -0.066162469274103751, 0.082537530725896249, 0.037974759336533557, -0.021325240663466443, 0.027774759336533557, -0.067425240663466443, 0.018925191254412770, -0.023174808745587230, 0.013525191254412770, -0.0013997260598779998, -0.075732338486404620, 0.046067661513595380, 0.030167661513595381 ) object <- logistic6_new(x, y, w, NULL, max_iter, NULL, NULL) result <- fit(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 6) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) object <- logistic6_new(x, y, w, c(0, 1, 1, 1, 1, 1), max_iter, NULL, NULL) result <- fit(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 6) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) }) test_that("fit_constrained: inequalities", { x <- ltd$D$x y <- ltd$D$y n <- length(y) w <- rep(1, n) k <- as.numeric(table(x)) max_iter <- 10000 estimated <- c( alpha = TRUE, delta = TRUE, eta = TRUE, phi = TRUE, nu = TRUE, xi = TRUE ) rss_value <- 0.050168602337768019 fitted_values <- rep( c( 0.84947145597244308, 0.83001285437491464, 0.62226246927410375, 0.50732524066346644, 0.33637480874558723, 0.14349972605987800, 0.092532338486404620, 0.092532338486404619 ), k ) residuals <- c( 0.0032285440275569165, -0.092371455972443084, 0.087528544027556916, -0.0025128543749146426, -0.052212854374914643, 0.054587145625085357, -0.066162469274103751, 0.082537530725896249, 0.037974759336533557, -0.021325240663466443, 0.027774759336533557, -0.067425240663466443, 0.018925191254412770, -0.023174808745587230, 0.013525191254412770, -0.0013997260598779998, -0.075732338486404620, 0.046067661513595380, 0.030167661513595381 ) object <- logistic6_new( x, y, w, NULL, max_iter, c(0.5, -1, 0.05, -5, 2, 0.5), c(1, -0.5, 5, 5, 10, 3) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 6) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values within the boundaries object <- logistic6_new( x, y, w, c(0.7, -0.6, 3, -1, 4, 1), max_iter, c(0.5, -1, 0.05, -5, 2, 0.5), c(1, -0.5, 5, 5, 10, 3) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 6) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values outside the boundaries object <- logistic6_new( x, y, w, c(-2, 2, 7, -8, 1, 5), max_iter, c(0.5, -1, 0.05, -5, 2, 0.5), c(1, -0.5, 5, 5, 10, 3) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 6) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) }) test_that("fit_constrained: equalities", { x <- ltd$D$x y <- ltd$D$y n <- length(y) w <- rep(1, n) k <- as.numeric(table(x)) max_iter <- 10000 estimated <- c( alpha = FALSE, delta = FALSE, eta = TRUE, phi = TRUE, nu = TRUE, xi = TRUE ) rss_value <- 0.062057350409983716 fitted_values <- rep( c( 0.79999935671542949, 0.79295099790131815, 0.62904933718751053, 0.51070978631265628, 0.32891952067935980, 0.15665231157393833, 0.090929983963630982, 0.090929983960543027 ), k ) residuals <- c( 0.052700643284570514, -0.042899356715429486, 0.13700064328457051, 0.034549002098681851, -0.015150997901318149, 0.091649002098681851, -0.072949337187510533, 0.075750662812489467, 0.034590213687343716, -0.024709786312656284, 0.024390213687343716, -0.070809786312656284, 0.026380479320640199, -0.015719520679359801, 0.020980479320640199, -0.014552311573938331, -0.074129983963630982, 0.047670016036369018, 0.031770016039456973 ) object <- logistic6_new( x, y, w, NULL, max_iter, c(0.8, -0.9, rep(-Inf, 4)), c(0.8, -0.9, rep(Inf, 4)) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 4) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values with same equalities object <- logistic6_new( x, y, w, c(0.8, -0.9, 1, 1, 1, 1), max_iter, c(0.8, -0.9, rep(-Inf, 4)), c(0.8, -0.9, rep(Inf, 4)) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 4) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values with different equalities object <- logistic6_new( x, y, w, c(0, 1, 1, 1, 1, 1), max_iter, c(0.8, -0.9, rep(-Inf, 4)), c(0.8, -0.9, rep(Inf, 