From c90fdefb4cd438ae71c613f676c2ff6631d0a7a3 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 25 Feb 2019 15:27:41 +0100 Subject: Static documentation rebuilt by current pkgdown --- R/nafta.R | 10 ++++-- docs/articles/FOCUS_D.html | 8 ++--- docs/articles/FOCUS_L.html | 42 +++++++++++----------- docs/articles/index.html | 2 +- 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 | 14 ++++---- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/AIC.mmkin.html | 2 +- docs/reference/CAKE_export.html | 2 +- docs/reference/DFOP.solution.html | 2 +- docs/reference/Extract.mmkin.html | 14 ++++---- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 2 +- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_datasets.html | 2 +- docs/reference/FOMC.solution.html | 2 +- docs/reference/HS.solution.html | 2 +- docs/reference/IORE.solution.html | 2 +- docs/reference/NAFTA_2015_datasets.html | 9 +++-- docs/reference/SFO.solution.html | 2 +- docs/reference/SFORB.solution.html | 2 +- docs/reference/add_err.html | 2 +- docs/reference/endpoints.html | 2 +- docs/reference/geometric_mean.html | 2 +- docs/reference/ilr.html | 2 +- docs/reference/index.html | 2 +- docs/reference/logLik.mkinfit.html | 2 +- docs/reference/logistic.solution.html | 2 +- docs/reference/max_twa_parent.html | 2 +- docs/reference/mccall81_245T.html | 14 ++++---- docs/reference/mkin_long_to_wide.html | 2 +- docs/reference/mkin_wide_to_long.html | 2 +- docs/reference/mkinds.html | 2 +- docs/reference/mkinerrmin.html | 2 +- docs/reference/mkinfit.html | 48 +++++++++++++------------- docs/reference/mkinmod.html | 4 +-- docs/reference/mkinparplot.html | 2 +- docs/reference/mkinplot.html | 2 +- docs/reference/mkinpredict.html | 6 ++-- docs/reference/mkinresplot.html | 2 +- docs/reference/mkinsub.html | 2 +- docs/reference/mmkin.html | 6 ++-- docs/reference/nafta.html | 9 +++-- docs/reference/plot.mkinfit.html | 2 +- docs/reference/plot.mmkin.html | 2 +- docs/reference/plot.nafta.html | 2 +- docs/reference/print.mkinds.html | 2 +- docs/reference/print.mkinmod.html | 2 +- docs/reference/print.nafta.html | 2 +- docs/reference/schaefer07_complex_case.html | 2 +- docs/reference/sigma_twocomp.html | 2 +- docs/reference/summary.mkinfit.html | 8 ++--- docs/reference/synthetic_data_for_UBA.html | 2 +- docs/reference/test_data_from_UBA_2014.html | 2 +- docs/reference/transform_odeparms.html | 26 +++++++------- tests/testthat/test_plots_twa.R | 2 ++ 62 files changed, 165 insertions(+), 149 deletions(-) diff --git a/R/nafta.R b/R/nafta.R index 102a9ad6..2af2404f 100644 --- a/R/nafta.R +++ b/R/nafta.R @@ -65,7 +65,10 @@ plot.nafta <- function(x, legend = FALSE, main = "auto", ...) { } print.nafta <- function(x, quiet = TRUE, ...) { - cat("Parameters:\n") + cat("Sums of squares:\n") + print(x$S) + print(x$S_c) + cat("\nParameters:\n") print(x$parameters) t_rep <- .evaluate_nafta_results(x$S, x$S_c, x$distimes, quiet = quiet) cat("\nDTx values:\n") @@ -95,8 +98,9 @@ print.nafta <- function(x, quiet = TRUE, ...) { t_rep <- t_IORE } else { if (!quiet) { - message("The representative half-life of the IORE model is longer than the one corresponding to the terminal degradation rate found with the DFOP model.") - message("The reprentative half-life obtained from the DFOP model may be used") + message("The representative half-life of the IORE model is longer than the one corresponding") + message("to the terminal degradation rate found with the DFOP model.") + message("The representative half-life obtained from the DFOP model may be used") } t_rep <- t_DFOP2 } diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index a470cdb6..0875ce0f 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -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:     Mon Feb 25 14:54:38 2019 
-## Date of summary: Mon Feb 25 14:54:38 2019 
+## Date of fit:     Mon Feb 25 15:25:02 2019 
+## Date of summary: Mon Feb 25 15:25:02 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 0.712 s
+## Fitted with method Port using 153 model solutions performed in 0.689 s
 ## 
 ## Weighting: none
 ## 
@@ -292,7 +292,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index e8a81075..14827789 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -111,8 +111,8 @@
 summary(m.L1.SFO)
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Mon Feb 25 14:54:40 2019 
-## Date of summary: Mon Feb 25 14:54:40 2019 
+## Date of fit:     Mon Feb 25 15:25:04 2019 
+## Date of summary: Mon Feb 25 15:25:04 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -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:     Mon Feb 25 14:54:42 2019 
-## Date of summary: Mon Feb 25 14:54:42 2019 
+## Date of fit:     Mon Feb 25 15:25:06 2019 
+## Date of summary: Mon Feb 25 15:25:06 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 1.529 s
+## Fitted with method Port using 611 model solutions performed in 1.516 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:     Mon Feb 25 14:54:42 2019 
-## Date of summary: Mon Feb 25 14:54:42 2019 
+## Date of fit:     Mon Feb 25 15:25:06 2019 
+## Date of summary: Mon Feb 25 15:25:06 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 0.199 s
+## Fitted with method Port using 81 model solutions performed in 0.198 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:     Mon Feb 25 14:54:44 2019 
-## Date of summary: Mon Feb 25 14:54:44 2019 
+## Date of fit:     Mon Feb 25 15:25:07 2019 
+## Date of summary: Mon Feb 25 15:25:07 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 0.853 s
+## Fitted with method Port using 336 model solutions performed in 0.85 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:     Mon Feb 25 14:54:45 2019 
-## Date of summary: Mon Feb 25 14:54:45 2019 
+## Date of fit:     Mon Feb 25 15:25:08 2019 
+## Date of summary: Mon Feb 25 15:25:09 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 0.348 s
+## Fitted with method Port using 137 model solutions performed in 0.346 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:     Mon Feb 25 14:54:45 2019 
-## Date of summary: Mon Feb 25 14:54:45 2019 
+## Date of fit:     Mon Feb 25 15:25:09 2019 
+## Date of summary: Mon Feb 25 15:25:09 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 0.112 s
+## Fitted with method Port using 46 model solutions performed in 0.111 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:     Mon Feb 25 14:54:45 2019 
-## Date of summary: Mon Feb 25 14:54:45 2019 
+## Date of fit:     Mon Feb 25 15:25:09 2019 
+## Date of summary: Mon Feb 25 15:25:09 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 0.165 s
+## Fitted with method Port using 66 model solutions performed in 0.164 s
 ## 
 ## Weighting: none
 ## 
@@ -724,7 +724,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
 
