Adapt saemix interface to saemix 3.0 on CRAN

1 files changed, 157 insertions, 8 deletions

diff --git a/test.log b/test.log
index 4d5012a0..019305bf 100644
--- a/test.log
+++ b/test.log
@@ -2,41 +2,190 @@
 Loading required package: parallel
 ℹ Testing mkin
 ✔ | F W S  OK | Context
+
+⠏ |         0 | AIC                                                             
+⠏ |         0 | AIC calculation                                                 
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [3.5s]
+
+⠏ |         0 | analytical                                                      
+⠏ |         0 | Analytical solutions for coupled models                         
+⠋ |         1 | Analytical solutions for coupled models                         
+⠙ |         2 | Analytical solutions for coupled models                         
+⠹ |         3 | Analytical solutions for coupled models                         
+⠸ |         4 | Analytical solutions for coupled models                         
+⠼ |         5 | Analytical solutions for coupled models                         
+✔ |         5 | Analytical solutions for coupled models [3.4s]
+
+⠏ |         0 | aw                                                              
+⠏ |         0 | Calculation of Akaike weights                                   
 ✔ |         5 | Calculation of Akaike weights
+
+⠏ |         0 | CAKE_export                                                     
+⠏ |         0 | Export dataset for reading into CAKE                            
 ✔ |         2 | Export dataset for reading into CAKE
+
+⠏ |         0 | confidence                                                      
+⠏ |         0 | Confidence intervals and p-values                               
+⠼ |         5 | Confidence intervals and p-values                               
+⠋ |        11 | Confidence intervals and p-values                               
+⠙ |        12 | Confidence intervals and p-values                               
 ✔ |        12 | Confidence intervals and p-values [1.0s]
-✔ |        14 | Error model fitting [5.0s]
+
+⠏ |         0 | error_models                                                    
+⠏ |         0 | Error model fitting                                             
+⠹ |         3 | Error model fitting                                             
+⠸ |         4 | Error model fitting                                             
+⠼ |         5 | Error model fitting                                             
+⠴ |         6 | Error model fitting                                             
+⠧ |         8 | Error model fitting                                             
+⠏ |        10 | Error model fitting                                             
+⠙ |        12 | Error model fitting                                             
+⠸ |        14 | Error model fitting                                             
+✔ |        14 | Error model fitting [4.9s]
+
+⠏ |         0 | f_time_norm                                                     
+⠏ |         0 | Time step normalisation                                         
 ✔ |         5 | Time step normalisation
+
+⠏ |         0 | FOCUS_chi2_error_level                                          
+⠏ |         0 | Calculation of FOCUS chi2 error levels                          
+⠙ |         2 | Calculation of FOCUS chi2 error levels                          
+⠸ |         4 | Calculation of FOCUS chi2 error levels                          
 ✔ |         4 | Calculation of FOCUS chi2 error levels [0.6s]
+
+⠏ |         0 | FOCUS_D_UBA_expertise                                           
+⠏ |         0 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
+⠋ |         1 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
+⠧ |         8 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
+⠏ |        10 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
 ✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
+
+⠏ |         0 | from_max_mean                                                   
+⠏ |         0 | Test fitting the decline of metabolites from their maximum      
+⠹ |         3 | Test fitting the decline of metabolites from their maximum      
+⠸ |         4 | Test fitting the decline of metabolites from their maximum      
 ✔ |         4 | Test fitting the decline of metabolites from their maximum [0.3s]
+
+⠏ |         0 | logistic                                                        
+⠏ |         0 | Fitting the logistic model                                      
+⠋ |         1 | Fitting the logistic model                                      
 ✔ |         1 | Fitting the logistic model [0.2s]
-✔ |     1  35 | Nonlinear mixed-effects models [26.8s]
+
+⠏ |         0 | mixed                                                           
+⠏ |         0 | Nonlinear mixed-effects models                                  
+⠙ |         2 | Nonlinear mixed-effects models                                  
+⠹ |         3 | Nonlinear mixed-effects models                                  
+⠸ |         4 | Nonlinear mixed-effects models                                  
+⠏ |        10 | Nonlinear mixed-effects models                                  
+⠙ |        12 | Nonlinear mixed-effects models                                  
+⠧ |        18 | Nonlinear mixed-effects models                                  
+⠙ |        22 | Nonlinear mixed-effects models                                  
+⠹ |        23 | Nonlinear mixed-effects models                                  
+✔ |     1  35 | Nonlinear mixed-effects models [26.6s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_mixed.R:161:3): saem results are reproducible for biphasic fits
 Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ────────────────────────────────────────────────────────────────────────────────
+
+⠏ |         0 | mkinds                                                          
+⠏ |         0 | Test dataset classes mkinds and mkindsg                         
 ✔ |         2 | Test dataset classes mkinds and mkindsg
+
+⠏ |         0 | mkinfit_errors                                                  
