Fix tests and rerun

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"