From 5ec8e1bad1aa7d79ee9c19bdd50be07f81a14278 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2022 22:11:02 +0100 Subject: Move two saem fits from setup script to skipped tests Save winbuilder/CRAN check time... --- ...t-for-saem-object-with-mkin-transformations.svg | 2502 ++++++++++++++++++++ ...t-for-saem-object-with-mkin-transformations.svg | 2502 -------------------- tests/testthat/setup_script.R | 3 - tests/testthat/test_mixed.R | 8 +- tests/testthat/test_multistart.R | 15 + tests/testthat/test_plot.R | 4 - 6 files changed, 2520 insertions(+), 2514 deletions(-) create mode 100644 tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg delete mode 100644 tests/testthat/_snaps/plot/mixed-model-fit-for-saem-object-with-mkin-transformations.svg (limited to 'tests') diff --git a/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg b/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg new file mode 100644 index 00000000..69fa6a4d --- /dev/null +++ b/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg @@ -0,0 +1,2502 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Population +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 + + + + + + + + + + + + + + + + + +0 +20 +40 +60 +80 +100 +120 + + + + + + + +0 +20 +40 +60 +80 +100 + + + + + + + + +Time +Residues parent + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index 2448886d..4e2f76ab 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -109,7 +109,4 @@ sfo_saem_1_reduced <- update(sfo_saem_1, no_random_effect = "parent_0") dfop_saem_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin", no_random_effect = c("parent_0", "g_qlogis")) -saem_dfop_sfo_m <- saem(mmkin_dfop_sfo, transformations = "mkin", quiet = TRUE) -saem_dfop_sfo_s <- saem(mmkin_dfop_sfo, transformations = "saemix", quiet = TRUE) - parallel::stopCluster(cl) diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index ab8dfc27..8c257738 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -46,6 +46,9 @@ test_that("nlme results are reproducible to some degree", { test_that("saemix results are reproducible for biphasic fits", { + skip_on_cran() + saem_dfop_sfo_s <- saem(mmkin_dfop_sfo, transformations = "saemix", quiet = TRUE) + test_summary <- summary(saem_dfop_sfo_s) test_summary$saemixversion <- "Dummy 0.0 for testing" test_summary$mkinversion <- "Dummy 0.0 for testing" @@ -65,11 +68,6 @@ test_that("saemix results are reproducible for biphasic fits", { expect_true(all(ci_dfop_sfo_s_s[, "lower"] < dfop_sfo_pop)) expect_true(all(ci_dfop_sfo_s_s[, "upper"] > dfop_sfo_pop)) - # k2 is not fitted well - ci_dfop_sfo_s_m <- summary(saem_dfop_sfo_m)$confint_back - expect_true(all(ci_dfop_sfo_s_m[no_k2, "lower"] < dfop_sfo_pop[no_k2])) - expect_true(all(ci_dfop_sfo_s_m[no_k1, "upper"] > dfop_sfo_pop[no_k1])) - # I tried to only do few iterations in routine tests as this is so slow # but then deSolve fails at some point (presumably at the switch between # the two types of iterations) diff --git a/tests/testthat/test_multistart.R b/tests/testthat/test_multistart.R index 3a511e06..91ef71f0 100644 --- a/tests/testthat/test_multistart.R +++ b/tests/testthat/test_multistart.R @@ -4,6 +4,7 @@ test_that("multistart works for saem.mmkin models", { skip_on_cran() # Save CRAN time set.seed(123456) saem_sfo_s_multi <- multistart(sfo_saem_1_reduced, n = 8, cores = n_cores) + anova_sfo <- anova(sfo_saem_1, sfo_saem_1_reduced, best(saem_sfo_s_multi), @@ -13,6 +14,17 @@ test_that("multistart works for saem.mmkin models", { expect_equal(round(anova_sfo, 1)["best(saem_sfo_s_multi)", "AIC"], 1302.2) expect_true(anova_sfo[3, "Pr(>Chisq)"] > 0.2) # Local: 1, win-builder: 0.4 + saem_dfop_sfo_m <- saem(mmkin_dfop_sfo, transformations = "mkin", quiet = TRUE) + dfop_sfo_pop <- attr(ds_dfop_sfo, "pop") + + # k2 is not fitted well (compare saem_dfop_sfo_s in test_mixed.R) + ci_dfop_sfo_s_m <- summary(saem_dfop_sfo_m)$confint_back + no_k1 <- c(1, 2, 3, 5, 6) + no_k2 <- c(1, 2, 3, 4, 6) + expect_true(all(ci_dfop_sfo_s_m[no_k2, "lower"] < dfop_sfo_pop[no_k2])) + expect_true(all(ci_dfop_sfo_s_m[no_k1, "upper"] > dfop_sfo_pop[no_k1])) + + set.seed(123456) saem_dfop_sfo_m_multi <- multistart(saem_dfop_sfo_m, n = 8, cores = n_cores) @@ -28,6 +40,9 @@ test_that("multistart works for saem.mmkin models", { tolerance = 1e-4) skip_on_travis() # Plots are platform dependent + plot_dfop_sfo_saem_m <- function() plot(saem_dfop_sfo_m) + vdiffr::expect_doppelganger("mixed model fit for saem object with mkin transformations", plot_dfop_sfo_saem_m) + llhist_sfo <- function() llhist(saem_sfo_s_multi) parplot_sfo <- function() parplot(saem_sfo_s_multi, ylim = c(0.5, 2)) vdiffr::expect_doppelganger("llhist for sfo fit", llhist_sfo) diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R index 01b0c1ee..f5da5982 100644 --- a/tests/testthat/test_plot.R +++ b/tests/testthat/test_plot.R @@ -41,7 +41,6 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", { f_uba_mmkin <- mmkin(list("DFOP-SFO" = dfop_sfo_uba), ds_uba, quiet = TRUE, cores = n_cores) f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin["DFOP-SFO", ]) - f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix") plot_dfop_sfo_mmkin <- function() plot(f_uba_dfop_sfo_mixed, pop_curve = TRUE) @@ -59,9 +58,6 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", { # Biphasic fits with lots of data and fits have lots of potential for differences plot_dfop_sfo_nlme <- function() plot(nlme_dfop_sfo) #plot_dfop_sfo_saem_s <- function() plot(saem_dfop_sfo_s) - plot_dfop_sfo_saem_m <- function() plot(saem_dfop_sfo_m) - - vdiffr::expect_doppelganger("mixed model fit for saem object with mkin transformations", plot_dfop_sfo_saem_m) # different results when working with eigenvalues plot_errmod_fit_D_obs_eigen <- function() plot_err(fit_D_obs_eigen, sep_obs = FALSE) -- cgit v1.2.1