diff --git a/docs/articles/index.html b/docs/articles/index.html
index b2b11a3f..a1c08835 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -140,7 +140,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index bffd19dd..24520f74 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -247,7 +247,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
 
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 83b05989..bf56eff2 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -136,7 +136,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
 
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index c3ee7415..48f08bfc 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -321,7 +321,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
 
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 4209d2bc..16f0cc7a 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -126,14 +126,14 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 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
+## 3     deSolve, compiled            3   2.328    1.000     2.327        0
+## 1 deSolve, not compiled            3  17.641    7.578    17.633        0
+## 2      Eigenvalue based            3   2.873    1.234     2.871        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
 ## 2          0         0

-
We see that using the compiled model is by a factor of around 7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.

+
We see that using the compiled model is by a factor of around 8 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.

 
 

 

@@ -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   4.162    1.000     4.158        0
-## 1 deSolve, not compiled            3  37.536    9.019    37.517        0
+## 2     deSolve, compiled            3   4.126    1.000     4.125        0
+## 1 deSolve, not compiled            3  37.487    9.086    37.467        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

@@ -190,7 +190,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
 
diff --git a/docs/authors.html b/docs/authors.html
index 78296059..1c3101aa 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -148,7 +148,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/index.html b/docs/index.html
index 1fe49776..75cf8c00 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -202,7 +202,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
 
