From be809ea23b256f627216958fcd90489ee0844ab8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 25 Feb 2019 14:50:13 +0100 Subject: Add plotting tests, add nafta to pkgdown --- docs/articles/FOCUS_D.html | 8 ++--- docs/articles/FOCUS_L.html | 44 +++++++++++++-------------- docs/articles/mkin.html | 2 +- docs/articles/twa.html | 2 +- docs/articles/web_only/FOCUS_Z.html | 2 +- docs/articles/web_only/compiled_models.html | 12 ++++---- docs/reference/Extract.mmkin.html | 12 ++++---- docs/reference/index.html | 6 ++++ docs/reference/mccall81_245T.html | 12 ++++---- docs/reference/mkinfit.html | 46 ++++++++++++++--------------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 4 +-- docs/reference/mmkin.html | 4 +-- docs/reference/summary.mkinfit.html | 6 ++-- docs/reference/transform_odeparms.html | 24 +++++++-------- 15 files changed, 96 insertions(+), 90 deletions(-) (limited to 'docs') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index ad8413dc..a470cdb6 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -85,7 +85,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2019-02-22

+

2019-02-25

@@ -163,8 +163,8 @@ 
summary(fit)
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:30 2019 
-## Date of summary: Fri Feb 22 20:48:31 2019 
+## Date of fit:     Mon Feb 25 14:54:38 2019 
+## Date of summary: Mon Feb 25 14:54:38 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -172,7 +172,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.731 s
+## Fitted with method Port using 153 model solutions performed in 0.712 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 17c7bf59..e8a81075 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -85,7 +85,7 @@
       
Example evaluation of FOCUS Laboratory Data L1 to L3

                         
Johannes Ranke

             
-            
2019-02-22

+            
2019-02-25

       
       
       
@@ -111,15 +111,15 @@
 summary(m.L1.SFO)
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:32 2019 
-## Date of summary: Fri Feb 22 20:48:32 2019 
+## Date of fit:     Mon Feb 25 14:54:40 2019 
+## Date of summary: Mon Feb 25 14:54:40 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.105 s
+## Fitted with method Port using 37 model solutions performed in 0.096 s
 ## 
 ## Weighting: none
 ## 
@@ -202,15 +202,15 @@
 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:34 2019 
-## Date of summary: Fri Feb 22 20:48:34 2019 
+## Date of fit:     Mon Feb 25 14:54:42 2019 
+## Date of summary: Mon Feb 25 14:54:42 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 611 model solutions performed in 1.604 s
+## Fitted with method Port using 611 model solutions performed in 1.529 s
 ## 
 ## Weighting: none
 ## 
@@ -297,15 +297,15 @@
 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:35 2019 
-## Date of summary: Fri Feb 22 20:48:35 2019 
+## Date of fit:     Mon Feb 25 14:54:42 2019 
+## Date of summary: Mon Feb 25 14:54:42 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.216 s
+## Fitted with method Port using 81 model solutions performed in 0.199 s
 ## 
 ## Weighting: none
 ## 
@@ -368,8 +368,8 @@
 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:36 2019 
-## Date of summary: Fri Feb 22 20:48:36 2019 
+## Date of fit:     Mon Feb 25 14:54:44 2019 
+## Date of summary: Mon Feb 25 14:54:44 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -378,7 +378,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.864 s
+## Fitted with method Port using 336 model solutions performed in 0.853 s
 ## 
 ## Weighting: none
 ## 
@@ -460,8 +460,8 @@
 
summary(mm.L3[["DFOP", 1]])

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:37 2019 
-## Date of summary: Fri Feb 22 20:48:38 2019 
+## Date of fit:     Mon Feb 25 14:54:45 2019 
+## Date of summary: Mon Feb 25 14:54:45 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -470,7 +470,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.362 s
+## Fitted with method Port using 137 model solutions performed in 0.348 s
 ## 
 ## Weighting: none
 ## 
@@ -561,15 +561,15 @@
 
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:38 2019 
-## Date of summary: Fri Feb 22 20:48:38 2019 
+## Date of fit:     Mon Feb 25 14:54:45 2019 
+## Date of summary: Mon Feb 25 14:54:45 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.123 s
+## Fitted with method Port using 46 model solutions performed in 0.112 s
 ## 
 ## Weighting: none
 ## 
@@ -621,15 +621,15 @@
 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:38 2019 
-## Date of summary: Fri Feb 22 20:48:38 2019 
+## Date of fit:     Mon Feb 25 14:54:45 2019 
+## Date of summary: Mon Feb 25 14:54:45 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.184 s
+## Fitted with method Port using 66 model solutions performed in 0.165 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 9baa44e4..bffd19dd 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -85,7 +85,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2019-02-22

+            
2019-02-25

       
       
       
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 8c340557..83b05989 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -85,7 +85,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2019-02-22

+            
2019-02-25

       
       
       
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index b1e2811c..c3ee7415 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -85,7 +85,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2019-02-22

+            
2019-02-25

       
       
       
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index fbf2de33..4209d2bc 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -85,7 +85,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2019-02-22

