test_that("Constructor", { x <- lltd$D$x y <- lltd$D$y m <- length(unique(x)) n <- length(y) w <- rep(1, n) max_iter <- 10000 stats <- lltd$stats_1 start <- c(0, 1, 1, 1) lower_bound <- c(0, -1, 0.5, 1) upper_bound <- c(3, 2, 2, 5) object <- loggompertz_new(x, y, w, NULL, max_iter, NULL, NULL) expect_true(inherits(object, "loggompertz")) expect_equal(object$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 <- loggompertz_new(x, y, w, start, max_iter, lower_bound, upper_bound) i <- c(1, 2) expect_true(inherits(object, "loggompertz")) 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$start, c(start[i], log(start[-i]))) expect_equal(object$lower_bound, c(lower_bound[i], log(lower_bound[-i]))) expect_equal(object$upper_bound, c(upper_bound[i], log(upper_bound[-i]))) w <- lltd$D$w stats <- lltd$stats_2 object <- loggompertz_new(x, y, w, NULL, max_iter, NULL, NULL) expect_true(inherits(object, "loggompertz")) 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$upper_bound) object <- loggompertz_new(x, y, w, start, max_iter, lower_bound, upper_bound) expect_true(inherits(object, "loggompertz")) expect_equal(object$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, c(start[i], log(start[-i]))) expect_equal(object$lower_bound, c(lower_bound[i], log(lower_bound[-i]))) expect_equal(object$upper_bound, c(upper_bound[i], log(upper_bound[-i]))) }) test_that("Constructor: errors", { x <- lltd$D$x y <- lltd$D$y w <- lltd$D$w max_iter <- 10000 expect_error( loggompertz_new(x, y, w, c(0, 1, 1), max_iter, NULL, NULL), "'start' must be of length 4" ) expect_error( loggompertz_new(x, y, w, c(0, 1, 1, 1, 1), max_iter, NULL, NULL), "'start' must be of length 4" ) expect_error( loggompertz_new(x, y, w, c(0, 1, 0, 1), max_iter, NULL, NULL), "parameter 'eta' cannot be negative nor zero" ) expect_error( loggompertz_new(x, y, w, c(0, 1, -1, 1), max_iter, NULL, NULL), "parameter 'eta' cannot be negative nor zero" ) expect_error( loggompertz_new(x, y, w, c(0, 1, 1, 0), max_iter, NULL, NULL), "parameter 'phi' cannot be negative nor zero" ) expect_error( loggompertz_new(x, y, w, c(0, 1, 1, -1), max_iter, NULL, NULL), "parameter 'phi' cannot be negative nor zero" ) expect_error( loggompertz_new(x, y, w, NULL, max_iter, rep(-Inf, 3), rep(Inf, 3)), "'lower_bound' must be of length 4" ) expect_error( loggompertz_new(x, y, w, NULL, max_iter, rep(-Inf, 3), rep(Inf, 4)), "'lower_bound' must be of length 4" ) expect_error( loggompertz_new(x, y, w, NULL, max_iter, rep(-Inf, 4), rep(Inf, 3)), "'upper_bound' must be of length 4" ) expect_error( loggompertz_new(x, y, w, NULL, max_iter, rep(-Inf, 4), c(1, 1, 0, Inf)), "'upper_bound[3]' cannot be negative nor zero", fixed = TRUE ) expect_error( loggompertz_new(x, y, w, NULL, max_iter, rep(-Inf, 4), c(1, 1, -1, Inf)), "'upper_bound[3]' cannot be negative nor zero", fixed = TRUE ) expect_error( loggompertz_new(x, y, w, NULL, max_iter, rep(-Inf, 4), c(1, 1, Inf, 0)), "'upper_bound[4]' cannot be negative nor zero", fixed = TRUE ) expect_error( loggompertz_new(x, y, w, NULL, max_iter, rep(-Inf, 4), c(1, 1, Inf, -1)), "'upper_bound[4]' cannot be negative nor zero", fixed = TRUE ) }) test_that("Function value", { x <- lltd$stats_1[, 1] theta <- lltd$theta_g m <- length(x) true_value <- c( 1, 0.99835911398420645, 0.82183032092156685, 0.57555097969061526, 0.42486123076253040, 0.33801933438930586, 0.15212234596215889, 0.15002124973437721 ) value <- loggompertz_fn(x, theta) expect_type(value, "double") expect_length(value, m) expect_equal(value, true_value) object <- structure(list(stats = lltd$stats_1), class = "loggompertz") value <- fn(object, object$stats[, 1], theta) expect_type(value, "double") expect_length(value, m) expect_equal(value, true_value) object <- structure(list(stats = lltd$stats_1), class = "loggompertz_fit") value <- fn(object, object$stats[, 1], theta) expect_type(value, "double") expect_length(value, m) expect_equal(value, true_value) }) test_that("Gradient (1)", { x <- lltd$stats_1[, 1] theta <- lltd$theta_g m <- length(x) true_gradient <- matrix( c( # alpha rep(1, m), # delta 0, 0.0019304541362277092, 0.20961138715109782, 0.49935178859927617, 0.67663384616172894, 0.77880078307140487, 0.99750312239746012, 0.99997500031249740, # eta 0, 0.0093970540520846307, 0.062120960821991612, -0.053740420946163813, -0.10559269877403762, -0.11471250798831215, -0.0063500361305660149, -0.00011258642934322865, # phi 0, 0.0041022150394838821, 0.11135604942402072, 0.11790250564149576, 0.089865432693354624, 0.066198066561069414, 0.00084787765403784111, 8.4997875026562279e-06 ), nrow = m, ncol = 4 ) G <- loggompertz_gradient(x, theta) expect_type(G, "double") expect_length(G, m * 4) expect_equal(G, true_gradient) }) test_that("Hessian (1)", { x <- lltd$stats_1[, 1] theta <- lltd$theta_g 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), # (delta, alpha) rep(0, m), # (delta, delta) rep(0, m), # (delta, eta) 0, -0.011055357708334860, -0.073083483319990132, 0.063224024642545663, 0.12422670444004426, 0.13495589175095547, 0.0074706307418423704, 0.00013245462275673958, # (delta, phi) 0, -0.0048261353405692731, -0.13100711696943614, -0.13870883016646560, -0.10572403846277015, -0.077880078307140487, -0.00099750312239746012, -9.9997500031249740e-06, # (eta, alpha) rep(0, m), # (eta, delta) 0, -0.011055357708334860, -0.073083483319990132, 0.063224024642545663, 0.12422670444004426, 0.13495589175095547, 0.0074706307418423704, 0.00013245462275673958, # (eta, eta) 0, -0.045204776057939509, -0.0077973141424894308, 0.0029938447029538161, 0.030242642409067612, 0.059634488615294076, 0.018975450654134089, 0.00059650372086101613, # (eta, phi) 0, -0.017682705989635783, 0.041700808527062246, 0.052382979149550082, 0.019194496020505641, -0.0013147191159589372, -0.0021097255890769194, -0.000040783552121669912, # (phi, alpha) rep(0, m), # (phi, delta) 0, -0.0048261353405692731, -0.13100711696943614, -0.13870883016646560, -0.10572403846277015, -0.077880078307140487, -0.00099750312239746012, -9.9997500031249740e-06, # (phi, eta) 0, -0.017682705989635783, 0.041700808527062246, 0.052382979149550082, 0.019194496020505641, -0.0013147191159589372, -0.0021097255890769194, -0.000040783552121669912, # (phi, phi) 0, -0.0094350945908129289, -0.047326321005208805, -0.0091701948832274482, 0.0039316126803342648, 0.0066198066561069414, 0.00016872765315353038, 1.6998725026562190e-06 ), dim = c(m, 4, 4) ) H <- loggompertz_hessian(x, theta) expect_type(H, "double") expect_length(H, m * 4 * 4) expect_equal(H, true_hessian) }) test_that("Gradient and Hessian (1)", { x <- lltd$stats_1[, 1] theta <- lltd$theta_g m <- length(x) true_gradient <- matrix( c( # alpha rep(1, m), # delta 0, 0.0019304541362277092, 0.20961138715109782, 0.49935178859927617, 0.67663384616172894, 0.77880078307140487, 0.99750312239746012, 0.99997500031249740, # eta 0, 0.0093970540520846307, 0.062120960821991612, -0.053740420946163813, -0.10559269877403762, -0.11471250798831215, -0.0063500361305660149, -0.00011258642934322865, # phi 0, 0.0041022150394838821, 0.11135604942402072, 0.11790250564149576, 0.089865432693354624, 0.066198066561069414, 0.00084787765403784111, 8.4997875026562279e-06 ), nrow = m, ncol = 4 ) true_hessian <- array( c( # (alpha, alpha) rep(0, m), # (alpha, delta) rep(0, m), # (alpha, eta) rep(0, m), # (alpha, phi) rep(0, m), # (delta, alpha) rep(0, m), # (delta, delta) rep(0, m), # (delta, eta) 0, -0.011055357708334860, -0.073083483319990132, 0.063224024642545663, 0.12422670444004426, 0.13495589175095547, 0.0074706307418423704, 0.00013245462275673958, # (delta, phi) 0, -0.0048261353405692731, -0.13100711696943614, -0.13870883016646560, -0.10572403846277015, -0.077880078307140487, -0.00099750312239746012, -9.9997500031249740e-06, # (eta, alpha) rep(0, m), # (eta, delta) 0, -0.011055357708334860, -0.073083483319990132, 0.063224024642545663, 0.12422670444004426, 0.13495589175095547, 0.0074706307418423704, 0.00013245462275673958, # (eta, eta) 0, -0.045204776057939509, -0.0077973141424894308, 0.0029938447029538161, 0.030242642409067612, 0.059634488615294076, 0.018975450654134089, 0.00059650372086101613, # (eta, phi) 0, -0.017682705989635783, 0.041700808527062246, 0.052382979149550082, 0.019194496020505641, -0.0013147191159589372, -0.0021097255890769194, -0.000040783552121669912, # (phi, alpha) rep(0, m), # (phi, delta) 0, -0.0048261353405692731, -0.13100711696943614, -0.13870883016646560, -0.10572403846277015, -0.077880078307140487, -0.00099750312239746012, -9.9997500031249740e-06, # (phi, eta) 0, -0.017682705989635783, 0.041700808527062246, 0.052382979149550082, 0.019194496020505641, -0.0013147191159589372, -0.0021097255890769194, -0.000040783552121669912, # (phi, phi) 0, -0.0094350945908129289, -0.047326321005208805, -0.0091701948832274482, 0.0039316126803342648, 0.0066198066561069414, 0.00016872765315353038, 1.6998725026562190e-06 ), dim = c(m, 4, 4) ) gh <- loggompertz_gradient_hessian(x, theta) expect_type(gh, "list") expect_type(gh$G, "double") expect_type(gh$H, "double") expect_length(gh$G, m * 4) expect_length(gh$H, m * 4 * 4) expect_equal(gh$G, true_gradient) expect_equal(gh$H, true_hessian) }) test_that("Gradient (2)", { x <- lltd$stats_1[, 