diff --git a/docs/news/index.html b/docs/news/index.html
index cd82d187..a66f5bbc 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -720,7 +720,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 7b40553c..2783dff9 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
 pandoc: 2.2.1
-pkgdown: 1.3.0
+pkgdown: 1.3.0.9000
 pkgdown_sha: ~
 articles:
   FOCUS_D: FOCUS_D.html
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html
index 3d10d36e..69552d5f 100644
--- a/docs/reference/AIC.mmkin.html
+++ b/docs/reference/AIC.mmkin.html
@@ -198,7 +198,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html
index 886c1922..74e77339 100644
--- a/docs/reference/CAKE_export.html
+++ b/docs/reference/CAKE_export.html
@@ -229,7 +229,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index 9bc215f0..40e2a0fa 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -196,7 +196,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 95b1558e..f86ff43a 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -280,7 +280,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.196       0.000       0.196 
+#>       0.196       0.000       0.198 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -469,8 +469,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x555559255c78>
-#> <environment: 0x55555add1128>
+#> <bytecode: 0x5555592a5fc0>
+#> <environment: 0x55555ba81950>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -492,8 +492,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555a1e9540>
-#> <environment: 0x55555add1128>
+#> <bytecode: 0x55555a5e0ee8>
+#> <environment: 0x55555ba81950>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -560,7 +560,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Mon Feb 25 14:52:43 2019"
+#> [1] "Mon Feb 25 15:23:07 2019"
 #> 
 #> $version
 #> [1] "0.9.48.1"
@@ -593,7 +593,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
index 9a43e010..9babae16 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -184,7 +184,7 @@ in this fit.

 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
index 663600dd..6e11464e 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -183,7 +183,7 @@ in this fit.

 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
index 58cab325..59219e45 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -184,7 +184,7 @@ in this fit.

 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
index f9cf0e11..67df3476 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -182,7 +182,7 @@ in this fit.

 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 56f58d03..7d38639b 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -180,7 +180,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index fe6944d3..43466474 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -210,7 +210,7 @@ The form given here differs slightly from the original reference by Gustafson
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 6997ebae..048a24c3 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -197,7 +197,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 103a1ae3..9646461c 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -211,7 +211,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/NAFTA_2015_datasets.html b/docs/reference/NAFTA_2015_datasets.html
index 9ef56fb0..be080428 100644
--- a/docs/reference/NAFTA_2015_datasets.html
+++ b/docs/reference/NAFTA_2015_datasets.html
@@ -152,7 +152,12 @@
     
 
     
Examples

-    
  nafta_evaluation <- nafta(MRID_555555)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding to the terminal degradation rate found with the DFOP model.
#> The reprentative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Parameters:
+    
  nafta_evaluation <- nafta(MRID_555555)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
+#>       SFO      IORE      DFOP 
+#> 1378.6832  615.7730  517.8836 
+#> [1] 717.4598
+#> 
+#> Parameters:
 #> $SFO
 #>                   Estimate       Pr(>t)        Lower        Upper
 #> parent_0      83.755751519 8.076390e-15 76.928220975 90.583282063
@@ -201,7 +206,7 @@
 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    

diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 325a4285..dd04ad1a 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -185,7 +185,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index f22b3af5..19566257 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -202,7 +202,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index c2db5b52..40f23bee 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -254,7 +254,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index e241c7b9..bd23c95a 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -191,7 +191,7 @@ with the advantage that the SFORB model can also be used for metabolites.

 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index e52ac866..e5a12b7d 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -171,7 +171,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 4c8af606..0ab8f0a3 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -193,7 +193,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 24f3df0c..24403ad6 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -485,7 +485,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index 1e3b5702..2f211431 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -231,7 +231,7 @@ In the case of iterative reweighting, the variances obtained by this
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index 728fbaa9..a30059fe 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -237,7 +237,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 2c10b624..17be80d5 100644
--- a/docs/reference/max_twa_parent.html
+++ b/docs/reference/max_twa_parent.html
@@ -193,7 +193,7 @@ guidance.

 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index bcc871d8..d4501489 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:     Mon Feb 25 14:53:05 2019 
-#> Date of summary: Mon Feb 25 14:53:05 2019 
+#> Date of fit:     Mon Feb 25 15:23:29 2019 
+#> Date of summary: Mon Feb 25 15:23:29 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 3.873 s
+#> Fitted with method Port using 574 model solutions performed in 3.852 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:     Mon Feb 25 14:53:07 2019 
-#> Date of summary: Mon Feb 25 14:53:07 2019 
+#> Date of fit:     Mon Feb 25 15:23:31 2019 
+#> Date of summary: Mon Feb 25 15:23:31 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 1.623 s
+#> Fitted with method Port using 246 model solutions performed in 1.604 s
 #> 
 #> Weighting: none
 #> 
@@ -362,7 +362,7 @@
 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index f8849a3e..f034f955 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -205,7 +205,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index 04eaff8b..e874f9bf 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -183,7 +183,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index 7a87c11e..a9362c2b 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -173,7 +173,7 @@ in order to be compatible with mkinfit

 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index c155a838..149006a5 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -209,7 +209,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.

