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-rw-r--r--test.log38
-rw-r--r--tests/testthat/print_saem_biphasic_s.txt40
-rw-r--r--tests/testthat/summary_DFOP_FOCUS_C.txt125
-rw-r--r--tests/testthat/test_plot.R4
-rw-r--r--tests/testthat/test_saem.R2
5 files changed, 98 insertions, 111 deletions
diff --git a/test.log b/test.log
index 70011abb..49a1a704 100644
--- a/test.log
+++ b/test.log
@@ -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"

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