4)) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 4) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) }) test_that("fit_constrained: equalities and inequalities", { x <- ltd$D$x y <- ltd$D$y n <- length(y) w <- rep(1, n) k <- as.numeric(table(x)) max_iter <- 10000 estimated <- c( alpha = FALSE, delta = FALSE, eta = TRUE, phi = TRUE, nu = TRUE, xi = TRUE ) rss_value <- 0.062057350409983716 fitted_values <- rep( c( 0.79999935671542949, 0.79295099790131815, 0.62904933718751053, 0.51070978631265628, 0.32891952067935980, 0.15665231157393833, 0.090929983963630982, 0.090929983960543027 ), k ) residuals <- c( 0.052700643284570514, -0.042899356715429486, 0.13700064328457051, 0.034549002098681851, -0.015150997901318149, 0.091649002098681851, -0.072949337187510533, 0.075750662812489467, 0.034590213687343716, -0.024709786312656284, 0.024390213687343716, -0.070809786312656284, 0.026380479320640199, -0.015719520679359801, 0.020980479320640199, -0.014552311573938331, -0.074129983963630982, 0.047670016036369018, 0.031770016039456973 ) object <- logistic6_new( x, y, w, NULL, max_iter, c(0.8, -0.9, 0.05, -5, 2, 1), c(0.8, -0.9, 3, 5, 6, 3) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 4) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values within the boundaries object <- logistic6_new( x, y, w, c(0.8, -0.9, 2, 0, 2.5, 1.2), max_iter, c(0.8, -0.9, 0.05, -5, 2, 1), c(0.8, -0.9, 3, 5, 6, 3) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 4) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values outside the boundaries object <- logistic6_new( x, y, w, c(0, 1, 5, -8, 10, 5), max_iter, c(0.8, -0.9, 0.05, -5, 2, 1), c(0.8, -0.9, 3, 5, 6, 3) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 4) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) }) test_that("fit (weighted)", { x <- ltd$D$x y <- ltd$D$y w <- ltd$D$w n <- length(y) k <- as.numeric(table(x)) max_iter <- 10000 # logistic6 model is basically unidentifiable: many parameters are # associated with the same residual sum of squares # there is no point in testing the values of `result$coefficients` estimated <- c( alpha = TRUE, delta = TRUE, eta = TRUE, phi = TRUE, nu = TRUE, xi = TRUE ) rss_value <- 0.026367789609414469 fitted_values <- rep( c( 0.85062856577440989, 0.85038705397619911, 0.68988971453996974, 0.50866177107419315, 0.30821950267475678, 0.17833789292363378, 0.087927106108376473, 0.087926555053940805 ), k ) residuals <- c( 0.0020714342255901108, -0.093528565774409889, 0.086371434225590111, -0.022887053976199108, -0.072587053976199108, 0.034212946023800892, -0.13378971453996974, 0.014910285460030258, 0.036638228925806847, -0.022661771074193153, 0.026438228925806847, -0.068761771074193153, 0.047080497325243221, 0.0049804973252432212, 0.041680497325243221, -0.036237892923633776, -0.071127106108376473, 0.050672893891623527, 0.034773444946059195 ) object <- logistic6_new(x, y, w, NULL, max_iter, NULL, NULL) result <- fit(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 6) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) object <- logistic6_new( x, y, w, c(1, -1, 1, 1, 1, 1), max_iter, NULL, NULL ) result <- fit(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 6) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) }) test_that("fit_constrained (weighted): inequalities", { x <- ltd$D$x y <- ltd$D$y w <- ltd$D$w n <- length(y) k <- as.numeric(table(x)) max_iter <- 10000 estimated <- c( alpha = TRUE, delta = TRUE, eta = TRUE, phi = TRUE, nu = TRUE, xi = TRUE ) rss_value <- 0.026367789609414469 fitted_values <- rep( c( 0.85062856577440989, 0.85038705397619911, 0.68988971453996974, 0.50866177107419315, 0.30821950267475678, 0.17833789292363378, 0.087927106108376473, 0.087926555053940805 ), k ) residuals <- c( 0.0020714342255901108, -0.093528565774409889, 0.086371434225590111, -0.022887053976199108, -0.072587053976199108, 