+⠏ |         0 | Special cases of mkinfit calls                                  
+⠇ |         9 | Special cases of mkinfit calls                                  
+⠏ |        10 | Special cases of mkinfit calls                                  
 ✔ |        10 | Special cases of mkinfit calls [0.4s]
-✔ |         1 | mkinfit features [0.4s]
+
+⠏ |         0 | mkinfit                                                         
+⠏ |         0 | mkinfit features                                                
+⠋ |         1 | mkinfit features                                                
+✔ |         1 | mkinfit features [0.3s]
+
+⠏ |         0 | mkinmod                                                         
+⠏ |         0 | mkinmod model generation and printing                           
+⠧ |         8 | mkinmod model generation and printing                           
 ✔ |         8 | mkinmod model generation and printing [0.2s]
+
+⠏ |         0 | mkinpredict_SFO_SFO                                             
+⠏ |         0 | Model predictions with mkinpredict                              
+⠋ |         1 | Model predictions with mkinpredict                              
 ✔ |         3 | Model predictions with mkinpredict [0.3s]
+
+⠏ |         0 | nafta                                                           
+⠏ |         0 | Evaluations according to 2015 NAFTA guidance                    
+⠙ |         2 | Evaluations according to 2015 NAFTA guidance                    
+⠇ |         9 | Evaluations according to 2015 NAFTA guidance                    
+⠏ |        10 | Evaluations according to 2015 NAFTA guidance                    
 ✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.5s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.2s]
+
+⠏ |         0 | nlme                                                            
+⠏ |         0 | Nonlinear mixed-effects models with nlme                        
+⠋ |         1 | Nonlinear mixed-effects models with nlme                        
+⠙ |         2 | Nonlinear mixed-effects models with nlme                        
+⠼ |         5 | Nonlinear mixed-effects models with nlme                        
+⠴ |         6 | Nonlinear mixed-effects models with nlme                        
+⠧ |         8 | Nonlinear mixed-effects models with nlme                        
+⠇ |         9 | Nonlinear mixed-effects models with nlme                        
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.3s]
+
+⠏ |         0 | nlmixr                                                          
+⠏ |         0 | plot                                                            
+⠏ |         0 | Plotting                                                        
+⠋ |         1 | Plotting                                                        
+⠇ |         9 | Plotting                                                        
+⠹ |        13 | Plotting                                                        
+⠼ |        15 | Plotting                                                        
 ✔ |        16 | Plotting [1.3s]
+
+⠏ |         0 | residuals                                                       
+⠏ |         0 | Residuals extracted from mkinfit models                         
 ✔ |         4 | Residuals extracted from mkinfit models
+
+⠏ |         0 | schaefer07_complex_case                                         
+⠏ |         0 | Complex test case from Schaefer et al. (2007) Piacenza paper    
+⠋ |         1 | Complex test case from Schaefer et al. (2007) Piacenza paper    
 ✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s]
-✔ |         7 | Fitting the SFORB model [3.8s]
+
+⠏ |         0 | SFORB                                                           
+⠏ |         0 | Fitting the SFORB model                                         
+⠋ |         1 | Fitting the SFORB model                                         
+⠼ |         5 | Fitting the SFORB model                                         
+✔ |         7 | Fitting the SFORB model [3.9s]
+
+⠏ |         0 | summary_old_objects                                             
+⠏ |         0 | Summaries of old mkinfit objects                                
 ✔ |         1 | Summaries of old mkinfit objects
+
+⠏ |         0 | summary                                                         
+⠏ |         0 | Summary                                                         
+⠸ |         4 | Summary                                                         
 ✔ |         4 | Summary [0.1s]
+
+⠏ |         0 | synthetic_data_for_UBA_2014                                     
+⠏ |         0 | Results for synthetic data established in expertise for UBA (Ranke 2014)
+⠋ |         1 | Results for synthetic data established in expertise for UBA (Ranke 2014)
+⠹ |         3 | Results for synthetic data established in expertise for UBA (Ranke 2014)
 ✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s]
-✔ |         9 | Hypothesis tests [8.6s]
+
+⠏ |         0 | tests                                                           
+⠏ |         0 | Hypothesis tests                                                
+⠼ |         5 | Hypothesis tests                                                
+⠴ |         6 | Hypothesis tests                                                
+⠧ |         8 | Hypothesis tests                                                
+⠇ |         9 | Hypothesis tests                                                
+✔ |         9 | Hypothesis tests [8.5s]
+
+⠏ |         0 | twa                                                             
+⠏ |         0 | Calculation of maximum time weighted average concentrations (TWAs)
+⠋ |         1 | Calculation of maximum time weighted average concentrations (TWAs)
+⠙ |         2 | Calculation of maximum time weighted average concentrations (TWAs)
+⠹ |         3 | Calculation of maximum time weighted average concentrations (TWAs)
+⠸ |         4 | Calculation of maximum time weighted average concentrations (TWAs)
 ✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 69.5 s
+Duration: 69.0 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting with saemix takes around 10 minutes when using deSolve (1)