diff options
| -rw-r--r-- | test.log | 38 | ||||
| -rw-r--r-- | tests/testthat/print_saem_biphasic_s.txt | 40 | ||||
| -rw-r--r-- | tests/testthat/summary_DFOP_FOCUS_C.txt | 125 | ||||
| -rw-r--r-- | tests/testthat/test_plot.R | 4 | ||||
| -rw-r--r-- | tests/testthat/test_saem.R | 2 |
5 files changed, 98 insertions, 111 deletions
@@ -3,14 +3,15 @@ Loading required package: parallel Testing mkin ✔ | OK F W S | Context ✔ | 5 | AIC calculation -✔ | 2 | Export dataset for reading into CAKE +✔ | 2 | Export dataset for reading into CAKE [0.2 s] ✔ | 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 [3.5 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 | Error model fitting [4.5 s] +✔ | 14 | Error model fitting [4.6 s] +✔ | 1 | Time step normalisation ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s] ✔ | 1 | Fitting the logistic model [0.2 s] ✔ | 1 | Test dataset class mkinds used in gmkin @@ -18,38 +19,19 @@ Testing mkin ✔ | 12 | Special cases of mkinfit calls [0.7 s] ✔ | 8 | mkinmod model generation and printing [0.2 s] ✔ | 3 | Model predictions with mkinpredict [0.4 s] -✔ | 14 2 | Evaluations according to 2015 NAFTA guidance [1.3 s] -──────────────────────────────────────────────────────────────────────────────── -Skip (test_nafta.R:25:5): Test data from Appendix B are correctly evaluated -Reason: getRversion() < "4.1.0" is TRUE - -Skip (test_nafta.R:53:5): Test data from Appendix D are correctly evaluated -Reason: getRversion() < "4.1.0" is TRUE -──────────────────────────────────────────────────────────────────────────────── -✔ | 9 | Nonlinear mixed-effects models [7.9 s] -✔ | 0 1 | Plotting [0.7 s] -──────────────────────────────────────────────────────────────────────────────── -Skip (test_plot.R:28:3): Plotting mkinfit and mmkin objects is reproducible -Reason: getRversion() < "4.1.0" is TRUE -──────────────────────────────────────────────────────────────────────────────── +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6 s] +✔ | 9 | Nonlinear mixed-effects models [7.7 s] +✔ | 18 | Plotting [2.1 s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 13 1 | Nonlinear mixed effects models fitted with SAEM from saemix [19.0 s] -──────────────────────────────────────────────────────────────────────────────── -Skip (test_saem.R:103:1): Simple models with metabolite can be fitted with saemix -Reason: empty test -──────────────────────────────────────────────────────────────────────────────── +✔ | 17 | Nonlinear mixed effects models fitted with SAEM from saemix [19.1 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] +✔ | 9 | Hypothesis tests [7.4 s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 59.7 s - -── Skipped tests ────────────────────────────────────────────────────────────── -● empty test (1) -● getRversion() < "4.1.0" is TRUE (3) +Duration: 62.0 s -[ FAIL 0 | WARN 0 | SKIP 4 | PASS 164 ] +[ FAIL 0 | WARN 0 | SKIP 0 | PASS 189 ] diff --git a/tests/testthat/print_saem_biphasic_s.txt b/tests/testthat/print_saem_biphasic_s.txt index 4d20117e..3c07b715 100644 --- a/tests/testthat/print_saem_biphasic_s.txt +++ b/tests/testthat/print_saem_biphasic_s.txt @@ -15,23 +15,23 @@ Likelihood computed by importance sampling 2692 2702 -1333 Fitted parameters: - estimate lower upper -parent_0 1.002e+02 99.302986 1.011e+02 -k_m1 2.182e-03 0.001576 2.788e-03 -f_parent_to_m1 4.883e-01 0.447687 5.289e-01 -k1 4.014e-02 0.023941 5.634e-02 -k2 1.517e-02 0.008507 2.184e-02 -g 5.007e-01 0.380534 6.208e-01 -Var.parent_0 1.511e+00 -0.551247 3.574e+00 -Var.k_m1 1.912e-02 -0.151313 1.896e-01 -Var.f_parent_to_m1 8.082e-02 0.018430 1.432e-01 -Var.k1 5.037e-01 0.095343 9.121e-01 -Var.k2 6.129e-01 0.124868 1.101e+00 -Var.g 7.107e-02 -0.244901 3.870e-01 -a.1 2.749e+00 2.568674 2.929e+00 -SD.parent_0 1.229e+00 0.390443 2.068e+00 -SD.k_m1 1.383e-01 -0.477984 7.545e-01 -SD.f_parent_to_m1 2.843e-01 0.174562 3.940e-01 -SD.k1 7.097e-01 0.422037 9.974e-01 -SD.k2 7.829e-01 0.471184 1.095e+00 -SD.g 2.666e-01 -0.326044 8.592e-01 + estimate lower upper +parent_0 1e+02 99.303 1e+02 +k_m1 2e-03 0.002 3e-03 +f_parent_to_m1 5e-01 0.448 5e-01 +k1 4e-02 0.024 6e-02 +k2 2e-02 0.009 2e-02 +g 5e-01 0.381 6e-01 +Var.parent_0 2e+00 -0.551 4e+00 +Var.k_m1 2e-02 -0.151 2e-01 +Var.f_parent_to_m1 8e-02 0.018 1e-01 +Var.k1 5e-01 0.095 9e-01 +Var.k2 6e-01 0.125 1e+00 +Var.g 7e-02 -0.245 4e-01 +a.1 3e+00 2.569 3e+00 +SD.parent_0 1e+00 0.390 2e+00 +SD.k_m1 1e-01 -0.478 8e-01 +SD.f_parent_to_m1 3e-01 0.175 4e-01 +SD.k1 7e-01 0.422 1e+00 +SD.k2 8e-01 0.471 1e+00 +SD.g 3e-01 -0.326 9e-01 diff --git a/tests/testthat/summary_DFOP_FOCUS_C.txt b/tests/testthat/summary_DFOP_FOCUS_C.txt index da3276e1..2b0210c0 100644 --- a/tests/testthat/summary_DFOP_FOCUS_C.txt +++ b/tests/testthat/summary_DFOP_FOCUS_C.txt @@ -1,77 +1,82 @@ -saemix version used for fitting: 3.1.9000 -mkin version used for pre-fitting: 0.9.50.4 -R version used for fitting: 4.0.3 -Date of fit: Wed Dec 9 08:16:28 2020 -Date of summary: Wed Dec 9 08:23:19 2020 +mkin version used for fitting: Dummy 0.0 for testing +R version used for fitting: Dummy R version for testing +Date of fit: Dummy date for testing +Date of summary: Dummy date for testing Equations: 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: -509 observations of 2 variable(s) grouped in 15 datasets Model predictions using solution type analytical -Fitted in 10.222 s using 300, 100 iterations +Fitted using test 0 model solutions performed in test time 0 s + +Error model: Constant variance -Variance model: Constant variance +Error model algorithm: OLS -Mean of starting values for individual parameters: - parent_0 k_m1 f_parent_to_m1 k1 k2 - 1.007005e+02 1.837381e-03 4.803953e-01 4.534096e-02 1.918378e-02 - g - 5.068235e-01 +Starting values for parameters to be optimised: + value type +parent_0 85.10 state +k1 0.10 deparm +k2 0.01 deparm +g 0.50 deparm -Fixed degradation parameter values: +Starting values for the transformed parameters actually optimised: + value lower upper +parent_0 85.100000 -Inf Inf +log_k1 -2.302585 -Inf Inf +log_k2 -4.605170 -Inf Inf +g_qlogis 0.000000 -Inf Inf + +Fixed parameter values: None Results: -Likelihood computed by importance sampling - AIC BIC logLik - 2692 2702 -1333 - -Optimised parameters: - est. lower upper -parent_0 1.002e+02 99.302986 1.011e+02 -k_m1 2.182e-03 0.001576 2.788e-03 -f_parent_to_m1 4.883e-01 0.447687 5.289e-01 -k1 4.014e-02 0.023941 5.634e-02 -k2 1.517e-02 0.008507 2.184e-02 -g 5.007e-01 0.380534 6.208e-01 - -Correlation: - prnt_0 k_m1 f_p__1 k1 k2 -k_m1 -0.152 -f_parent_to_m1 -0.138 0.396 -k1 0.085 -0.036 -0.026 -k2 0.005 0.067 0.018 -0.043 -g -0.075 -0.113 -0.029 -0.248 -0.263 - -Random effects: - est. lower