1] theta <- lltd$theta_g m <- length(x) true_gradient <- matrix( c( # alpha rep(1, m), # delta 0, 0.0019304541362277092, 0.20961138715109782, 0.49935178859927617, 0.67663384616172894, 0.77880078307140487, 0.99750312239746012, 0.99997500031249740, # log_eta 0, 0.018794108104169261, 0.12424192164398322, -0.10748084189232763, -0.21118539754807525, -0.22942501597662429, -0.012700072261132030, -0.00022517285868645729, # log_phi 0, 0.020511075197419411, 0.55678024712010359, 0.58951252820747881, 0.44932716346677312, 0.33099033280534707, 0.0042393882701892055, 0.000042498937513281139 ), nrow = m, ncol = 4 ) G <- loggompertz_gradient_2(x, theta) expect_type(G, "double") expect_length(G, m * 4) expect_equal(G, true_gradient) }) test_that("Hessian (2)", { x <- lltd$stats_1[, 1] theta <- lltd$theta_g m <- length(x) true_hessian <- array( c( # (alpha, alpha) rep(0, m), # (alpha, delta) rep(0, m), # (alpha, log_eta) rep(0, m), # (alpha, log_phi) rep(0, m), # (delta, alpha) rep(0, m), # (delta, delta) rep(0, m), # (delta, log_eta) 0, -0.022110715416669719, -0.14616696663998026, 0.12644804928509133, 0.24845340888008853, 0.26991178350191093, 0.014941261483684741, 0.00026490924551347917, # (delta, log_phi) 0, -0.024130676702846366, -0.65503558484718070, -0.69354415083232801, -0.52862019231385073, -0.38940039153570243, -0.0049875156119873006, -0.000049998750015624870, # (log_eta, alpha) rep(0, m), # (log_eta, delta) 0, -0.022110715416669719, -0.14616696663998026, 0.12644804928509133, 0.24845340888008853, 0.26991178350191093, 0.014941261483684741, 0.00026490924551347917, # (log_eta, log_eta) 0, -0.16202499612758877, 0.093052665074025501, -0.095505463080512362, -0.090214827911804800, 0.0091129384845520113, 0.063201730355404326, 0.0021608420247576072, # (log_eta, log_phi) 0, -0.17682705989635783, 0.41700808527062246, 0.52382979149550082, 0.19194496020505641, -0.013147191159589372, -0.021097255890769194, -0.00040783552121669912, # (log_phi, alpha) rep(0, m), # (log_phi, delta) 0, -0.024130676702846366, -0.65503558484718070, -0.69354415083232801, -0.52862019231385073, -0.38940039153570243, -0.0049875156119873006, -0.000049998750015624870, # (log_phi, log_eta) 0, -0.17682705989635783, 0.41700808527062246, 0.52382979149550082, 0.19194496020505641, -0.013147191159589372, -0.021097255890769194, -0.00040783552121669912, # (log_phi, log_phi) 0, -0.21536628957290381, -0.62637777801011654, 0.36025765612679261, 0.54761748047512974, 0.49648549920802060, 0.0084575795990274650, 0.000084995750079686615 ), dim = c(m, 4, 4) ) H <- loggompertz_hessian_2(x, theta) expect_type(H, "double") expect_length(H, m * 4 * 4) expect_equal(H, true_hessian) }) test_that("Gradient and Hessian (2)", { x <- lltd$stats_1[, 1] theta <- lltd$theta_g m <- length(x) true_gradient <- matrix( c( # alpha rep(1, m), # delta 0, 0.0019304541362277092, 0.20961138715109782, 0.49935178859927617, 0.67663384616172894, 0.77880078307140487, 0.99750312239746012, 0.99997500031249740, # log_eta 0, 0.018794108104169261, 0.12424192164398322, -0.10748084189232763, -0.21118539754807525, -0.22942501597662429, -0.012700072261132030, -0.00022517285868645729, # log_phi 0, 0.020511075197419411, 0.55678024712010359, 0.58951252820747881, 0.44932716346677312, 0.33099033280534707, 0.0042393882701892055, 0.000042498937513281139 ), nrow = m, ncol = 4 ) true_hessian <- array( c( # (alpha, alpha) rep(0, m), # (alpha, delta) rep(0, m), # (alpha, log_eta) rep(0, m), # (alpha, log_phi) rep(0, m), # (delta, alpha) rep(0, m), # (delta, delta) rep(0, m), # (delta, log_eta) 0, -0.022110715416669719, -0.14616696663998026, 0.12644804928509133, 0.24845340888008853, 0.26991178350191093, 0.014941261483684741, 0.00026490924551347917, # (delta, log_phi) 0, -0.024130676702846366, -0.65503558484718070, -0.69354415083232801, -0.52862019231385073, -0.38940039153570243, -0.0049875156119873006, -0.000049998750015624870, # (log_eta, alpha) rep(0, m), # (log_eta, delta) 0, -0.022110715416669719, -0.14616696663998026, 0.12644804928509133, 0.24845340888008853, 0.26991178350191093, 0.014941261483684741, 0.00026490924551347917, # (log_eta, log_eta) 0, -0.16202499612758877, 0.093052665074025501, -0.095505463080512362, -0.090214827911804800, 0.0091129384845520113, 0.063201730355404326, 0.0021608420247576072, # (log_eta, log_phi) 0, -0.17682705989635783, 0.41700808527062246, 0.52382979149550082, 0.19194496020505641, -0.013147191159589372, -0.021097255890769194, -0.00040783552121669912, # (log_phi, alpha) rep(0, m), # (log_phi, delta) 