+            
2019-02-25

       
       
       
@@ -126,9 +126,9 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.484    1.000     2.483        0
-## 1 deSolve, not compiled            3  17.963    7.231    17.951        0
-## 2      Eigenvalue based            3   3.146    1.267     3.144        0
+## 3     deSolve, compiled            3   2.394    1.000     2.388    0.004
+## 1 deSolve, not compiled            3  17.923    7.487    17.910    0.000
+## 2      Eigenvalue based            3   3.021    1.262     3.018    0.000
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -157,8 +157,8 @@
 }

 
## Successfully compiled differential equation model from auto-generated C code.

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.232    1.000     4.226    0.004
-## 1 deSolve, not compiled            3  37.946    8.966    37.924    0.000
+## 2     deSolve, compiled            3   4.162    1.000     4.158        0
+## 1 deSolve, not compiled            3  37.536    9.019    37.517        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index e3285ed3..95b1558e 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -280,7 +280,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.201       0.000       0.200 
+#>       0.196       0.000       0.196 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -469,8 +469,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x555559103bf0>
-#> <environment: 0x55555a51ba10>
+#> <bytecode: 0x555559255c78>
+#> <environment: 0x55555add1128>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -492,8 +492,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555a537b00>
-#> <environment: 0x55555a51ba10>
+#> <bytecode: 0x55555a1e9540>
+#> <environment: 0x55555add1128>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -560,7 +560,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Fri Feb 22 20:46:31 2019"
+#> [1] "Mon Feb 25 14:52:43 2019"
 #> 
 #> $version
 #> [1] "0.9.48.1"
diff --git a/docs/reference/index.html b/docs/reference/index.html
index f31a72fe..24f3df0c 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -151,6 +151,12 @@
           
mmkin() 

         
         
Fit one or more kinetic models with one or more state variables to one or more datasets

+      
+        
+        
+          
nafta() 

+        
+        
Evaluate parent kinetics using the NAFTA guidance

       
     
       
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 7b3418de..bcc871d8 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -160,8 +160,8 @@
                          anisole = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  
    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
     summary(fit.1, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:46:54 2019 
-#> Date of summary: Fri Feb 22 20:46:54 2019 
+#> Date of fit:     Mon Feb 25 14:53:05 2019 
+#> Date of summary: Mon Feb 25 14:53:05 2019 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -171,7 +171,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 574 model solutions performed in 4.461 s
+#> Fitted with method Port using 574 model solutions performed in 3.873 s
 #> 
 #> Weighting: none
 #> 
@@ -249,8 +249,8 @@
                    fixed_parms = "k_phenol_sink", quiet = TRUE)
     summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:46:56 2019 
-#> Date of summary: Fri Feb 22 20:46:56 2019 
+#> Date of fit:     Mon Feb 25 14:53:07 2019 
+#> Date of summary: Mon Feb 25 14:53:07 2019 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -260,7 +260,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.709 s
+#> Fitted with method Port using 246 model solutions performed in 1.623 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index dfdddb25..80278890 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -438,15 +438,15 @@
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:46:59 2019 
-#> Date of summary: Fri Feb 22 20:46:59 2019 
+#> Date of fit:     Mon Feb 25 14:53:09 2019 
+#> Date of summary: Mon Feb 25 14:53:09 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 64 model solutions performed in 0.185 s
+#> Fitted with method Port using 64 model solutions performed in 0.168 s
 #> 
 #> Weighting: none
 #> 
@@ -515,7 +515,7 @@
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#>        User      System verstrichen 
-#>       1.071       0.000       1.072 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       1.038       0.000       1.039 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -590,7 +590,7 @@
 #> Model cost at call  146 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>        User      System verstrichen 
-#>       0.852       0.000       0.852 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.827       0.000       0.827 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -628,8 +628,8 @@
                       m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(f.noweight)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:47:11 2019 
-#> Date of summary: Fri Feb 22 20:47:11 2019 
+#> Date of fit:     Mon Feb 25 14:53:22 2019 
+#> Date of summary: Mon Feb 25 14:53:22 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -637,7 +637,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.864 s
+#> Fitted with method Port using 186 model solutions performed in 0.898 s
 #> 
 #> Weighting: none
 #> 
@@ -745,8 +745,8 @@
 #>   120       m1    33.31  28.78984  4.520e+00
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
 summary(f.irls)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:47:14 2019 
-#> Date of summary: Fri Feb 22 20:47:14 2019 
+#> Date of fit:     Mon Feb 25 14:53:24 2019 
+#> Date of summary: Mon Feb 25 14:53:24 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -754,7 +754,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 551 model solutions performed in 2.584 s
+#> Fitted with method Port using 551 model solutions performed in 2.572 s
 #> 
 #> Weighting: none
 #> 
@@ -867,8 +867,8 @@
 #>   120       m1    33.31  28.80898  4.501e+00 2.722
f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE)
 summary(f.w.mean)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:47:15 2019 
-#> Date of summary: Fri Feb 22 20:47:15 2019 
+#> Date of fit:     Mon Feb 25 14:53:25 2019 
+#> Date of summary: Mon Feb 25 14:53:25 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -876,7 +876,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 155 model solutions performed in 0.716 s
+#> Fitted with method Port using 155 model solutions performed in 0.709 s
 #> 
 #> Weighting: mean
 #> 
@@ -985,8 +985,8 @@
                      quiet = TRUE)
 summary(f.w.value)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:47:16 2019 
-#> Date of summary: Fri Feb 22 20:47:16 2019 
+#> Date of fit:     Mon Feb 25 14:53:26 2019 
+#> Date of summary: Mon Feb 25 14:53:26 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -994,7 +994,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 174 model solutions performed in 0.83 s
+#> Fitted with method Port using 174 model solutions performed in 0.81 s
 #> 
 #> Weighting: manual
 #> 
@@ -1105,8 +1105,8 @@
 f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
 summary(f.w.man)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:47:17 2019 
-#> Date of summary: Fri Feb 22 20:47:17 2019 
+#> Date of fit:     Mon Feb 25 14:53:28 2019 
+#> Date of summary: Mon Feb 25 14:53:28 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1114,7 +1114,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 270 model solutions performed in 1.286 s
+#> Fitted with method Port using 270 model solutions performed in 1.25 s
 #> 
 #> Weighting: manual
 #> 
@@ -1223,8 +1223,8 @@
                        reweight.method = "obs")
 summary(f.w.man.irls)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:47:21 2019 
-#> Date of summary: Fri Feb 22 20:47:21 2019 
+#> Date of fit:     Mon Feb 25 14:53:31 2019 
+#> Date of summary: Mon Feb 25 14:53:31 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1232,7 +1232,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 692 model solutions performed in 3.38 s
+#> Fitted with method Port using 692 model solutions performed in 3.302 s
 #> 
 #> Weighting: manual
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 64fba5e5..ba26c686 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -231,7 +231,7 @@ For the definition of model types and their parameters, the equations given
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file622753352edd.c 2> file622753352edd.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file481263217c00.c 2> file481263217c00.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 2b4c33aa..738eeb9d 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -325,7 +325,7 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "eigen")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.004       0.000       0.003 
  system.time(
+#>       0.003       0.000       0.003 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
@@ -335,7 +335,7 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.039       0.000       0.040 

