Add some more tests

10 files changed, 83 insertions, 47 deletions

diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R
index 79139d12..b6b6c830 100644
--- a/R/nlme.mmkin.R
+++ b/R/nlme.mmkin.R
@@ -193,7 +193,8 @@ nlme.mmkin <- function(model, data = "auto",
   val$mkinmod <- model[[1]]$mkinmod
   val$data <- thisCall[["data"]]
   val$mmkin <- model
-  val$mean_dp_start <- ifelse(is.list(start), start$fixed, start)
+  if (is.list(start)) val$mean_dp_start <- start$fixed
+  else val$mean_dp_start <- start
   val$transform_rates <- model[[1]]$transform_rates
   val$transform_fractions <- model[[1]]$transform_fractions
   val$solution_type <- model[[1]]$solution_type
diff --git a/man/saem.Rd b/man/saem.Rd
index 00e9aeda..0c066dd2 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -34,6 +34,7 @@ saemix_model(
   transformations = c("mkin", "saemix"),
   degparms_start = numeric(),
   test_log_parms = FALSE,
+  conf.level = 0.6,
   verbose = FALSE,
   ...
 )
diff --git a/test.log b/test.log
index 5c8f1802..b044e6a0 100644
--- a/test.log
+++ b/test.log
@@ -3,45 +3,51 @@ Loading required package: parallel
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [3.4s]
+✔ |         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]
+✔ |        12 | Confidence intervals and p-values [1.1s]
 ⠋ |         1 | Dimethenamid data from 2018                                     
-✔ |        24 | Dimethenamid data from 2018 [37.1s]
-✔ |        14 | Error model fitting [6.8s]
+✔ |     1  25 | Dimethenamid data from 2018 [49.7s]
+────────────────────────────────────────────────────────────────────────────────
+Skip (test_dmta.R:147:3): 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 [7.0s]
 ✔ |         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]
 ✔ |         4 | Test fitting the decline of metabolites from their maximum [0.5s]
 ✔ |         1 | Fitting the logistic model [0.3s]
-✔ |     1  12 | Nonlinear mixed-effects models [0.2s]
+⠴ |         6 | Nonlinear mixed-effects models                                  
+✔ |     1  15 | Nonlinear mixed-effects models [2.4s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_mixed.R:67:3): saemix results are reproducible for biphasic fits
 Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ────────────────────────────────────────────────────────────────────────────────
-✔ |         2 | Test dataset classes mkinds and mkindsg
+✔ |         3 | Test dataset classes mkinds and mkindsg
 ✔ |        10 | Special cases of mkinfit calls [0.6s]
 ✔ |         1 | mkinfit features [0.5s]
 ✔ |         8 | mkinmod model generation and printing [0.2s]
 ✔ |         3 | Model predictions with mkinpredict [0.4s]
 ✔ |        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 [9.2s]
 ✔ |        16 | Plotting [1.5s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |        23 | saemix_parent [29.0s]
+✔ |        23 | saemix_parent [30.4s]
 ✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6s]
 ✔ |         7 | Fitting the SFORB model [4.5s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         4 | Summary [0.1s]
-✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5s]
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.6s]
 ✔ |         9 | Hypothesis tests [9.4s]
 ✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 115.2 s
+Duration: 133.2 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
+• 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 1 | PASS 230 ]
+[ FAIL 0 | WARN 0 | SKIP 2 | PASS 235 ]
diff --git a/tests/testthat/dimethenamid_2018.txt b/tests/testthat/dimethenamid_2018.txt
new file mode 100644
index 00000000..513acff9
--- /dev/null
+++ b/tests/testthat/dimethenamid_2018.txt
@@ -0,0 +1,24 @@
+<mkindsg> holding 7 mkinds objects
+Title $title:  Aerobic soil degradation data on dimethenamid-P from the EU assessment in 2018 
+Occurrence of observed compounds $observed_n:
+DMTAP   M23   M27   M31  DMTA 
+    3     7     7     7     4 
+Time normalisation factors $f_time_norm:
+[1] 1.0000000 0.9706477 1.2284784 1.2284784 0.6233856 0.7678922 0.6733938
+Meta information $meta:
+                     study  usda_soil_type study_moisture_ref_type rel_moisture
+Calke        Unsworth 2014      Sandy loam                     pF2         1.00
+Borstel  Staudenmaier 2009            Sand                     pF1         0.50
+Elliot 1        Wendt 1997       Clay loam                   pF2.5         0.75
+Elliot 2        Wendt 1997       Clay loam                   pF2.5         0.75
+Flaach          König 1996 Sandy clay loam                     pF1         0.40
+BBA 2.2         König 1995      Loamy sand                     pF1         0.40
+BBA 2.3         König 1995      Sandy loam                     pF1         0.40
+         study_ref_moisture temperature
+Calke                    NA          20
+Borstel               23.00          20
+Elliot 1              33.37          23
+Elliot 2              33.37          23
+Flaach                   NA          20
+BBA 2.2                  NA          20
+BBA 2.3                  NA          20
diff --git a/print_nlmixr_saem_biphasic.txt b/tests/testthat/print_nlmixr_saem_biphasic.txt
index 5cf80f0f..5cf80f0f 100644
--- a/print_nlmixr_saem_biphasic.txt
+++ b/tests/testthat/print_nlmixr_saem_biphasic.txt
diff --git a/print_nlmixr_saem_biphasic_tc.txt b/tests/testthat/print_nlmixr_saem_biphasic_tc.txt
index ad59005d..2f940bfe 100644
--- a/print_nlmixr_saem_biphasic_tc.txt
+++ b/tests/testthat/print_nlmixr_saem_biphasic_tc.txt
@@ -11,6 +11,7 @@ Data:
 507 observations of 2 variable(s) grouped in 15 datasets
 