0, -0.024130676702846366, -0.65503558484718070, -0.69354415083232801, -0.52862019231385073, -0.38940039153570243, -0.0049875156119873006, -0.000049998750015624870, # (log_phi, log_eta) 0, -0.17682705989635783, 0.41700808527062246, 0.52382979149550082, 0.19194496020505641, -0.013147191159589372, -0.021097255890769194, -0.00040783552121669912, # (log_phi, log_phi) 0, -0.21536628957290381, -0.62637777801011654, 0.36025765612679261, 0.54761748047512974, 0.49648549920802060, 0.0084575795990274650, 0.000084995750079686615 ), dim = c(m, 4, 4) ) gh <- loggompertz_gradient_hessian_2(x, theta) expect_type(gh, "list") expect_type(gh$G, "double") expect_type(gh$H, "double") expect_length(gh$G, m * 4) expect_length(gh$H, m * 4 * 4) expect_equal(gh$G, true_gradient) expect_equal(gh$H, true_hessian) object <- structure(list(stats = lltd$stats_1), class = "loggompertz") gh <- gradient_hessian(object, theta) expect_type(gh, "list") expect_type(gh$G, "double") expect_type(gh$H, "double") expect_length(gh$G, m * 4) expect_length(gh$H, m * 4 * 4) expect_equal(gh$G, true_gradient) expect_equal(gh$H, true_hessian) }) test_that("Value of the RSS", { theta <- lltd$theta_g theta[3:4] <- log(theta[3:4]) true_value <- 0.32075900098848013 object <- structure( list(stats = lltd$stats_1, m = nrow(lltd$stats_1)), class = "loggompertz" ) 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]) rss_fn <- rss_fixed(object, known_param) expect_type(rss_fn, "closure") value <- rss_fn(theta[2:3]) expect_type(value, "double") expect_length(value, 1) expect_equal(value, true_value) }) test_that("Gradient and Hessian of the RSS", { theta <- lltd$theta_g theta[3:4] <- log(theta[3:4]) true_gradient <- c( 2.2653108698938061, 0.73068466091804248, -0.075702268537242359, 0.57850423102806821 ) true_hessian <- matrix( c( # alpha 19, 8.2261048577719928, -1.0136637259706368, 5.2206369313459388, # delta 8.2261048577719928, 6.0552995869783359, -0.70635145977914647, 1.9088026101488051, # log_eta -1.0136637259706368, -0.70635145977914647, 0.17854179243952868, -0.20592244468846133, # log_phi 5.2206369313459388, 1.9088026101488051, -0.20592244468846133, 2.7235196164555188 ), nrow = 4, ncol = 4 ) object <- structure( list(stats = lltd$stats_1, m = nrow(lltd$stats_1)), class = "loggompertz" ) rss_gh <- rss_gradient_hessian(object) expect_type(rss_gh, "closure") gh <- rss_gh(theta) expect_type(gh$G, "double") expect_type(gh$H, "double") expect_length(gh$G, 4) expect_length(gh$H, 4 * 4) expect_equal(gh$G, true_gradient) expect_equal(gh$H, true_hessian) known_param <- c(theta[1], NA, NA, theta[4]) rss_gh <- rss_gradient_hessian_fixed(object, known_param) expect_type(rss_gh, "closure") gh <- rss_gh(theta[2:3]) expect_type(gh$G, "double") expect_type(gh$H, "double") expect_length(gh$G, 2) expect_length(gh$H, 2 * 2) expect_equal(gh$G, true_gradient[2:3]) expect_equal(gh$H, true_hessian[2:3, 2:3]) }) test_that("mle_asy", { x <- lltd$D$x y <- lltd$D$y w <- rep(1, length(y)) max_iter <- 10000 theta <- c(0, 1, 0.63524784841453301, 1.6101961281319852) true_value <- c( 0.83777215113750696, -0.75729507682865963, 0.63524784841453301, 1.6101961281319852 ) object <- loggompertz_new(x, y, w, NULL, max_iter, NULL, NULL) result <- mle_asy(object, theta) expect_type(result, "double") expect_length(result, 4) expect_equal(result, true_value) }) test_that("fit", { x <- lltd$D$x y <- lltd$D$y n <- length(y) w <- rep(1, n) k <- as.numeric(table(x)) max_iter <- 10000 estimated <- c(alpha = TRUE, delta = TRUE, eta = TRUE, phi = TRUE) rss_value <- 0.073630385904407914 theta <- c( alpha = 0.83777215113750696, delta = -0.75729507682865963, eta = exp(0.63524784841453301), phi = exp(1.6101961281319852) ) fitted_values <- rep( c( 0.83777215113750696, 0.83509727314890451, 0.67312406791826807, 0.46539726317063078, 0.33641138140141234, 0.26005233684193214, 0.083128285791155688, 0.080511485993225808 ), k ) residuals <- c( 0.014927848862493037, -0.080672151137506963, 0.099227848862493037, -0.0075972731489045085, -0.057297273148904508, 0.049502726851095492, -0.11702406791826807, 0.031675932081731933, 0.079902736829369223, 0.020602736829369223, 0.069702736829369223, -0.025497263170630777, 0.018888618598587661, -0.023211381401412339, 0.013488618598587661, -0.11795233684193214, -0.066328285791155688, 0.055471714208844312, 0.042188514006774192 ) object <- loggompertz_new(x, y, w, NULL, max_iter, NULL, NULL) result <- fit(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$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$weights, w) object <- loggompertz_new(x, y, w, c(0, 1, 1, 1), max_iter, NULL, NULL) result <- fit(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$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$weights, w) }) test_that("fit_constrained: inequalities", { x <- lltd$D$x y <- lltd$D$y n <- length(y) w <- rep(1, n) k <- as.numeric(table(x)) max_iter <- 10000 estimated <- c(alpha = TRUE, delta = TRUE, eta = TRUE, phi = TRUE) rss_value <- 0.073630385904407914 theta <- c( alpha = 0.83777215113750696, delta = -0.75729507682865963, eta = exp(0.63524784841453301), phi = exp(1.6101961281319852) ) fitted_values <- rep( c( 0.83777215113750696, 0.83509727314890451, 0.67312406791826807, 0.46539726317063078, 0.33641138140141234, 0.26005233684193214, 0.083128285791155688, 0.080511485993225808 ), k ) residuals <- c( 0.014927848862493037, -0.080672151137506963, 0.099227848862493037, -0.0075972731489045085, -0.057297273148904508, 0.049502726851095492, -0.11702406791826807, 0.031675932081731933, 0.079902736829369223, 0.020602736829369223, 0.069702736829369223, -0.025497263170630777, 0.018888618598587661, -0.023211381401412339, 0.013488618598587661, -0.11795233684193214, -0.066328285791155688, 0.055471714208844312, 0.042188514006774192 ) object <- loggompertz_new( x, y, w, NULL, max_iter, c(0.5, -1, 1, 3), c(1, -0.5, 5, 12) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$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$weights, w) # initial values within the boundaries object <- loggompertz_new( x, y, w, c(0.6, -0.6, 4, 8), max_iter, c(0.5, -1, 1, 3), c(1, -0.5, 5, 12) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$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$weights, w) # initial values outside the boundaries object <- loggompertz_new( x, y, w, c(-2, 2, 7, 1), max_iter, c(0.5, -1, 1, 3), c(1, -0.5, 5, 12) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$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$weights, w) }) test_that("fit_constrained: equalities", { x <- lltd$D$x y <- lltd$D$y n <- length(y) w <- rep(1, n) k <- as.numeric(table(x)) max_iter <- 10000 estimated <- c(alpha = FALSE, delta = FALSE, eta = TRUE, phi = TRUE) rss_value <- 0.17654034036023363 theta <- c( alpha = 0.8, delta = -0.9, eta = exp(0.34256135717772634), phi = exp(1.8046122081510387) ) fitted_values <- rep( c( 0.8, 0.79248376718906222, 0.65161512055560499, 0.47490216690684499, 0.34359567627384339, 0.25186908386433202, -0.082746689754940315, -0.099320242477951822 ), k ) residuals <- c( 0.0527, -0.0429, 0.137, 0.035016232810937784, -0.014683767189062216, 0.092116232810937784, -0.095515120555604989, 0.053184879444395011, 0.070397833093155009, 0.011097833093155009, 0.060197833093155009, -0.035002166906844991, 0.011704323726156605, -0.030395676273843395, 0.0063043237261566051, -0.10976908386433202, 0.099546689754940315, 0.22134668975494032, 0.22202024247795182 ) object <- loggompertz_new( x, y, w, NULL, max_iter, c(0.8, -0.9, rep(-Inf, 2)), c(0.8, -0.9, rep(Inf, 2)) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 2) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values with same equalities object <- loggompertz_new( x, y, w, c(0.8, -0.9, 1, 1), max_iter, c(0.8, -0.9, rep(-Inf, 2)), c(0.8, -0.9, rep(Inf, 2)) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 2) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values with different equalities object <- loggompertz_new( x, y, w, c(0, 1, 1, 1), max_iter, c(0.8, -0.9, rep(-Inf, 2)), c(0.8, -0.9, rep(Inf, 2)) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 2) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) }) test_that("fit_constrained: equalities and inequalities", { x <- lltd$D$x y <- lltd$D$y n <- length(y) w <- rep(1, n) k <- as.numeric(table(x)) max_iter <- 10000 estimated <- c(alpha = FALSE, delta = FALSE, eta = TRUE, phi = TRUE) rss_value <- 0.17654034036023363 theta <- c( alpha = 0.8, delta = -0.9, eta = exp(0.34256135717772634), phi = exp(1.8046122081510387) ) fitted_values <- rep( c( 0.8, 0.79248376718906222, 0.65161512055560499, 0.47490216690684499, 0.34359567627384339, 0.25186908386433202, -0.082746689754940315, -0.099320242477951822 ), k ) residuals <- c( 0.0527, -0.0429, 0.137, 0.035016232810937784, -0.014683767189062216, 0.092116232810937784, -0.095515120555604989, 0.053184879444395011, 0.070397833093155009, 0.011097833093155009, 0.060197833093155009, -0.035002166906844991, 0.011704323726156605, -0.030395676273843395, 0.0063043237261566051, -0.10976908386433202, 0.099546689754940315, 0.22134668975494032, 0.22202024247795182 ) object <- loggompertz_new( x, y, w, NULL, max_iter, c(0.8, -0.9, 1, 3), c(0.8, -0.9, 5, 12) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 2) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values within the boundaries object <- loggompertz_new( x, y, w, c(0.8, -0.9, 3, 7), max_iter, c(0.8, -0.9, 1, 3), c(0.8, -0.9, 5, 12) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 2) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values outside the boundaries object <- loggompertz_new( x, y, w, c(0, 1, 8, 1), max_iter, c(0.8, -0.9, 1, 3), c(0.8, -0.9, 5, 12) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 2) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) }) test_that("fit (weighted)", { x <- lltd$D$x y <- lltd$D$y w <- lltd$D$w n <- length(y) k <- as.numeric(table(x)) max_iter <- 10000 estimated <- c(alpha = TRUE, delta = TRUE, eta = TRUE, phi = TRUE) rss_value <- 0.035138156284360913 theta <- c( alpha = 0.84575428432937011, delta = -0.76656134360156587, eta = exp(0.89238310459026989), phi = exp(1.6622042309903930) ) fitted_values <- rep( c( 0.84575428432937011, 0.84573608713048233, 0.73789083646643889, 0.47593010582855891, 0.31155933858113756, 0.22406801104864969, 0.079774485527624186, 0.079195048422139125 ), k ) residuals <- c( 0.0069457156706298950, -0.088654284329370105, 0.091245715670629895, -0.018236087130482331, -0.067936087130482331, 0.038863912869517669, -0.18179083646643889, -0.033090836466438890, 0.069369894171441088, 0.010069894171441088, 0.059169894171441088, -0.036030105828558912, 0.043740661418862440, 0.0016406614188624399, 0.038340661418862440, -0.081968011048649687, -0.062974485527624186, 0.058825514472375814, 0.043504951577860875 ) object <- loggompertz_new(x, y, w, NULL, max_iter, NULL, NULL) result <- fit(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$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$weights, w) object <- loggompertz_new(x, y, w, c(0, 1, 1, 1), max_iter, NULL, NULL) result <- fit(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$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$weights, w) }) test_that("fit_constrained (weighted): inequalities", { x <- lltd$D$x y <- lltd$D$y w <- lltd$D$w n <- length(y) k <- as.numeric(table(x)) max_iter <- 10000 estimated <- c(alpha = TRUE, delta = TRUE, eta = TRUE, phi = TRUE) rss_value <- 0.035138156284360913 theta <- c( alpha = 0.84575428432937011, delta = -0.76656134360156587, eta = exp(0.89238310459026989), phi = exp(1.6622042309903930) ) fitted_values <- rep( c( 0.84575428432937011, 0.84573608713048233, 0.73789083646643889, 0.47593010582855891, 0.31155933858113756, 0.22406801104864969, 0.079774485527624186, 0.079195048422139125 ), k ) residuals <- c( 0.0069457156706298950, -0.088654284329370105, 0.091245715670629895, -0.018236087130482331, -0.067936087130482331, 0.038863912869517669, -0.18179083646643889, -0.033090836466438890, 0.069369894171441088, 0.010069894171441088, 0.059169894171441088, -0.036030105828558912, 0.043740661418862440, 0.0016406614188624399, 0.038340661418862440, -0.081968011048649687, -0.062974485527624186, 0.058825514472375814, 0.043504951577860875 ) object <- loggompertz_new( x, y, w, NULL, max_iter, c(0.5, -1, 1, 3), c(1, -0.5, 5, 12) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$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$weights, w) # initial values within the boundaries object <- loggompertz_new( x, y, w, c(0.6, -0.6, 4, 8), max_iter, c(0.5, -1, 1, 3), c(1, -0.5, 5, 12) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$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$weights, w) # initial values outside the boundaries object <- loggompertz_new( x, y, w, c(-2, 2, 7, 1), max_iter, c(0.5, -1, 1, 3), c(1, -0.5, 5, 12) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$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$weights, w) }) test_that("fit_constrained (weighted): equalities", { x <- lltd$D$x y <- lltd$D$y w <- lltd$D$w n <- length(y) k <- as.numeric(table(x)) max_iter <- 10000 estimated <- c(alpha = FALSE, delta = FALSE, eta = TRUE, phi = TRUE) rss_value <- 0.12152790634234742 theta <- c( alpha = 0.8, delta = -0.9, eta = exp(0.67344700327430744), phi = exp(1.8267797417585254) ) fitted_values <- rep( c( 0.8, 0.79991222146934487, 0.71604576658544182, 0.49162778848529489, 0.31063536742142226, 0.19268868846616760, -0.096135387777275743, -0.099957631352575174 ), k ) residuals <- c( 0.0527, -0.0429, 0.137, 0.027587778530655130, -0.022112221469344870, 0.084687778530655130, -0.15994576658544182, -0.011245766585441821, 0.053672211514705107, -0.0056277884852948934, 0.043472211514705107, -0.051727788485294893, 0.044664632578577739, 0.0025646325785777394, 0.039264632578577739, -0.050588688466167597, 