+#>       0.047       0.000       0.047 

   
    # Predict from a fitted model
     f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Model cost at call  1 :  552.5739 
 #> Model cost at call  3 :  552.5739 
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 71ec89e8..1a60e3ea 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -191,8 +191,8 @@
 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.052       0.044       7.383 
time_1
#>        User      System verstrichen 
-#>      23.652       0.004      23.672 

+#>       0.036       0.039       7.196 
time_1
#>        User      System verstrichen 
+#>      22.818       0.000      22.834 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340480   0.2659520   0.7505686   0.2494314 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 39ef962c..f0d4a060 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -208,15 +208,15 @@
     
Examples

     
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:48:16 2019 
-#> Date of summary: Fri Feb 22 20:48:16 2019 
+#> Date of fit:     Mon Feb 25 14:54:24 2019 
+#> Date of summary: Mon Feb 25 14:54:24 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.088 s
+#> Fitted with method Port using 35 model solutions performed in 0.085 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 9d18fbb2..1071a932 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -202,8 +202,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:48:24 2019 
-#> Date of summary: Fri Feb 22 20:48:24 2019 
+#> Date of fit:     Mon Feb 25 14:54:32 2019 
+#> Date of summary: Mon Feb 25 14:54:32 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -211,7 +211,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.717 s
+#> Fitted with method Port using 153 model solutions performed in 0.704 s
 #> 
 #> Weighting: none
 #> 
@@ -278,8 +278,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
 summary(fit.2, data=FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:48:26 2019 
-#> Date of summary: Fri Feb 22 20:48:26 2019 
+#> Date of fit:     Mon Feb 25 14:54:34 2019 
+#> Date of summary: Mon Feb 25 14:54:34 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -287,7 +287,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 350 model solutions performed in 1.661 s
+#> Fitted with method Port using 350 model solutions performed in 1.62 s
 #> 
 #> Weighting: none
 #> 
@@ -366,8 +366,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:48:27 2019 
-#> Date of summary: Fri Feb 22 20:48:27 2019 
+#> Date of fit:     Mon Feb 25 14:54:35 2019 
+#> Date of summary: Mon Feb 25 14:54:35 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -375,7 +375,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.871 s
+#> Fitted with method Port using 186 model solutions performed in 0.856 s
 #> 
 #> Weighting: none
 #> 
@@ -450,8 +450,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:48:28 2019 
-#> Date of summary: Fri Feb 22 20:48:28 2019 
+#> Date of fit:     Mon Feb 25 14:54:36 2019 
+#> Date of summary: Mon Feb 25 14:54:36 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -459,7 +459,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 104 model solutions performed in 0.484 s
+#> Fitted with method Port using 104 model solutions performed in 0.482 s
 #> 
 #> Weighting: none
 #> 
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