diff options
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | GNUmakefile | 5 | ||||
| -rw-r--r-- | test.log | 20 | ||||
| -rw-r--r-- | test_dev.log | 117 | ||||
| -rw-r--r-- | tests/testthat/print_mmkin_biphasic_mixed.txt | 26 | ||||
| -rw-r--r-- | tests/testthat/print_mmkin_sfo_1_mixed.txt | 19 | ||||
| -rw-r--r-- | tests/testthat/setup_script.R | 1 | ||||
| -rw-r--r-- | tests/testthat/test_mixed.R | 2 | ||||
| -rw-r--r-- | tests/testthat/test_saemix_parent.R | 6 |
9 files changed, 107 insertions, 91 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 41237793..c2aefe50 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 1.1.0 -Date: 2022-03-02 +Date: 2022-03-03 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", diff --git a/GNUmakefile b/GNUmakefile index 75a18e58..d6a6d9b5 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -57,6 +57,9 @@ build-no-vignettes: $(TGZVNR) install: build "$(RBIN)/R" CMD INSTALL $(TGZ) +devinstall: build + "$(RDEVBIN)/R" CMD INSTALL $(TGZ) + quickinstall: build-no-vignettes "$(RBIN)/R" CMD INSTALL $(TGZVNR) @@ -82,7 +85,7 @@ test: install "$(RBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee test.log sed -i -e "s/.*\r.*\r//" test.log -devtest: install +devtest: devinstall "$(RDEVBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee test_dev.log sed -i -e "s/\r.*\r//" test_dev.log @@ -3,17 +3,17 @@ Loading required package: parallel ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [4.2s] +✔ | 5 | Analytical solutions for coupled models [4.3s] ✔ | 5 | Calculation of Akaike weights ✔ | 2 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.0s] ⠋ | 1 | Dimethenamid data from 2018 -✔ | 1 27 | Dimethenamid data from 2018 [63.0s] +✔ | 1 27 | Dimethenamid data from 2018 [62.6s] ──────────────────────────────────────────────────────────────────────────────── -Skip (test_dmta.R:162:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data +Skip (test_dmta.R:164:3): 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 [6.8s] +✔ | 14 | Error model fitting [6.9s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.8s] ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.1s] @@ -31,21 +31,21 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.3s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.1s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.0s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.4s] ✔ | 16 | Plotting [1.5s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 23 | saemix_parent [29.8s] -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6s] +✔ | 23 | saemix parent models [29.4s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.7s] ✔ | 7 | Fitting the SFORB model [4.4s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 4 | Summary [0.1s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5s] -✔ | 9 | Hypothesis tests [9.6s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.6s] +✔ | 9 | Hypothesis tests [9.4s] ✔ | 2 | tffm0 ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 144.7 s +Duration: 144.3 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) diff --git a/test_dev.log b/test_dev.log index df159d1e..041804e9 100644 --- a/test_dev.log +++ b/test_dev.log @@ -1,62 +1,81 @@ -Loading mkin +ℹ Loading mkin Loading required package: parallel -Testing mkin -✔ | OK F W S | Context -✔ | 5 | AIC calculation -✔ | 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 [3.4 s] -✔ | 5 | Analytical solutions for coupled models [3.1 s] -✔ | 5 | Calculation of Akaike weights -✔ | 14 | Confidence intervals and p-values [1.2 s] -✔ | 14 | Error model fitting [5.8 s] -✔ | 5 | Time step normalisation -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s] -✔ | 1 | Fitting the logistic model [0.2 s] -✔ | 5 3 | Nonlinear mixed-effects models [0.1 s] +ℹ Testing mkin +✔ | F W S OK | Context +✔ | 5 | AIC calculation +✔ | 5 | Analytical solutions for coupled models [14.4s] +✔ | 5 | Calculation of Akaike weights +✔ | 2 | Export dataset for reading into CAKE +✔ | 12 | Confidence intervals and p-values [1.0s] +⠋ | 1 | Dimethenamid data from 2018 +✔ | 1 27 | Dimethenamid data from 2018 [124.8s] ──────────────────────────────────────────────────────────────────────────────── -Skip (test_mixed.R:4:3): Parent fits using saemix are correctly implemented -Reason: !saemix_available is TRUE - -Skip (test_mixed.R:94:3): Print methods work -Reason: !saemix_available is TRUE - -Skip (test_mixed.R:118:3): saem results are reproducible for biphasic fits -Reason: !saemix_available is TRUE +Skip (test_dmta.R:164:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data +Reason: Fitting this ODE model with saemix takes about 15 minutes on my system ──────────────────────────────────────────────────────────────────────────────── -✔ | 2 | Test dataset classes mkinds and mkindsg -✔ | 1 | mkinfit features [0.3 s] -✔ | 10 | Special cases of mkinfit calls [0.3 s] -✔ | 8 | mkinmod model generation and printing [0.2 s] -✔ | 3 | Model predictions with mkinpredict [0.3 s] -✔ | 14 2 | Evaluations according to 2015 NAFTA guidance [2.2 s] +✔ | 14 | Error model fitting [6.8s] +✔ | 5 | Time step normalisation +✔ | 4 | Calculation of FOCUS chi2 error levels [0.8s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.5s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.6s] +✔ | 1 | Fitting the logistic model [0.3s] +⠇ | 1 8 | Nonlinear mixed-effects models +✖ | 1 1 13 | Nonlinear mixed-effects models [1.5s] ──────────────────────────────────────────────────────────────────────────────── -Skip (test_nafta.R:25:5): Test data from Appendix B are correctly evaluated -Reason: getRversion() >= "4.1.0" is TRUE +Failure (test_mixed.R:5:3): Print methods work +Results have changed from known value recorded in 'print_mmkin_dfop_1_mixed.txt'. -Skip (test_nafta.R:53:5): Test data from Appendix D are correctly evaluated -Reason: getRversion() >= "4.1.0" is TRUE +old[18:21] vs new[18:21] + "" + "Mean fitted parameters:" + "parent_0 log_k1 log_k2 g_qlogis " +- " 100.06 -2.68 -5.57 0.01 " ++ " 100.06 -2.68 -5.58 0.01 " + +Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits +Reason: Fitting with saemix takes around 10 minutes when using deSolve ──────────────────────────────────────────────────────────────────────────────── -✔ | 9 | Nonlinear mixed-effects models [7.9 s] -✔ | 0 1 | Plotting [0.7 s] +✔ | 3 | Test dataset classes mkinds and mkindsg +✔ | 10 | Special cases of mkinfit calls [0.6s] +✔ | 3 | mkinfit features [1.1s] +✔ | 8 | mkinmod model generation and printing [0.2s] +✔ | 3 | Model predictions with mkinpredict [0.3s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.1s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.5s] +✖ | 2 14 | Plotting [1.5s] ──────────────────────────────────────────────────────────────────────────────── -Skip (test_plot.R:18:3): Plotting mkinfit, mmkin and mixed model objects is reproducible -Reason: getRversion() >= "4.1.0" is TRUE +Failure (test_plot.R:42:3): 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:42:2 + 3. testthat::expect_snapshot_file(...) + +Failure (test_plot.R:50:3): Plotting mkinfit, mmkin and mixed model objects is reproducible +Snapshot of `testcase` to 'plot/mixed-model-fit-for-saem-object-with-mkin-transformations.svg' has changed +Run `testthat::snapshot_review('plot/')` to review changes +Backtrace: + 1. vdiffr::expect_doppelganger(...) + at test_plot.R:50:2 + 3. testthat::expect_snapshot_file(...) ──────────────────────────────────────────────────────────────────────────────── -✔ | 4 | Residuals extracted from mkinfit models -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s] -✔ | 4 | Summary [0.1 s] -✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s] -✔ | 9 | Hypothesis tests [7.7 s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0 s] +✔ | 4 | Residuals extracted from mkinfit models +✔ | 23 | saemix_parent [28.7s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [12.2s] +✔ | 7 | Fitting the SFORB model [16.1s] +✔ | 1 | Summaries of old