 Likelihood:
+
    AIC  BIC logLik
   2400 2468  -1184
 
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index bfa70005..4b99ad67 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -204,10 +204,10 @@ saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE)
 saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE)
 
 # nlmixr saem
-tmp <- capture_output(nlmixr_saem_biphasic <- nlmixr(mmkin_biphasic, est = "saem",
-    control = nlmixr::saemControl(nBurn = 300, nEm = 100, nmc = 9, print = 0)))
-tmp <- capture_output(nlmixr_saem_biphasic_tc <- nlmixr(mmkin_biphasic_tc, est = "saem",
-    control = nlmixr::saemControl(nBurn = 300, nEm = 100, nmc = 9, print = 0)))
+tmp <- suppressMessages(capture.output(nlmixr_saem_biphasic <- nlmixr(mmkin_biphasic, est = "saem",
+    control = nlmixr::saemControl(nBurn = 300, nEm = 100, nmc = 9, print = 0))))
+tmp <- suppressMessages(capture.output(nlmixr_saem_biphasic_tc <- nlmixr(mmkin_biphasic_tc, est = "saem",
+    control = nlmixr::saemControl(nBurn = 300, nEm = 100, nmc = 9, print = 0))))
 # The FOCEI fit takes too long...
 #tmp <- capture_output(nlmixr_focei_biphasic <- nlmixr(mmkin_biphasic, est = "focei",
 #    control = nlmixr::foceiControl(print = 0)))
diff --git a/tests/testthat/summary_nlmixr_saem_biphasic.txt b/tests/testthat/summary_nlmixr_saem_biphasic.txt
index c5c1fe78..f1cdc47b 100644
--- a/tests/testthat/summary_nlmixr_saem_biphasic.txt
+++ b/tests/testthat/summary_nlmixr_saem_biphasic.txt
@@ -13,7 +13,7 @@ d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
            exp(-k2 * time))) * parent - k_m1 * m1
 
 Data:
-508 observations of 2 variable(s) grouped in 15 datasets
+507 observations of 2 variable(s) grouped in 15 datasets
 
 Degradation model predictions using RxODE
 
@@ -23,9 +23,9 @@ Variance model: Constant variance
 
 Mean of starting values for individual parameters:
        parent_0        log_k_m1 f_parent_qlogis          log_k1          log_k2 
-         100.74           -5.43           -0.05           -2.85           -4.57 
+         100.67           -5.38           -0.09           -2.74           -4.51 
        g_qlogis 
-          -0.15 
+          -0.18 
 
 Mean of starting values for error model parameters:
 sigma_parent     sigma_m1 
@@ -38,39 +38,39 @@ Results:
 
 Likelihood calculated by gauss3_1.6  
    AIC  BIC logLik
-  2465 2525  -1219
+  2510 2569  -1241
 
 Optimised parameters:
                   est. lower  upper
-parent_0        100.54  99.7 101.40
-log_k_m1         -5.44  -5.6  -5.24
-f_parent_qlogis  -0.06  -0.2   0.05
-log_k1           -2.81  -3.0  -2.65
-log_k2           -4.62  -4.8  -4.41
-g_qlogis         -0.14  -0.4   0.17
+parent_0        100.49  99.6 101.37
+log_k_m1         -5.36  -5.5  -5.20
+f_parent_qlogis  -0.09  -0.3   0.08
+log_k1           -2.78  -3.0  -2.59
+log_k2           -4.51  -4.7  -4.35
+g_qlogis         -0.12  -0.5   0.21
 