upper -SD.parent_0 1.2293 0.3904 2.0682 -SD.k_m1 0.1383 -0.4780 0.7545 -SD.f_parent_to_m1 0.2843 0.1746 0.3940 -SD.k1 0.7097 0.4220 0.9974 -SD.k2 0.7829 0.4712 1.0946 -SD.g 0.2666 -0.3260 0.8592 - -Variance model: - est. lower upper -a.1 2.749 2.569 2.929 - -Resulting formation fractions: - ff -parent_m1 0.4883 -parent_sink 0.5117 + AIC BIC logLik + 29.02372 30.00984 -9.511861 + +Optimised, transformed parameters with symmetric confidence intervals: + Estimate Std. Error Lower Upper +parent_0 85.0000 0.66620 83.1500 86.8500 +log_k1 -0.7775 0.03380 -0.8713 -0.6836 +log_k2 -4.0260 0.13100 -4.3890 -3.6620 +g_qlogis 1.7660 0.08218 1.5380 1.9940 +sigma 0.6962 0.16410 0.2406 1.1520 + +Parameter correlation: +[1] "Correlation matrix is platform dependent, not tested" + +Backtransformed parameters: +Confidence intervals for internally transformed parameters are asymmetric. +t-test (unrealistically) based on the assumption of normal distribution +for estimators of untransformed parameters. + Estimate t value Pr(>t) Lower Upper +parent_0 85.00000 127.600 1.131e-08 83.15000 86.85000 +k1 0.45960 29.580 3.887e-06 0.41840 0.50480 +k2 0.01785 7.636 7.901e-04 0.01241 0.02568 +g 0.85390 83.310 6.221e-08 0.82310 0.88020 +sigma 0.69620 4.243 6.618e-03 0.24060 1.15200 + +FOCUS Chi2 error levels in percent: + err.min n.optim df +All data 2.661 4 5 +parent 2.661 4 5 Estimated disappearance times: - DT50 DT90 DT50back DT50_k1 DT50_k2 -parent 27.07 110.1 33.14 17.27 45.68 -m1 317.69 1055.4 NA NA NA + DT50 DT90 DT50back DT50_k1 DT50_k2 +parent 1.887 21.25 6.397 1.508 38.83 + +Data: + time variable observed predicted residual + 0 parent 85.1 85.003 0.09726 + 1 parent 57.9 58.039 -0.13912 + 3 parent 29.9 30.054 -0.15351 + 7 parent 14.6 13.866 0.73388 + 14 parent 9.7 9.787 -0.08657 + 28 parent 6.6 7.532 -0.93205 + 63 parent 4.0 4.033 -0.03269 + 91 parent 3.9 2.447 1.45348 + 119 parent 0.6 1.484 -0.88424 diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R index bafcd561..4d815d33 100644 --- a/tests/testthat/test_plot.R +++ b/tests/testthat/test_plot.R @@ -32,10 +32,10 @@ test_that("Plotting mkinfit and mmkin objects is reproducible", { plot_err_sfo_sfo <- function() plot_err(f_sfo_sfo_desolve) vdiffr::expect_doppelganger("plot_err for FOCUS D", plot_err_sfo_sfo) - plot_errmod_fit_obs_1 <- function() plot_err(fit_obs_1, sep_obs = FALSE) + plot_errmod_fit_tc_1 <- function() plot_err(fit_tc_1, sep_obs = FALSE) vdiffr::expect_doppelganger("plot_errmod with SFO_lin_a_tc", plot_errmod_fit_tc_1) - plot_errmod_fit_tc_1 <- function() plot_err(fit_tc_1, sep_obs = FALSE) + plot_errmod_fit_obs_1 <- function() plot_err(fit_obs_1, sep_obs = FALSE) vdiffr::expect_doppelganger("plot_errmod with SFO_lin_a_obs", plot_errmod_fit_obs_1) skip_on_travis() diff --git a/tests/testthat/test_saem.R b/tests/testthat/test_saem.R index d41efbfa..37456ed4 100644 --- a/tests/testthat/test_saem.R +++ b/tests/testthat/test_saem.R @@ -102,7 +102,7 @@ test_that("Parent only models can be fitted with saemix", { test_that("Simple models with metabolite can be fitted with saemix", { - expect_known_output(print(saem_biphasic_s), "print_saem_biphasic_s.txt") + expect_known_output(print(saem_biphasic_s, digits = 1), "print_saem_biphasic_s.txt") test_summary <- summary(saem_biphasic_s) test_summary$saemixversion <- "Dummy 0.0 for testing" |