0.11293538777727574, 0.23473538777727574, 0.22265763135257517 ) object <- loggompertz_new( x, y, w, NULL, max_iter, c(0.8, -0.9, rep(-Inf, 2)), c(0.8, -0.9, rep(Inf, 2)) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 2) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values with same equalities object <- loggompertz_new( x, y, w, c(0.8, -0.9, 1, 1), max_iter, c(0.8, -0.9, rep(-Inf, 2)), c(0.8, -0.9, rep(Inf, 2)) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 2) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values with different equalities object <- loggompertz_new( x, y, w, c(0, 1, 1, 1), max_iter, c(0.8, -0.9, rep(-Inf, 2)), c(0.8, -0.9, rep(Inf, 2)) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_false(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 2) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) }) test_that("fit_constrained (weighted): equalities and inequalities", { x <- lltd$D$x y <- lltd$D$y w <- lltd$D$w n <- length(y) k <- as.numeric(table(x)) max_iter <- 10000 estimated <- c(alpha = FALSE, delta = FALSE, eta = TRUE, phi = TRUE) rss_value <- 0.12152790634234742 theta <- c( alpha = 0.8, delta = -0.9, eta = exp(0.67344700327430744), phi = exp(1.8267797417585254) ) fitted_values <- rep( c( 0.8, 0.79991222146934487, 0.71604576658544182, 0.49162778848529489, 0.31063536742142226, 0.19268868846616760, -0.096135387777275743, -0.099957631352575174 ), k ) residuals <- c( 0.0527, -0.0429, 0.137, 0.027587778530655130, -0.022112221469344870, 0.084687778530655130, -0.15994576658544182, -0.011245766585441821, 0.053672211514705107, -0.0056277884852948934, 0.043472211514705107, -0.051727788485294893, 0.044664632578577739, 0.0025646325785777394, 0.039264632578577739, -0.050588688466167597, 0.11293538777727574, 0.23473538777727574, 0.22265763135257517 ) object <- loggompertz_new( x, y, w, NULL, max_iter, c(0.8, -0.9, 1, 3), c(0.8, -0.9, 5, 12) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 2) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values within the boundaries object <- loggompertz_new( x, y, w, c(0.8, -0.9, 3, 7), max_iter, c(0.8, -0.9, 1, 3), c(0.8, -0.9, 5, 12) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 2) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) # initial values outside the boundaries object <- loggompertz_new( x, y, w, c(0, 1, 8, 1), max_iter, c(0.8, -0.9, 1, 3), c(0.8, -0.9, 5, 12) ) result <- fit_constrained(object) expect_true(inherits(result, "loggompertz_fit")) expect_true(inherits(result, "loglogistic")) expect_true(result$converged) expect_true(result$constrained) expect_equal(result$estimated, estimated) expect_equal(result$coefficients, theta, tolerance = 1.0e-6) expect_equal(result$rss, rss_value) expect_equal(result$df.residual, object$n - 2) expect_equal(result$fitted.values, fitted_values, tolerance = 1.0e-6) expect_equal(result$residuals, residuals, tolerance = 1.0e-6) expect_equal(result$weights, w) }) test_that("fisher_info", { x <- lltd$D$x y <- lltd$D$y w <- lltd$D$w max_iter <- 10000 theta <- lltd$theta_g names(theta) <- c("alpha", "delta", "eta", "phi") sigma <- lltd$sigma true_value <- matrix(c( # alpha 6206.96, 2748.9449629599373, -189.18362192800753, 344.04436069543435, -28355.127259362132, # delta 2748.9449629599373, 2023.9485432497464, -124.69711327516109, 134.06347723771206, -10502.299351663864, # eta -189.18362192800753, -124.69711327516109, 23.773250144905426, -11.783571918074014, 850.51618712697142, # phi 344.04436069543435, 134.06347723771206, -11.783571918074014, 29.686894742510176, -1441.3142462178932, # sigma -28355.127259362132, -10502.299351663864, 850.51618712697142, -1441.3142462178932, 113909.14953385276 ), nrow = 5, ncol = 5 ) rownames(true_value) <- colnames(true_value) <- c( "alpha", "delta", "eta", "phi", "sigma" ) object <- loggompertz_new(x, y, w, NULL, max_iter, NULL, NULL) fim <- fisher_info(object, theta, sigma) expect_type(fim, "double") expect_length(fim, 5 * 5) expect_equal(fim, true_value) }) test_that("drda: 'lower_bound' argument errors", { x <- lltd$D$x y <- lltd$D$y expect_error( drda( y ~ x, mean_function = "loggompertz", lower_bound = c("a", "b", "c", "d") ), "'lower_bound' must be a numeric vector" ) expect_error( drda( y ~ x, mean_function = "loggompertz", lower_bound = matrix(-Inf, nrow = 4, ncol = 2), upper_bound = rep(Inf, 4) ), "'lower_bound' must be a numeric vector" ) expect_error( drda( y ~ x, mean_function = "loggompertz", lower_bound = rep(-Inf, 5), upper_bound = rep(Inf, 4) ), "'lower_bound' and 'upper_bound' must have the same