 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 80278890..ffc87dfb 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:     Mon Feb 25 14:53:09 2019 
-#> Date of summary: Mon Feb 25 14:53:09 2019 
+#> Date of fit:     Mon Feb 25 15:23:34 2019 
+#> Date of summary: Mon Feb 25 15:23:34 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 0.168 s
+#> Fitted with method Port using 64 model solutions performed in 0.163 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 
-#>       1.038       0.000       1.039 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       1.011       0.000       1.012 
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 
-#>       0.827       0.000       0.827 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.826       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:     Mon Feb 25 14:53:22 2019 
-#> Date of summary: Mon Feb 25 14:53:22 2019 
+#> Date of fit:     Mon Feb 25 15:23:46 2019 
+#> Date of summary: Mon Feb 25 15:23:46 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 0.898 s
+#> Fitted with method Port using 186 model solutions performed in 0.849 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:     Mon Feb 25 14:53:24 2019 
-#> Date of summary: Mon Feb 25 14:53:24 2019 
+#> Date of fit:     Mon Feb 25 15:23:48 2019 
+#> Date of summary: Mon Feb 25 15:23:48 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 2.572 s
+#> Fitted with method Port using 551 model solutions performed in 2.529 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:     Mon Feb 25 14:53:25 2019 
-#> Date of summary: Mon Feb 25 14:53:25 2019 
+#> Date of fit:     Mon Feb 25 15:23:49 2019 
+#> Date of summary: Mon Feb 25 15:23:49 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 0.709 s
+#> Fitted with method Port using 155 model solutions performed in 0.707 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:     Mon Feb 25 14:53:26 2019 
-#> Date of summary: Mon Feb 25 14:53:26 2019 
+#> Date of fit:     Mon Feb 25 15:23:50 2019 
+#> Date of summary: Mon Feb 25 15:23:50 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 0.81 s
+#> Fitted with method Port using 174 model solutions performed in 0.803 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:     Mon Feb 25 14:53:28 2019 
-#> Date of summary: Mon Feb 25 14:53:28 2019 
+#> Date of fit:     Mon Feb 25 15:23:52 2019 
+#> Date of summary: Mon Feb 25 15:23:52 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 1.25 s
+#> Fitted with method Port using 270 model solutions performed in 1.242 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:     Mon Feb 25 14:53:31 2019 
-#> Date of summary: Mon Feb 25 14:53:31 2019 
+#> Date of fit:     Mon Feb 25 15:23:55 2019 
+#> Date of summary: Mon Feb 25 15:23:55 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 3.302 s
+#> Fitted with method Port using 692 model solutions performed in 3.263 s
 #> 
 #> Weighting: manual
 #> 
@@ -1373,7 +1373,7 @@
 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index ba26c686..48693b0c 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 file481263217c00.c 2> file481263217c00.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file6703f4535ea.c 2> file6703f4535ea.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
@@ -288,7 +288,7 @@ For the definition of model types and their parameters, the equations given
 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 7438e0e0..f0706605 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -175,7 +175,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 2f386d45..2eed795a 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -169,7 +169,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 738eeb9d..5d786bac 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 
-#>       0.003       0.000       0.003 
  system.time(
+#>       0.003       0.000       0.004 
  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 
-#>       0.047       0.000       0.047 

+#>       0.040       0.000       0.039 

   
    # 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 
@@ -396,7 +396,7 @@
 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index 702e50eb..e1ba5acb 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -222,7 +222,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 95689f48..3e0bdcbd 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -200,7 +200,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 1a60e3ea..29684bad 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 
-#>       0.036       0.039       7.196 
time_1
#>        User      System verstrichen 
-#>      22.818       0.000      22.834 

+#>       0.040       0.038       7.255 
time_1
#>        User      System verstrichen 
+#>      22.747       0.000      22.761 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340480   0.2659520   0.7505686   0.2494314 
@@ -237,7 +237,7 @@
 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html
index c74c3939..071ea132 100644
--- a/docs/reference/nafta.html
+++ b/docs/reference/nafta.html
@@ -175,7 +175,12 @@
     
 
     
