Some more tests

6 files changed, 196 insertions, 69 deletions

diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R
index 27c2ce6c..3f50c42d 100644
--- a/R/summary.saem.mmkin.R
+++ b/R/summary.saem.mmkin.R
@@ -207,11 +207,11 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3)
     tc = "Two-component variance function"), "\n")
 
   cat("\nMean of starting values for individual parameters:\n")
-  print(x$mean_dp_start)
+  print(x$mean_dp_start, digits = digits)
 
   cat("\nFixed degradation parameter values:\n")
   if(length(x$fixed$value) == 0) cat("None\n")
-  else print(x$fixed)
+  else print(x$fixed, digits = digits)
 
   cat("\nResults:\n\n")
   cat("Likelihood computed by importance sampling\n")
diff --git a/tests/testthat/print_saem_biphasic_s.txt b/tests/testthat/print_saem_biphasic_s.txt
new file mode 100644
index 00000000..4d20117e
--- /dev/null
+++ b/tests/testthat/print_saem_biphasic_s.txt
@@ -0,0 +1,37 @@
+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
+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
+
+Likelihood computed by importance sampling
+   AIC  BIC logLik
+  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
diff --git a/tests/testthat/summary_DFOP_FOCUS_C.txt b/tests/testthat/summary_DFOP_FOCUS_C.txt
index 2b0210c0..da3276e1 100644
--- a/tests/testthat/summary_DFOP_FOCUS_C.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_C.txt
@@ -1,82 +1,77 @@
-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 
+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 
 
 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
 
-Model predictions using solution type analytical 
-
-Fitted using test 0 model solutions performed in test time 0 s
+Data:
+509 observations of 2 variable(s) grouped in 15 datasets
 
-Error model: Constant variance 
+Model predictions using solution type analytical 
 
-Error model algorithm: OLS 
+Fitted in 10.222 s using 300, 100 iterations
 
-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
+Variance model: Constant variance 
 
-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
+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 
 
-Fixed parameter values:
+Fixed degradation parameter values:
 None
 
 Results:
 
-       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
+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
 
 Estimated disappearance times:
-        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
+         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
diff --git a/tests/testthat/summary_saem_biphasic_s.txt b/tests/testthat/summary_saem_biphasic_s.txt
new file mode 100644
index 00000000..b5777ce1
--- /dev/null
+++ b/tests/testthat/summary_saem_biphasic_s.txt
@@ -0,0 +1,77 @@
+saemix version used for fitting:      Dummy 0.0 for testing 
+mkin version used for pre-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 test time 0 s using 300, 100 iterations
+
+Variance model: Constant variance 
+
+Mean of starting values for individual parameters:
+      parent_0           k_m1 f_parent_to_m1             k1             k2 
+       1.0e+02        1.8e-03        4.8e-01        4.5e-02        1.9e-02 
+             g 
+       5.1e-01 
+
+Fixed degradation parameter values:
+None
+
+Results:
+
+Likelihood computed by importance sampling
+   AIC  BIC logLik
+  2692 2702  -1333
+
+Optimised parameters:
+                  est.   lower   upper
+parent_0       1.0e+02 99.3030 1.0e+02
+k_m1           2.2e-03  0.0016 2.8e-03
+f_parent_to_m1 4.9e-01  0.4477 5.3e-01
+k1             4.0e-02  0.0239 5.6e-02
+k2             1.5e-02  0.0085 2.2e-02
+g              5.0e-01  0.3805 6.2e-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       1.23  0.39  2.07
+SD.k_m1           0.14 -0.48  0.75
+SD.f_parent_to_m1 0.28  0.17  0.39
+SD.k1             0.71  0.42  1.00
+SD.k2             0.78  0.47  1.09
+SD.g              0.27 -0.33  0.86
+
+Variance model:
+    est. lower upper
+a.1  2.7   2.6   2.9
+
+Resulting formation fractions:
+              ff
+parent_m1   0.49
+parent_sink 0.51
+
+Estimated disappearance times:
+       DT50 DT90 DT50back DT50_k1 DT50_k2
+parent   27  110       33      17      46
+m1      318 1055       NA      NA      NA
diff --git a/tests/testthat/test_f_time_norm.R b/tests/testthat/test_f_time_norm.R
new file mode 100644
index 00000000..790cce8b
--- /dev/null
+++ b/tests/testthat/test_f_time_norm.R
@@ -0,0 +1,6 @@
+context("Time step normalisation")
+
+test_that("Simple temperature and moisture normalisation works", {
+  expect_equal(round(f_time_norm_focus(25, 20, 25), 2), 1.37)
+})
+
diff --git a/tests/testthat/test_saem.R b/tests/testthat/test_saem.R
index 0b6d4531..d41efbfa 100644
--- a/tests/testthat/test_saem.R
+++ b/tests/testthat/test_saem.R
@@ -102,15 +102,27 @@ 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")
+
+  test_summary <- summary(saem_biphasic_s)
+  test_summary$saemixversion <- "Dummy 0.0 for testing"
+  test_summary$mkinversion <- "Dummy 0.0 for testing"
+  test_summary$Rversion <- "Dummy R version for testing"
+  test_summary$date.fit <- "Dummy date for testing"
+  test_summary$date.summary <- "Dummy date for testing"
+  test_summary$time <- c(elapsed = "test time 0")
+
+  expect_known_output(print(test_summary, digits = 2), "summary_saem_biphasic_s.txt")
+
   dfop_sfo_pop <- as.numeric(dfop_sfo_pop)
   ci_dfop_sfo_s_s <- summary(saem_biphasic_s)$confint_back
   expect_true(all(ci_dfop_sfo_s_s[, "lower"] < dfop_sfo_pop))
   expect_true(all(ci_dfop_sfo_s_s[, "upper"] > dfop_sfo_pop))
 
-  # The following does not work, the k1 and k2 are not fitted well
+  # The following does not work, as k1 and k2 are not fitted well
   ci_dfop_sfo_s_m <- summary(saem_biphasic_m)$confint_back
   # expect_true(all(ci_dfop_sfo_s_m[, "lower"] < dfop_sfo_pop))
-  #expect_true(all(ci_dfop_sfo_s_m[, "upper"] > dfop_sfo_pop))
+  # expect_true(all(ci_dfop_sfo_s_m[, "upper"] > dfop_sfo_pop))
 
   # Somehow this does not work at the moment. But it took forever (~ 10 min) anyways...
   #saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve", quiet = TRUE)