length" ) expect_error( drda( y ~ x, mean_function = "loggompertz", lower_bound = c( 0, -Inf, -Inf, -Inf), upper_bound = c(-1, Inf, Inf, Inf) ), "'lower_bound' cannot be larger than 'upper_bound'" ) expect_error( drda( y ~ x, mean_function = "loggompertz", lower_bound = c(Inf, -Inf, -Inf, -Inf), upper_bound = c(Inf, Inf, Inf, Inf) ), "'lower_bound' cannot be equal to infinity" ) expect_error( drda( y ~ x, mean_function = "loggompertz", lower_bound = rep(-Inf, 5), upper_bound = rep(Inf, 5) ), "'lower_bound' must be of length 4" ) }) test_that("drda: 'upper_bound' argument errors", { x <- lltd$D$x y <- lltd$D$y expect_error( drda( y ~ x, mean_function = "loggompertz", upper_bound = c("a", "b", "c", "d") ), "'upper_bound' must be a numeric vector" ) expect_error( drda( y ~ x, mean_function = "loggompertz", lower_bound = rep(-Inf, 4), upper_bound = matrix(Inf, nrow = 4, ncol = 2) ), "'upper_bound' must be a numeric vector" ) expect_error( drda( y ~ x, mean_function = "loggompertz", lower_bound = c(-Inf, -Inf, -Inf, -Inf), upper_bound = c(-Inf, Inf, Inf, Inf) ), "'upper_bound' cannot be equal to -infinity" ) expect_error( drda( y ~ x, mean_function = "loggompertz", lower_bound = rep(-Inf, 5), upper_bound = rep(Inf, 5) ), "'lower_bound' must be of length 4" ) }) test_that("drda: 'start' argument errors", { x <- lltd$D$x y <- lltd$D$y expect_error( drda( y ~ x, mean_function = "loggompertz", start = c("a", "b", "c", "d") ), "'start' must be a numeric vector" ) expect_error( drda( y ~ x, mean_function = "loggompertz", start = c(0, Inf, 1, 1) ), "'start' must be finite" ) expect_error( drda( y ~ x, mean_function = "loggompertz", start = c(-Inf, 1, 1, 1) ), "'start' must be finite" ) expect_error( drda( y ~ x, mean_function = "loggompertz", start = rep(1, 5) ), "'start' must be of length 4" ) expect_error( drda( y ~ x, mean_function = "loggompertz", start = c(0, 1, -1, 1) ), "parameter 'eta' cannot be negative nor zero" ) expect_error( drda( y ~ x, mean_function = "loggompertz", start = c(0, 1, 0, 1) ), "parameter 'eta' cannot be negative nor zero" ) expect_error( drda( y ~ x, mean_function = "loggompertz", start = c(0, 1, 1, -1) ), "parameter 'phi' cannot be negative nor zero" ) expect_error( drda( y ~ x, mean_function = "loggompertz", start = c(0, 1, 1, 0) ), "parameter 'phi' cannot be negative nor zero" ) }) test_that("nauc: decreasing", { x <- lltd$D$x y <- lltd$D$y w <- lltd$D$w result <- drda(y ~ x, weights = w, mean_function = "loggompertz") expect_equal(nauc(result), 0.085299967613769906, tolerance = 1.0e-6) expect_equal(nauc(result, xlim = c(0, 2)), 0.84575366076886644) expect_equal(nauc(result, ylim = c(0.3, 0.7)), 0.0059283502711447546) expect_equal(nauc(result, xlim = c(0, 2), ylim = c(0.3, 0.7)), 1.0) expect_equal( nauc(result, xlim = c(5, 8), ylim = c(0.3, 0.7)), 0.33844687600885550 ) expect_equal(nauc(result, xlim = c(10, 15), ylim = c(0.3, 0.7)), 0.0) }) test_that("naac: decreasing", { x <- lltd$D$x y <- lltd$D$y w <- lltd$D$w result <- drda(y ~ x, weights = w, mean_function = "loggompertz") expect_equal(naac(result), 1 - 0.085299967613769906) expect_equal(naac(result, xlim = c(0, 2)), 1 - 0.84575366076886644) expect_equal(naac(result, ylim = c(0.3, 0.7)), 1 - 0.0059283502711447546) expect_equal(naac(result, xlim = c(0, 2), ylim = c(0.3, 0.7)), 0.0) expect_equal( naac(result, xlim = c(5, 8), ylim = c(0.3, 0.7)), 1 - 0.33844687600885550 ) expect_equal(naac(result, xlim = c(10, 15), ylim = c(0.3, 0.7)), 1.0) }) test_that("nauc: increasing", { x <- lltd$D$x y <- rev(lltd$D$y) w <- lltd$D$w result <- drda(y ~ x, weights = w, mean_function = "loggompertz") expect_equal(nauc(result), 0.88478280795251264) expect_equal(nauc(result, xlim = c(0, 2)), 0.129049490857619206) expect_equal(nauc(result, ylim = c(0.3, 0.7)), 0.99551714173529925) expect_equal(nauc(result, xlim = c(0, 2), ylim = c(0.3, 0.7)), 0.0) expect_equal( nauc(result, xlim = c(5, 8), ylim = c(0.3, 0.7)), 0.85655631688941921 ) expect_equal(nauc(result, xlim = c(9, 12), ylim = c(0.3, 0.7)), 1.0) }) test_that("naac: increasing", { x <- lltd$D$x y <- rev(lltd$D$y) w <- lltd$D$w result <- drda(y ~ x, weights = w, mean_function = "loggompertz") expect_equal(naac(result), 1 - 0.88478280795251264) expect_equal(naac(result, xlim = c(0, 2)), 1 - 0.129049490857619206) expect_equal(naac(result, ylim = c(0.3, 0.7)), 1 - 0.99551714173529925) expect_equal(naac(result, xlim = c(0, 2), ylim = c(0.3, 0.7)), 1.0) expect_equal( naac(result, xlim = c(5, 8), ylim = c(0.3, 0.7)), 1 - 0.85655631688941921 ) expect_equal(naac(result, xlim = c(9, 12), ylim = c(0.3, 0.7)), 0.0) })