Examples

-    
  nafta_evaluation <- nafta(MRID_555555)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding to the terminal degradation rate found with the DFOP model.
#> The reprentative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Parameters:
+    
  nafta_evaluation <- nafta(MRID_555555)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
+#>       SFO      IORE      DFOP 
+#> 1378.6832  615.7730  517.8836 
+#> [1] 717.4598
+#> 
+#> Parameters:
 #> $SFO
 #>                   Estimate       Pr(>t)        Lower        Upper
 #> parent_0      83.755751519 8.076390e-15 76.928220975 90.583282063
@@ -227,7 +232,7 @@
 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    

diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index b46da2f1..44ac2967 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -291,7 +291,7 @@ plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, …
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index acea2def..dd7b619d 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -215,7 +215,7 @@ If the current plot device is a tikz device,
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html
index ccc98b23..76da1ffa 100644
--- a/docs/reference/plot.nafta.html
+++ b/docs/reference/plot.nafta.html
@@ -178,7 +178,7 @@ plot(x, legend = FALSE, main = "auto", …)

 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index e4e142d7..1d858500 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -162,7 +162,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index d5e128a7..ace71925 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -183,7 +183,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/print.nafta.html b/docs/reference/print.nafta.html
index dc9373f7..ac276857 100644
--- a/docs/reference/print.nafta.html
+++ b/docs/reference/print.nafta.html
@@ -166,7 +166,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 410c95d8..b7ba3d96 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -213,7 +213,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index 01b0d542..f44a1c14 100644
--- a/docs/reference/sigma_twocomp.html
+++ b/docs/reference/sigma_twocomp.html
@@ -192,7 +192,7 @@ This is the error model used for example by Werner et al. (1978). The model
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index f0d4a060..9afaf13a 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:     Mon Feb 25 14:54:24 2019 
-#> Date of summary: Mon Feb 25 14:54:24 2019 
+#> Date of fit:     Mon Feb 25 15:24:48 2019 
+#> Date of summary: Mon Feb 25 15:24:48 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 0.085 s
+#> Fitted with method Port using 35 model solutions performed in 0.086 s
 #> 
 #> Weighting: none
 #> 
@@ -300,7 +300,7 @@
 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index b2b55805..6363db6f 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -301,7 +301,7 @@ summary(fit)
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 39f6d364..b3ec4699 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -226,7 +226,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 1071a932..6861f712 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:     Mon Feb 25 14:54:32 2019 
-#> Date of summary: Mon Feb 25 14:54:32 2019 
+#> Date of fit:     Mon Feb 25 15:24:56 2019 
+#> Date of summary: Mon Feb 25 15:24:56 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 0.704 s
+#> Fitted with method Port using 153 model solutions performed in 0.737 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:     Mon Feb 25 14:54:34 2019 
-#> Date of summary: Mon Feb 25 14:54:34 2019 
+#> Date of fit:     Mon Feb 25 15:24:58 2019 
+#> Date of summary: Mon Feb 25 15:24:58 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 1.62 s
+#> Fitted with method Port using 350 model solutions performed in 1.593 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:     Mon Feb 25 14:54:35 2019 
-#> Date of summary: Mon Feb 25 14:54:35 2019 
+#> Date of fit:     Mon Feb 25 15:24:59 2019 
+#> Date of summary: Mon Feb 25 15:24:59 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 0.856 s
+#> Fitted with method Port using 186 model solutions performed in 0.858 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:     Mon Feb 25 14:54:36 2019 
-#> Date of summary: Mon Feb 25 14:54:36 2019 
+#> Date of fit:     Mon Feb 25 15:25:00 2019 
+#> Date of summary: Mon Feb 25 15:25:00 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 0.482 s
+#> Fitted with method Port using 104 model solutions performed in 0.473 s
 #> 
 #> Weighting: none
 #> 
@@ -534,7 +534,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.3.0.9000.

 

       
    
diff --git a/tests/testthat/test_plots_twa.R b/tests/testthat/test_plots_twa.R
index fe0ba325..0014f738 100644
--- a/tests/testthat/test_plots_twa.R
+++ b/tests/testthat/test_plots_twa.R
@@ -52,9 +52,11 @@ context("Plotting")
 
 test_that("Plotting mmkin objects is reproducible", {
   skip_on_cran()
+  plot_sep_FOCUS_C_SFO <- function() plot_sep(fits[[, "FOCUS_C"]])
   mmkin_FOCUS_C <- function() plot(fits[, "FOCUS_C"])
   mmkin_SFO <- function() plot(fits["SFO",])
 
+  vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with sep = TRUE", plot_sep_FOCUS_C_SFO)
   vdiffr::expect_doppelganger("mmkin plot for FOCUS C", mmkin_FOCUS_C)
   vdiffr::expect_doppelganger("mmkin plot for SFO (FOCUS C and D)", mmkin_SFO)
 })
-- 
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