diff options
| -rw-r--r-- | log/build.log | 2 | ||||
| -rw-r--r-- | log/test.log | 36 | ||||
| -rw-r--r-- | tests/testthat/print_dfop_saemix_1.txt | 24 | ||||
| -rw-r--r-- | tests/testthat/test_mixed.R | 2 |
4 files changed, 44 insertions, 20 deletions
diff --git a/log/build.log b/log/build.log index 5ac21b0d..c4f9b8a2 100644 --- a/log/build.log +++ b/log/build.log @@ -5,5 +5,5 @@ * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories -* building ‘mkin_1.1.2.tar.gz’ +* building ‘mkin_1.2.0.tar.gz’ diff --git a/log/test.log b/log/test.log index 0e2ca6b2..b4298c40 100644 --- a/log/test.log +++ b/log/test.log @@ -1,38 +1,38 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.4s] +✔ | 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 [63.1s] +✔ | 1 12 | Dimethenamid data from 2018 [31.7s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_dmta.R:98:3): 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 [5.5s] +✔ | 14 | Error model fitting [5.0s] ✔ | 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 [0.4s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] ✔ | 1 | Fitting the logistic model [0.2s] -✔ | 7 | Batch fitting and diagnosing hierarchical kinetic models [28.6s] -✔ | 1 12 | Nonlinear mixed-effects models [0.6s] +✔ | 7 | Batch fitting and diagnosing hierarchical kinetic models [14.4s] +✔ | 1 12 | Nonlinear mixed-effects models [0.3s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_mixed.R:74:3): 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 [1.1s] -✔ | 3 | mkinfit features [1.7s] -✔ | 8 | mkinmod model generation and printing [0.4s] -✔ | 3 | Model predictions with mkinpredict [0.6s] -✔ | 7 | Multistart method for saem.mmkin models [93.9s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [7.0s] -✔ | 9 | Nonlinear mixed-effects models with nlme [13.0s] -✔ | 16 | Plotting [11.3s] +✔ | 10 | Special cases of mkinfit calls [0.4s] +✔ | 3 | mkinfit features [0.7s] +✔ | 8 | mkinmod model generation and printing [0.2s] +✔ | 3 | Model predictions with mkinpredict [0.3s] +✔ | 7 | Multistart method for saem.mmkin models [38.1s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.4s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.6s] +✔ | 16 | Plotting [9.8s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [72.6s] +✔ | 1 36 | saemix parent models [72.0s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_saemix_parent.R:152:3): We can also use mkin solution methods for saem Reason: This still takes almost 2.5 minutes although we do not solve ODEs @@ -43,11 +43,11 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs ✔ | 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 [8.1s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] +✔ | 9 | Hypothesis tests [8.3s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.1s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 324.3 s +Duration: 208.6 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) diff --git a/tests/testthat/print_dfop_saemix_1.txt b/tests/testthat/print_dfop_saemix_1.txt new file mode 100644 index 00000000..f427b3e6 --- /dev/null +++ b/tests/testthat/print_dfop_saemix_1.txt @@ -0,0 +1,24 @@ +Kinetic nonlinear mixed-effects model fit by SAEM +Structural model: +d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * + time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) + * parent + +Data: +270 observations of 1 variable(s) grouped in 15 datasets + +Likelihood computed by importance sampling + AIC BIC logLik + 1409 1415 -695 + +Fitted parameters: + estimate lower upper +parent_0 100.04 98.89 101.20 +log_k1 -4.12 -4.24 -4.00 +log_k2 -2.67 -2.90 -2.44 +g_qlogis 0.43 0.22 0.64 +a.1 0.92 0.67 1.16 +b.1 0.05 0.04 0.06 +SD.log_k1 0.22 0.14 0.30 +SD.log_k2 0.36 0.21 0.51 +SD.g_qlogis 0.14 -0.11 0.39 diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index 8e4d668b..646b6110 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -11,7 +11,7 @@ test_that("Print methods work", { expect_known_output(print(mixed(mmkin_sfo_1), digits = 2), "print_mmkin_sfo_1_mixed.txt") expect_known_output(print(dfop_nlme_1, digits = 1), "print_dfop_nlme_1.txt") - expect_known_output(print(sfo_saem_1_reduced, digits = 1), "print_sfo_saem_1_reduced.txt") + expect_known_output(print(dfop_saemix_1, digits = 1), "print_dfop_saemix_1.txt") }) test_that("nlme results are reproducible to some degree", { |