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-rw-r--r--log/test.log139
-rw-r--r--tests/testthat/test_dmta.R7
2 files changed, 108 insertions, 38 deletions
diff --git a/log/test.log b/log/test.log
index c872cb1d..6d5bc470 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,50 +1,117 @@
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [3.1s]
+✔ | 5 | Analytical solutions for coupled models [1.5s]
✔ | 5 | Calculation of Akaike weights
✔ | 3 | Export dataset for reading into CAKE
-✔ | 6 | Use of precompiled symbols in mkinpredict [5.3s]
-✔ | 12 | Confidence intervals and p-values
-✔ | 1 12 | Dimethenamid data from 2018 [31.5s]
-✔ | 14 | Error model fitting [5.6s]
+✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s]
+✔ | 12 | Confidence intervals and p-values [0.4s]
+✔ | 1 12 | Dimethenamid data from 2018 [13.2s]
+────────────────────────────────────────────────────────────────────────────────
+Skip ('test_dmta.R:88:3'): Different backends get consistent results for SFO-SFO3+, dimethenamid data
+Reason: Fitting this ODE model with saemix takes about 5 minutes on my new system
+────────────────────────────────────────────────────────────────────────────────
+✔ | 14 | Error model fitting [2.5s]
✔ | 5 | Time step normalisation
-✔ | 4 | Calculation of FOCUS chi2 error levels
-✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
-✔ | 4 | Test fitting the decline of metabolites from their maximum
-✔ | 1 | Fitting the logistic model
-✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [43.1s]
-✔ | 2 16 | Nonlinear mixed-effects models [441.3s]
+✔ | 4 | Calculation of FOCUS chi2 error levels [0.3s]
+✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.4s]
+✔ | 4 | Test fitting the decline of metabolites from their maximum [0.2s]
+✔ | 1 | Fitting the logistic model [0.1s]
+✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.0s]
+✖ | 1 2 15 | Nonlinear mixed-effects models [149.2s]
+────────────────────────────────────────────────────────────────────────────────
+Failure ('test_mixed.R:21:3'): 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:80:3'): saemix results are reproducible for biphasic fits
+Reason: Fitting with saemix takes around 10 minutes when using deSolve
+
+Skip ('test_mixed.R:133:3'): SFO-SFO saemix specific analytical solution work
+Reason: This is seldom used, so save some time
+────────────────────────────────────────────────────────────────────────────────
✔ | 3 | Test dataset classes mkinds and mkindsg
-✔ | 10 | Special cases of mkinfit calls
-✔ | 3 | mkinfit features
+✔ | 10 | Special cases of mkinfit calls [0.3s]
+✔ | 3 | mkinfit features [0.5s]
✔ | 8 | mkinmod model generation and printing
-✔ | 3 | Model predictions with mkinpredict
-✔ | 12 | Multistart method for saem.mmkin models [71.6s]
-✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.7s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [10.1s]
-✔ | 15 | Plotting [12.1s]
+✔ | 3 | Model predictions with mkinpredict [0.1s]
+✖ | 3 9 | Multistart method for saem.mmkin models [23.2s]
+────────────────────────────────────────────────────────────────────────────────
+Failure ('test_multistart.R:44:3'): 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:55:3'): 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:56:3'): 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 [1.6s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [3.8s]
+✖ | 1 14 | Plotting [4.7s]
+────────────────────────────────────────────────────────────────────────────────
+Failure ('test_plot.R:55:3'): 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 [81.8s]
-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s]
+✔ | 1 36 | saemix parent models [31.4s]
+────────────────────────────────────────────────────────────────────────────────
+Skip ('test_saemix_parent.R:143:3'): 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 [0.5s]
✔ | 11 | Processing of residue series
-✔ | 10 | Fitting the SFORB model [3.8s]
+✔ | 10 | Fitting the SFORB model [1.7s]
✔ | 1 | Summaries of old mkinfit objects
✔ | 5 | Summary
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s]
-✔ | 9 | Hypothesis tests [7.3s]
-✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [1.5s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s]
+✔ | 9 | Hypothesis tests [2.9s]
+✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 731.0 s
-
-── Skipped tests (4) ───────────────────────────────────────────────────────────
-• Fitting this ODE model with saemix takes about 15 minutes on my system (1):
- 'test_dmta.R:88:3'
-• Fitting with saemix takes around 10 minutes when using deSolve (1):
- 'test_mixed.R:80:3'
-• This is seldom used, so save some time (1): 'test_mixed.R:133:3'
-• This still takes almost 2.5 minutes although we do not solve ODEs (1):
- 'test_saemix_parent.R:143:3'
-
-[ FAIL 0 | WARN 0 | SKIP 4 | PASS 281 ]
+Duration: 262.6 s
+
+── Skipped tests ──────────────────────────────────────────────────────────────
+• Fitting this ODE model with saemix takes about 5 minutes on my new system (1)
+• Fitting with saemix takes around 10 minutes when using deSolve (1)
+• This is seldom used, so save some time (1)
+• This still takes almost 2.5 minutes although we do not solve ODEs (1)
+
+[ FAIL 5 | WARN 0 | SKIP 4 | PASS 276 ]
diff --git a/tests/testthat/test_dmta.R b/tests/testthat/test_dmta.R
index cd6de341..3941cae1 100644
--- a/tests/testthat/test_dmta.R
+++ b/tests/testthat/test_dmta.R
@@ -85,9 +85,12 @@ test_that("Different backends get consistent results for SFO-SFO3+, dimethenamid
"Iteration 5, LME step.*not converge")
ints_nlme_mets <- intervals(nlme_sfo_sfo3p_tc, which = "fixed")
- skip("Fitting this ODE model with saemix takes about 15 minutes on my system")
+ skip("Fitting this ODE model with saemix takes about 5 minutes on my new system")
+ # August 2023: Please refer to the mkin vignette for the currently
+ # recommended way to fit the DMTA pathway data with saemix
+
# As DFOP is overparameterised and leads to instabilities and errors, we
- # need to use SFO.
+ # need to use SFO with nlme
# saem_saemix_sfo_sfo3p_tc <- saem(dmta_sfo_sfo3p_tc)
# The fit above, using SFO for the parent leads to low values of DMTA_0
# (confidence interval from 84.4 to 92.8) which is not consistent with what

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