0.034212946023800892, -0.13378971453996974, 0.014910285460030258, 0.036638228925806847, -0.022661771074193153, 0.026438228925806847, -0.068761771074193153, 0.047080497325243221, 0.0049804973252432212, 0.041680497325243221, -0.036237892923633776, -0.071127106108376473, 0.050672893891623527, 0.034773444946059195 ) object <- logistic6_new( x, y, w, NULL, max_iter, c(0.5, -1, 0.05, -5, 0.5, 0), c(1, -0.5, 3, 5, 3, 2) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 6) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values within the boundaries object <- logistic6_new( x, y, w, c(0.7, -0.6, 1, 2, 2.5, 1.8), max_iter, c(0.5, -1, 0.05, -5, 0.5, 0), c(1, -0.5, 3, 5, 3, 2) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 6) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values outside the boundaries object <- logistic6_new( x, y, w, c(-2, -5, 4, -8, 4, 3), 10000, c(0.5, -1, 0.05, -5, 0.5, 0), c(1, -0.5, 3, 5, 3, 2) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 6) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) }) test_that("fit_constrained (weighted): equalities", { x <- ltd$D$x y <- ltd$D$y w <- ltd$D$w n <- length(y) k <- as.numeric(table(x)) max_iter <- 10000 estimated <- c( alpha = FALSE, delta = FALSE, eta = TRUE, phi = TRUE, nu = TRUE, xi = TRUE ) rss_value <- 0.032325384005503981 fitted_values <- rep( c( 0.89996907976852931, 0.87386569158187010, 0.63652439966625265, 0.51281254109481959, 0.33374773386909931, 0.14206152371471766, 0.093890198677872793, 0.093890198677872789 ), k ) residuals <- c( -0.047269079768529308, -0.14286907976852931, 0.037030920231470692, -0.046365691581870097, -0.096065691581870097, 0.010734308418129903, -0.080424399666252655, 0.068275600333747345, 0.032487458905180414, -0.026812541094819586, 0.022287458905180414, -0.072912541094819586, 0.021552266130900692, -0.020547733869099308, 0.016152266130900692, 0.000038476285282337392, -0.077090198677872793, 0.044709801322127207, 0.028809801322127211 ) object <- logistic6_new( x, y, w, NULL, max_iter, c(0.9, -0.9, rep(-Inf, 4)), c(0.9, -0.9, rep(Inf, 4)) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 4) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values with same equalities object <- logistic6_new( x, y, w, c(0.9, -0.9, 1, 1, 1, 1), max_iter, c(0.9, -0.9, rep(-Inf, 4)), c(0.9, -0.9, rep(Inf, 4)) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 4) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values with different equalities object <- logistic6_new( x, y, w, c(0, 1, 1, 1, 1, 1), max_iter, c(0.9, -0.9, rep(-Inf, 4)), c(0.9, -0.9, rep(Inf, 4)) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 4) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) }) test_that("fit_constrained (weighted): equalities and inequalities", { x <- ltd$D$x y <- ltd$D$y w <- ltd$D$w n <- length(y) k <- as.numeric(table(x)) max_iter <- 10000 estimated <- c( alpha = FALSE, delta = FALSE, eta = TRUE, phi = TRUE, nu = TRUE, xi = TRUE ) rss_value <- 0.032325384005503981 fitted_values <- rep( c( 0.89996907976852931, 0.87386569158187010, 0.63652439966625265, 0.51281254109481959, 0.33374773386909931, 0.14206152371471766, 0.093890198677872793, 0.093890198677872789 ), k ) residuals <- c( -0.047269079768529308, -0.14286907976852931, 0.037030920231470692, -0.046365691581870097, -0.096065691581870097, 0.010734308418129903, -0.080424399666252655, 0.068275600333747345, 0.032487458905180414, -0.026812541094819586, 0.022287458905180414, -0.072912541094819586, 0.021552266130900692, -0.020547733869099308, 0.016152266130900692, 0.000038476285282337392, -0.077090198677872793, 0.044709801322127207, 0.028809801322127211 ) object <- logistic6_new( x, y, w, NULL, max_iter, c(0.9, -0.9, 0.05, -5, 5, 0.5), c(0.9, -0.9, 3, 5, 12, 4) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 4) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values