 Correlation: 
-                prnt_0 lg_k_1 f_prn_ log_k1 log_k2
-log_k_m1        -0.224                            
-f_parent_qlogis -0.401  0.335                     
-log_k1           0.119  0.083  0.019              
-log_k2          -0.019  0.237  0.142  0.395       
-g_qlogis         0.083 -0.282 -0.218 -0.532 -0.544
+                pr_0 l__1 f_p_ lg_1 lg_2
+log_k_m1        -0.3                    
+f_parent_qlogis -0.2  0.3               
+log_k1           0.1  0.1  0.0          
+log_k2           0.0  0.3  0.1  0.4     
+g_qlogis         0.0 -0.3 -0.1 -0.5 -0.7
 
 Random effects (omega):
                     eta.parent_0 eta.log_k_m1 eta.f_parent_qlogis eta.log_k1
-eta.parent_0                0.05          0.0                0.00       0.00
-eta.log_k_m1                0.00          0.1                0.00       0.00
-eta.f_parent_qlogis         0.00          0.0                0.03       0.00
-eta.log_k1                  0.00          0.0                0.00       0.05
-eta.log_k2                  0.00          0.0                0.00       0.00
-eta.g_qlogis                0.00          0.0                0.00       0.00
+eta.parent_0                 0.2         0.00                0.00       0.00
+eta.log_k_m1                 0.0         0.05                0.00       0.00
+eta.f_parent_qlogis          0.0         0.00                0.09       0.00
+eta.log_k1                   0.0         0.00                0.00       0.09
+eta.log_k2                   0.0         0.00                0.00       0.00
+eta.g_qlogis                 0.0         0.00                0.00       0.00
                     eta.log_k2 eta.g_qlogis
 eta.parent_0              0.00          0.0
 eta.log_k_m1              0.00          0.0
 eta.f_parent_qlogis       0.00          0.0
 eta.log_k1                0.00          0.0
-eta.log_k2                0.08          0.0
+eta.log_k2                0.03          0.0
 eta.g_qlogis              0.00          0.1
 
 Variance model:
@@ -80,11 +80,11 @@ sigma_parent     sigma_m1
 Backtransformed parameters:
                 est. lower upper
 parent_0       1e+02 1e+02 1e+02
-k_m1           4e-03 4e-03 5e-03
-f_parent_to_m1 5e-01 5e-01 5e-01
+k_m1           5e-03 4e-03 6e-03
+f_parent_to_m1 5e-01 4e-01 5e-01
 k1             6e-02 5e-02 7e-02
-k2             1e-02 8e-03 1e-02
-g              5e-01 4e-01 5e-01
+k2             1e-02 9e-03 1e-02
+g              5e-01 4e-01 6e-01
 
 Resulting formation fractions:
              ff
@@ -93,5 +93,5 @@ parent_sink 0.5
 
 Estimated disappearance times:
        DT50 DT90 DT50back DT50_k1 DT50_k2
-parent   27  170       51      12      70
-m1      160  532       NA      NA      NA
+parent   25  152       46      11      63
+m1      147  488       NA      NA      NA
diff --git a/tests/testthat/test_dmta.R b/tests/testthat/test_dmta.R
index 22fa9d95..7b130999 100644
--- a/tests/testthat/test_dmta.R
+++ b/tests/testthat/test_dmta.R
@@ -139,8 +139,9 @@ dmta_sfo_sfo3p_tc <- mmkin(list("SFO-SFO3+" = sfo_sfo3p),
 
 test_that("Different backends get consistent results for SFO-SFO3+, dimethenamid data", {
 
-  nlme_sfo_sfo3p_tc <- nlme(dmta_sfo_sfo3p_tc,
-    start = mean_degparms(dmta_sfo_sfo3p_tc, test_log_parms = TRUE))
+  expect_warning(nlme_sfo_sfo3p_tc <- nlme(dmta_sfo_sfo3p_tc,
+    start = mean_degparms(dmta_sfo_sfo3p_tc, test_log_parms = TRUE)),
+    "Iteration 5, LME step.*not converge")
   ints_nlme_mets <- intervals(nlme_sfo_sfo3p_tc, which = "fixed")
 
   skip("Fitting this ODE model with saemix takes about 15 minutes on my system")
diff --git a/tests/testthat/test_mkinds.R b/tests/testthat/test_mkinds.R
index 5ce3619b..c10a3f5b 100644
--- a/tests/testthat/test_mkinds.R
+++ b/tests/testthat/test_mkinds.R
@@ -8,4 +8,6 @@ test_that("An mkinds object can be created and printed", {
 test_that("An mkindsg object can be created and printed", {
   testdata_group <- mkindsg$new("Experimental X", experimental_data_for_UBA_2019[6:10])
   expect_known_output(print(testdata_group), "experimental_data_for_UBA_2019_mkindsg.txt")
+
+  expect_known_output(print(dimethenamid_2018), "dimethenamid_2018.txt")
 })