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-rw-r--r--log/test.log32
-rw-r--r--log/test_dev.log114
-rw-r--r--tests/testthat/test_mixed.R3
3 files changed, 112 insertions, 37 deletions
diff --git a/log/test.log b/log/test.log
index 897bf896..0b9aa7eb 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,11 +1,11 @@
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [3.5s]
+✔ | 5 | Analytical solutions for coupled models [3.3s]
✔ | 5 | Calculation of Akaike weights
✔ | 3 | Export dataset for reading into CAKE
-✔ | 12 | Confidence intervals and p-values [1.2s]
-✔ | 1 12 | Dimethenamid data from 2018 [33.2s]
+✔ | 12 | Confidence intervals and p-values [1.1s]
+✔ | 1 12 | Dimethenamid data from 2018 [33.3s]
────────────────────────────────────────────────────────────────────────────────
Skip ('test_dmta.R:98'): Different backends get consistent results for SFO-SFO3+, dimethenamid data
Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
@@ -14,40 +14,40 @@ Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
✔ | 5 | Time step normalisation
✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s]
✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
-✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s]
-✔ | 1 | Fitting the logistic model [0.2s]
-✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [24.7s]
-✔ | 1 11 | Nonlinear mixed-effects models [13.1s]
+✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s]
+✔ | 1 | Fitting the logistic model [0.3s]
+✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [25.5s]
+✔ | 1 11 | Nonlinear mixed-effects models [13.2s]
────────────────────────────────────────────────────────────────────────────────
-Skip ('test_mixed.R:77'): saemix results are reproducible for biphasic fits
+Skip ('test_mixed.R:78'): saemix results are reproducible for biphasic fits
Reason: Fitting with saemix takes around 10 minutes when using deSolve
────────────────────────────────────────────────────────────────────────────────
✔ | 3 | Test dataset classes mkinds and mkindsg
-✔ | 10 | Special cases of mkinfit calls [0.4s]
+✔ | 10 | Special cases of mkinfit calls [0.5s]
✔ | 3 | mkinfit features [0.7s]
✔ | 8 | mkinmod model generation and printing [0.2s]
✔ | 3 | Model predictions with mkinpredict [0.3s]
-✔ | 12 | Multistart method for saem.mmkin models [49.5s]
+✔ | 12 | Multistart method for saem.mmkin models [51.1s]
✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [8.8s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [9.2s]
✔ | 15 | Plotting [10.3s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 1 36 | saemix parent models [72.5s]
+✔ | 1 36 | saemix parent models [73.7s]
────────────────────────────────────────────────────────────────────────────────
Skip ('test_saemix_parent.R:143'): We can also use mkin solution methods for saem
Reason: This still takes almost 2.5 minutes although we do not solve ODEs
────────────────────────────────────────────────────────────────────────────────
-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s]
✔ | 11 | Processing of residue series
✔ | 10 | Fitting the SFORB model [3.8s]
✔ | 1 | Summaries of old mkinfit objects
✔ | 5 | Summary [0.2s]
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
-✔ | 9 | Hypothesis tests [8.2s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.4s]
+✔ | 9 | Hypothesis tests [8.8s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 246.1 s
+Duration: 251.2 s
── Skipped tests ──────────────────────────────────────────────────────────────
• Fitting this ODE model with saemix takes about 15 minutes on my system (1)
diff --git a/log/test_dev.log b/log/test_dev.log
index 527d28ed..1612e32d 100644
--- a/log/test_dev.log
+++ b/log/test_dev.log
@@ -1,57 +1,131 @@
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [3.2s]
+✔ | 5 | Analytical solutions for coupled models [3.3s]
✔ | 5 | Calculation of Akaike weights
✔ | 3 | Export dataset for reading into CAKE
-✔ | 12 | Confidence intervals and p-values [1.0s]
-✔ | 1 12 | Dimethenamid data from 2018 [31.3s]
+✔ | 12 | Confidence intervals and p-values [1.1s]
+✔ | 1 12 | Dimethenamid data from 2018 [33.8s]
────────────────────────────────────────────────────────────────────────────────
Skip ('test_dmta.R:98'): Different backends get consistent results for SFO-SFO3+, dimethenamid data
Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
────────────────────────────────────────────────────────────────────────────────
-✔ | 14 | Error model fitting [5.2s]
+✔ | 14 | Error model fitting [5.7s]
✔ | 5 | Time step normalisation
✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s]
✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
-✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s]
+✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s]
✔ | 1 | Fitting the logistic model [0.2s]
-✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [23.5s]
-✔ | 1 12 | Nonlinear mixed-effects models [0.3s]
+✖ | 1 9 | Batch fitting and diagnosing hierarchical kinetic models [25.5s]
────────────────────────────────────────────────────────────────────────────────
-Skip ('test_mixed.R:74'): saemix results are reproducible for biphasic fits
+Failure ('test_mhmkin.R:55'): Multiple hierarchical kinetic models can be fitted and diagnosed
+Results have changed from known value recorded in 'illparms_hfits_synth_no_ranef_auto.txt'.
+
+ old | new
+[1] " error" | " error" [1]
+[2] "degradation const tc " | "degradation const tc " [2]
+[3] " SFO sd(parent_0)" | " SFO sd(parent_0)" [3]
+[4] " FOMC b.1 " - " FOMC " [4]
+────────────────────────────────────────────────────────────────────────────────
+✖ | 1 1 10 | Nonlinear mixed-effects models [13.4s]
+────────────────────────────────────────────────────────────────────────────────
+Failure ('test_mixed.R:20'): Print methods work
+Results have changed from known value recorded in 'print_dfop_saem_1.txt'.
