diff options
| -rw-r--r-- | test.log | 45 | ||||
| -rw-r--r-- | tests/testthat/print_sfo_saem_1.txt (renamed from tests/testthat/print_sfo_saemix_1.txt) | 2 | ||||
| -rw-r--r-- | tests/testthat/test_mixed.R | 2 | ||||
| -rw-r--r-- | tests/testthat/test_plot.R | 6 |
4 files changed, 11 insertions, 44 deletions
@@ -6,7 +6,7 @@ Testing mkin ✔ | 2 | Export dataset for reading into CAKE ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.0 s] ✔ | 4 | Calculation of FOCUS chi2 error levels [0.5 s] -✔ | 7 | Fitting the SFORB model [3.6 s] +✔ | 7 | Fitting the SFORB model [3.5 s] ✔ | 5 | Analytical solutions for coupled models [3.2 s] ✔ | 5 | Calculation of Akaike weights ✔ | 14 | Confidence intervals and p-values [1.2 s] @@ -14,33 +14,7 @@ Testing mkin ✔ | 3 | Time step normalisation ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s] ✔ | 1 | Fitting the logistic model [0.2 s] -⠏ | 8 2 | Nonlinear mixed effects models -LL by is "-1333.17 (df=13)" - -LL by is "-1333.17 (df=13)" - -LL by is "-1336.30 (df=13)" -
✖ | 11 2 | Nonlinear mixed effects models [6.4 s] -──────────────────────────────────────────────────────────────────────────────── -ERROR (test_mixed.R:11:3): Parent only models can be fitted using nonlinear mixed effects models -Error: object 'sfo_saem_1' not found -Backtrace: - 1. base::summary(sfo_saem_1) test_mixed.R:11:2 - -FAILURE (test_mixed.R:91:3): Print methods work -Results have changed from known value recorded in 'print_sfo_saemix_1.txt'. - -old[6:11] vs new[6:13] - "Data:" - "264 observations of 1 variable(s) grouped in 15 datasets" - "" - "Likelihood computed by importance sampling" -+ " " -+ "LL by is \"-653.97 (df=6)\"" - " AIC BIC logLik" - " 1320 1324 -654" - "" -──────────────────────────────────────────────────────────────────────────────── +✔ | 31 | Nonlinear mixed effects models [27.5 s] ✔ | 2 | Test dataset classes mkinds and mkindsg ✔ | 1 | mkinfit features [0.3 s] ✔ | 12 | Special cases of mkinfit calls [0.8 s] @@ -48,21 +22,16 @@ old[6:11] vs new[6:13] ✔ | 3 | Model predictions with mkinpredict [0.4 s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6 s] ✔ | 9 | Nonlinear mixed-effects models [7.8 s] -✖ | 15 1 | Plotting [1.9 s] -──────────────────────────────────────────────────────────────────────────────── -FAILURE (test_plot.R:39:3): Plotting mkinfit and mmkin objects is reproducible -Figures don't match: mixed-model-fit-for-nlme-object.svg - -──────────────────────────────────────────────────────────────────────────────── +✔ | 16 | Plotting [1.9 s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6 s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s] ✔ | 4 | Summary [0.1 s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s] ✔ | 9 | Hypothesis tests [7.3 s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 48.1 s +Duration: 69.3 s -[ FAIL 3 | WARN 0 | SKIP 0 | PASS 183 ] +[ FAIL 0 | WARN 0 | SKIP 0 | PASS 204 ] diff --git a/tests/testthat/print_sfo_saemix_1.txt b/tests/testthat/print_sfo_saem_1.txt index 9dd4f175..d341e9e7 100644 --- a/tests/testthat/print_sfo_saemix_1.txt +++ b/tests/testthat/print_sfo_saem_1.txt @@ -6,8 +6,6 @@ Data: 264 observations of 1 variable(s) grouped in 15 datasets Likelihood computed by importance sampling - -LL by is "-653.97 (df=6)" AIC BIC logLik 1320 1324 -654 diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index 6fc6c2f0..7798be8a 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -88,7 +88,7 @@ test_that("Print methods work", { expect_known_output(print(fits, digits = 2), "print_mmkin_parent.txt") expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt") expect_known_output(print(nlme_biphasic, digits = 1), "print_nlme_biphasic.txt") - expect_known_output(print(sfo_saemix_1, digits = 1), "print_sfo_saemix_1.txt") + expect_known_output(print(sfo_saem_1, digits = 1), "print_sfo_saem_1.txt") }) test_that("nlme results are reproducible", { diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R index b0bf2c8f..22f4307f 100644 --- a/tests/testthat/test_plot.R +++ b/tests/testthat/test_plot.R @@ -35,14 +35,14 @@ test_that("Plotting mkinfit and mmkin objects is reproducible", { plot_biphasic_mmkin <- function() plot(f_uba_dfop_sfo_mixed) vdiffr::expect_doppelganger("mixed model fit for mmkin object", plot_biphasic_mmkin) - plot_biphasic_nlme <- function() plot(dfop_nlme_1) - vdiffr::expect_doppelganger("mixed model fit for nlme object", plot_biphasic_nlme) - plot_biphasic_saem_s <- function() plot(f_uba_dfop_sfo_saem) vdiffr::expect_doppelganger("mixed model fit for saem object with saemix transformations", plot_biphasic_saem_s) skip_on_travis() + plot_biphasic_nlme <- function() plot(dfop_nlme_1) + vdiffr::expect_doppelganger("mixed model fit for nlme object", plot_biphasic_nlme) + #plot_biphasic_mmkin <- function() plot(mixed(mmkin_biphasic)) # Biphasic fits with lots of data and fits have lots of potential for differences plot_biphasic_nlme <- function() plot(nlme_biphasic) |