mkinfit objects +✔ | 4 | Summary [0.1s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [19.0s] +✔ | 9 | Hypothesis tests [67.6s] +✔ | 2 | tffm0 +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 41.2 s +Duration: 314.2 s ── Skipped tests ────────────────────────────────────────────────────────────── -● !saemix_available is TRUE (3) -● getRversion() >= "4.1.0" is TRUE (3) +• 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) -[ FAIL 0 | WARN 0 | SKIP 6 | PASS 160 ] +[ FAIL 3 | WARN 0 | SKIP 2 | PASS 237 ] diff --git a/tests/testthat/print_mmkin_biphasic_mixed.txt b/tests/testthat/print_mmkin_biphasic_mixed.txt deleted file mode 100644 index 712c813a..00000000 --- a/tests/testthat/print_mmkin_biphasic_mixed.txt +++ /dev/null @@ -1,26 +0,0 @@ -Kinetic model fitted by nonlinear regression to each dataset -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 -d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) - * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * - exp(-k2 * time))) * parent - k_m1 * m1 - -Data: -507 observations of 2 variable(s) grouped in 15 datasets - -<mmkin> object -Status of individual fits: - - dataset -model 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 - DFOP-SFO OK OK OK OK OK OK OK OK OK OK OK OK OK OK OK - -OK: No warnings - -Mean fitted parameters: - parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 - 100.648 -5.380 -0.093 -2.736 -4.534 - g_qlogis - -0.142 diff --git a/tests/testthat/print_mmkin_sfo_1_mixed.txt b/tests/testthat/print_mmkin_sfo_1_mixed.txt new file mode 100644 index 00000000..33e5bf5c --- /dev/null +++ b/tests/testthat/print_mmkin_sfo_1_mixed.txt @@ -0,0 +1,19 @@ +Kinetic model fitted by nonlinear regression to each dataset +Structural model: +d_parent/dt = - k_parent * parent + +Data: +262 observations of 1 variable(s) grouped in 15 datasets + +<mmkin> object +Status of individual fits: + + dataset +model 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + SFO OK OK OK OK OK OK OK OK OK OK OK OK OK OK OK + +OK: No warnings + +Mean fitted parameters: + parent_0 log_k_parent + 99.9 -3.3 diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index ca0ca313..ec96fbc2 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -187,7 +187,6 @@ mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc", cores = n_ mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE, cores = n_cores) mmkin_biphasic <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE, cores = n_cores, error_model = "tc") -mmkin_biphasic_mixed <- mixed(mmkin_biphasic) # nlme dfop_nlme_1 <- nlme(mmkin_dfop_1) diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index 798dd01f..ae8743af 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -2,7 +2,7 @@ context("Nonlinear mixed-effects models") test_that("Print methods work", { expect_known_output(print(fits[, 2:3], digits = 2), "print_mmkin_parent.txt") - expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt") + 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, digits = 1), "print_sfo_saem_1.txt") diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R index 2f05c175..8beceba9 100644 --- a/tests/testthat/test_saemix_parent.R +++ b/tests/testthat/test_saemix_parent.R @@ -1,3 +1,5 @@ +context("saemix parent models") + test_that("Parent fits using saemix are correctly implemented", { expect_error(saem(fits), "Only row objects") @@ -63,9 +65,9 @@ test_that("Parent fits using saemix are correctly implemented", { expect_true(all(rel_diff_mmkin[c("parent_0", "k1")] < 0.20)) expect_true(all(rel_diff_mmkin_tested[c("parent_0", "k1", "k2")] < 0.20)) - # We get < 15% deviations with transformations made in mkin + # We get < 20% deviations with transformations made in mkin rel_diff_1 <- (s_dfop_s1$confint_back[, "est."] - dfop_pop) / dfop_pop - expect_true(all(rel_diff_1 < 0.15)) + expect_true(all(rel_diff_1 < 0.20)) # We get < 20% deviations with transformations made in saemix rel_diff_2 <- (s_dfop_s2$confint_back[, "est."] - dfop_pop) / dfop_pop |