+
+old[13:23] vs new[13:23]
+ ""
+ "Fitted parameters:"
+ " estimate lower upper"
+- "parent_0 99.92 98.77 101.06"
++ "parent_0 99.96 98.82 101.11"
+- "log_k1 -2.72 -2.95 -2.50"
++ "log_k1 -2.71 -2.94 -2.49"
+- "log_k2 -4.14 -4.27 -4.01"
++ "log_k2 -4.14 -4.26 -4.01"
+- "g_qlogis -0.35 -0.53 -0.16"
++ "g_qlogis -0.36 -0.54 -0.17"
+- "a.1 0.92 0.68 1.16"
++ "a.1 0.93 0.69 1.17"
+ "b.1 0.05 0.04 0.06"
+ "SD.log_k1 0.37 0.23 0.51"
+and 1 more ...
+
+Skip ('test_mixed.R:77'): saemix results are reproducible for biphasic fits
Reason: Fitting with saemix takes around 10 minutes when using deSolve
────────────────────────────────────────────────────────────────────────────────
✔ | 3 | Test dataset classes mkinds and mkindsg
✔ | 10 | Special cases of mkinfit calls [0.5s]
-✔ | 3 | mkinfit features [0.7s]
+✔ | 3 | mkinfit features [0.8s]
✔ | 8 | mkinmod model generation and printing [0.2s]
✔ | 3 | Model predictions with mkinpredict [0.3s]
-✔ | 9 | Multistart method for saem.mmkin models [35.2s]
+✖ | 4 8 | Multistart method for saem.mmkin models [53.5s]
+────────────────────────────────────────────────────────────────────────────────
+Failure ('test_multistart.R:44'): multistart works for saem.mmkin models
+Snapshot of `testcase` to 'multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg' has changed
+Run `testthat::snapshot_review('multistart/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger(...)
+ at test_multistart.R:44:2
+ 3. testthat::expect_snapshot_file(...)
+
+Failure ('test_multistart.R:49'): multistart works for saem.mmkin models
+Snapshot of `testcase` to 'multistart/parplot-for-sfo-fit.svg' has changed
+Run `testthat::snapshot_review('multistart/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger("parplot for sfo fit", parplot_sfo)
+ at test_multistart.R:49:2
+ 3. testthat::expect_snapshot_file(...)
+
+Failure ('test_multistart.R:55'): multistart works for saem.mmkin models
+Snapshot of `testcase` to 'multistart/llhist-for-dfop-sfo-fit.svg' has changed
+Run `testthat::snapshot_review('multistart/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger("llhist for dfop sfo fit", llhist_dfop_sfo)
+ at test_multistart.R:55:2
+ 3. testthat::expect_snapshot_file(...)
+
+Failure ('test_multistart.R:56'): multistart works for saem.mmkin models
+Snapshot of `testcase` to 'multistart/parplot-for-dfop-sfo-fit.svg' has changed
+Run `testthat::snapshot_review('multistart/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo)
+ at test_multistart.R:56:2
+ 3. testthat::expect_snapshot_file(...)
+────────────────────────────────────────────────────────────────────────────────
✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.5s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [8.3s]
-✔ | 16 | Plotting [10.0s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [9.2s]
+✖ | 1 14 | Plotting [10.5s]
+────────────────────────────────────────────────────────────────────────────────
+Failure ('test_plot.R:55'): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Snapshot of `testcase` to 'plot/mixed-model-fit-for-nlme-object.svg' has changed
+Run `testthat::snapshot_review('plot/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger(...)
+ at test_plot.R:55:2
+ 3. testthat::expect_snapshot_file(...)
+────────────────────────────────────────────────────────────────────────────────
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 1 36 | saemix parent models [63.3s]
+✔ | 1 36 | saemix parent models [74.3s]
────────────────────────────────────────────────────────────────────────────────
Skip ('test_saemix_parent.R:143'): We can also use mkin solution methods for saem
Reason: This still takes almost 2.5 minutes although we do not solve ODEs
────────────────────────────────────────────────────────────────────────────────
-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.3s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s]
✔ | 11 | Processing of residue series
-✔ | 10 | Fitting the SFORB model [3.5s]
+✔ | 10 | Fitting the SFORB model [3.9s]
✔ | 1 | Summaries of old mkinfit objects
✔ | 5 | Summary [0.2s]
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s]
-✔ | 9 | Hypothesis tests [7.5s]
-✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.4s]
+✔ | 9 | Hypothesis tests [8.8s]
+✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.1s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 204.4 s
+Duration: 256.2 s
── Skipped tests ──────────────────────────────────────────────────────────────
• Fitting this ODE model with saemix takes about 15 minutes on my system (1)
• Fitting with saemix takes around 10 minutes when using deSolve (1)
• This still takes almost 2.5 minutes although we do not solve ODEs (1)
-[ FAIL 0 | WARN 0 | SKIP 3 | PASS 269 ]
+[ FAIL 7 | WARN 0 | SKIP 3 | PASS 263 ]
+Error while shutting down parallel: unable to terminate some child processes
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index 8c257738..39a332f5 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -16,7 +16,8 @@ test_that("Print methods work", {
expect_known_output(print(sfo_saem_1_reduced, digits = 1), "print_sfo_saem_1_reduced.txt")
skip_on_cran() # The following test is platform dependent and fails on
- # win-builder with current (18 Nov 2022) R-devel and on the Fedora CRAN check systems
+ # win-builder with current (18 Nov 2022) R-devel, on the Linux R-devel CRAN check systems
+ # and also using R-devel locally
expect_known_output(print(dfop_saem_1, digits = 1), "print_dfop_saem_1.txt")
})

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