within the boundaries object <- logistic6_new( x, y, w, c(0.9, -0.9, 2, 0, 11, 1), max_iter, c(0.9, -0.9, 0.05, -5, 5, 0.5), c(0.9, -0.9, 3, 5, 12, 4) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 4) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values outside the boundaries object <- logistic6_new( x, y, w, c(0, 1, 5, -8, 3, 6), max_iter, c(0.9, -0.9, 0.05, -5, 5, 0.5), c(0.9, -0.9, 3, 5, 12, 4) ) result <- fit_constrained(object) expect_true(inherits(result, "logistic6_fit")) expect_true(inherits(result, "logistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 4) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) }) test_that("fisher_info", { x <- ltd$D$x y <- ltd$D$y w <- ltd$D$w max_iter <- 10000 theta <- ltd$theta_6 names(theta) <- c("alpha", "delta", "eta", "phi", "nu", "xi") sigma <- ltd$sigma true_value <- matrix(c( # alpha 6206.96, 2093.9776752822887, 153.30946172983291, 153.11183995442809, -221.36872037331707, 148.97949961445271, 11595.531011291549, # delta 2093.9776752822887, 1437.5265454670404, -14.586523790688970, 40.797335330545767, -120.18243242866359, 134.67400631342478, 10406.248038205941, # eta 153.30946172983291, -14.586523790688970, -2.2648840073304669, 16.727779439929406, -5.9742410009604452, -3.5836831170680006, -1060.9581981747777, # phi 153.11183995442809, 40.797335330545767, 16.727779439929406, -12.239261546191805, -7.8866010818907720, 5.4396548685774482, -201.51541062927098, # nu -221.36872037331707, -120.18243242866359, -5.9742410009604452, -7.8866010818907720, 4.3346830493633020, -3.2808483355079093, -358.18422398482191, # xi 148.97949961445271, 134.67400631342478, -3.5836831170680006, 5.4396548685774482, -3.2808483355079093, 17.822668367095048, 900.77323828870695, # sigma 11595.531011291549, 10406.248038205941, -1060.9581981747777, -201.51541062927098, -358.18422398482191, 900.77323828870695, 139735.83919814804 ), nrow = 7, ncol = 7 ) rownames(true_value) <- colnames(true_value) <- c( "alpha", "delta", "eta", "phi", "nu", "xi", "sigma" ) object <- logistic6_new(x, y, w, NULL, max_iter, NULL, NULL) fim <- fisher_info(object, theta, sigma) expect_type(fim, "double") expect_length(fim, 7 * 7) expect_equal(fim, true_value) }) test_that("drda: 'lower_bound' argument errors", { x <- ltd$D$x y <- ltd$D$y expect_error( drda( y ~ x, mean_function = "logistic6", lower_bound = c("a", "b", "c", "d", "e", "f") ), "'lower_bound' must be a numeric vector" ) expect_error( drda( y ~ x, mean_function = "logistic6", lower_bound = matrix(-Inf, nrow = 6, ncol = 2), upper_bound = rep(Inf, 6) ), "'lower_bound' must be a numeric vector" ) expect_error( drda( y ~ x, mean_function = "logistic6", lower_bound = rep(-Inf, 7), upper_bound = rep(Inf, 6) ), "'lower_bound' and 'upper_bound' must have the same length" ) expect_error( drda( y ~ x, mean_function = "logistic6", lower_bound = c( 0, -Inf, -Inf, -Inf, -Inf, -Inf), upper_bound = c(-1, Inf, Inf, Inf, Inf, Inf) ), "'lower_bound' cannot be larger than 'upper_bound'" ) expect_error( drda( y ~ x, mean_function = "logistic6", lower_bound = c(Inf, -Inf, -Inf, -Inf, -Inf, -Inf), upper_bound = c(Inf, Inf, Inf, Inf, Inf, Inf) ), "'lower_bound' cannot be equal to infinity" ) expect_error( drda( y ~ x, mean_function = "logistic6", lower_bound = rep(-Inf, 7), upper_bound = rep(Inf, 7) ), "'lower_bound' must be of length 6" ) }) test_that("drda: 'upper_bound' argument errors", { x <- ltd$D$x y <- ltd$D$y expect_error( drda( y ~ x, mean_function = "logistic6", upper_bound = c("a", "b", "c", "d", "e", "f") ), "'upper_bound' must be a numeric vector" ) expect_error( drda( y ~ x, mean_function = "logistic6", lower_bound = rep(-Inf, 6), upper_bound = matrix(Inf, nrow = 6, ncol = 2) ), "'upper_bound' must be a numeric vector" ) expect_error( drda( y ~ x, mean_function = "logistic6", lower_bound = c(-Inf, -Inf, -Inf, -Inf, -Inf, -Inf), upper_bound = c(-Inf, Inf, Inf, Inf, Inf, Inf) ), "'upper_bound' cannot be equal to -infinity" ) expect_error( drda( y ~ x, mean_function = "logistic6", lower_bound = rep(-Inf, 7), upper_bound = rep(Inf, 7) ), "'lower_bound' must be of length 6" ) }) test_that("drda: 'start' argument errors", { x <- ltd$D$x y <- ltd$D$y expect_error( drda( y ~ x, mean_function = "logistic6", start = c("a", "b", "c", "d", "e", "f") ), "'start' must be a numeric vector" ) expect_error( drda( y ~ x, mean_function = "logistic6", start = c(0, Inf, 1, 1, 1, 1) ), "'start' must be finite" ) expect_error( drda( y ~ x, mean_function = "logistic6", start = c(-Inf, 1, 1, 1, 1, 1) ), "'start' must be finite" ) expect_error( drda( y ~ x, mean_function = "logistic6", start = c(1, 1, 1, 1, 1, 1, 1) ), "'start' must be of length 6" ) expect_error( drda( y ~ x, mean_function = "logistic6", start = c(0, 1, -1, 1, 1, 1) ), "parameter 'eta' cannot be negative nor zero" ) expect_error( drda( y ~ x, mean_function = "logistic6", start = c(0, 1, 0, 1, 1, 1) ), "parameter 'eta' cannot be negative nor zero" ) expect_error( drda( y ~ x, mean_function = "logistic6", start = c(0, 1, 1, 1, -1, 1) ), "parameter 'nu' cannot be negative nor zero" ) expect_error( drda( y ~ x, mean_function = "logistic6", start = c(0, 1, 1, 1, 0, 1) ), "parameter 'nu' cannot be negative nor zero" ) expect_error( drda( y ~ x, mean_function = "logistic6", start = c(0, 1, 1, 1, 1, -1) ), "parameter 'xi' cannot be negative nor zero" ) expect_error( drda( y ~ x, mean_function = "logistic6", start = c(0, 1, 1, 1, 1, 0) ), "parameter 'xi' cannot be negative nor zero" ) }) test_that("nauc: decreasing", { x <- ltd$D$x y <- ltd$D$y w <- ltd$D$w result <- drda(y ~ x, weights = w, mean_function = "logistic6") expect_equal(nauc(result), 0.42753516878440054) expect_equal(nauc(result, xlim = c(-2, 2)), 0.40530818958837455) expect_equal(nauc(result, ylim = c(0.3, 0.7)), 0.40513264312426645) expect_equal(nauc(result, xlim = c(-15, -10), ylim = c(0.3, 0.7)), 1.0) expect_equal( nauc(result, xlim = c(1, 5), ylim = c(0.3, 0.7)), 0.019678613960958503 ) expect_equal(nauc(result, xlim = c(10, 15), ylim = c(0.3, 0.7)), 0.0) }) test_that("naac: decreasing", { x <- ltd$D$x y <- ltd$D$y w <- ltd$D$w result <- drda(y ~ x, weights = w, mean_function = "logistic6") expect_equal(naac(result), 1 - 0.42753516878440054) expect_equal(naac(result, xlim = c(-2, 2)), 1 - 0.40530818958837455) expect_equal(naac(result, ylim = c(0.3, 0.7)), 1 - 0.40513264312426645) expect_equal(naac(result, xlim = c(-15, -10), ylim = c(0.3, 0.7)), 0.0) expect_equal( naac(result, xlim = c(1, 5), ylim = c(0.3, 0.7)), 1 - 0.019678613960958503 ) expect_equal(naac(result, xlim = c(10, 15), ylim = c(0.3, 0.7)), 1.0) }) test_that("nauc: increasing", { x <- ltd$D$x y <- rev(ltd$D$y) w <- ltd$D$w result <- drda(y ~ x, weights = w, mean_function = "logistic6") expect_equal(nauc(result), 0.65302073661957048) expect_equal(nauc(result, xlim = c(-2, 2)), 0.65733232476226463) expect_equal(nauc(result, ylim = c(0.3, 0.7)), 0.74700167012690062) expect_equal(nauc(result, xlim = c(-25, -18), ylim = c(0.3, 0.7)), 0.0) expect_equal( nauc(result, xlim = c(-5, -1), ylim = c(0.3, 0.7)), 0.62649140813097662 ) expect_equal(nauc(result, xlim = c(9, 12), ylim = c(0.3, 0.7)), 1.0) }) test_that("naac: increasing", { x <- ltd$D$x y <- rev(ltd$D$y) w <- ltd$D$w result <- drda(y ~ x, weights = w, mean_function = "logistic6") expect_equal(naac(result), 1 - 0.65302073661957048) expect_equal(naac(result, xlim = c(-2, 2)), 1 - 0.65733232476226463) expect_equal(naac(result, ylim = c(0.3, 0.7)), 1 - 0.74700167012690062) expect_equal(naac(result, xlim = c(-25, -18), ylim = c(0.3, 0.7)), 1.0) expect_equal( naac(result, xlim = c(-5, -1), ylim = c(0.3, 0.7)), 1 - 0.62649140813097662 ) expect_equal(naac(result, xlim = c(9, 12), ylim = c(0.3, 0.7)), 0.0) })