From b2cbfc35e4c2b3f8dbb2e9d83ab1f4b358427896 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 14 Sep 2018 17:20:20 +0200 Subject: Update NEWS Static documentation rebuilt by pkgdown --- docs/articles/FOCUS_D.html | 6 ++-- docs/articles/FOCUS_L.html | 38 ++++++++++++------------ docs/articles/web_only/compiled_models.html | 12 ++++---- docs/news/index.html | 22 ++++++++++---- docs/reference/Extract.mmkin.html | 12 ++++---- docs/reference/mccall81_245T.html | 12 ++++---- docs/reference/mkinfit.html | 46 ++++++++++++++--------------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 2 +- docs/reference/mmkin.html | 4 +-- docs/reference/summary.mkinfit.html | 6 ++-- docs/reference/transform_odeparms.html | 24 +++++++-------- 12 files changed, 98 insertions(+), 88 deletions(-) (limited to 'docs') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 6dde02d4..a90cb7fb 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -162,8 +162,8 @@ 
summary(fit)
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 16:50:31 2018 
-## Date of summary: Fri Sep 14 16:50:31 2018 
+## Date of fit:     Fri Sep 14 17:17:43 2018 
+## Date of summary: Fri Sep 14 17:17:44 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -171,7 +171,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.728 s
+## Fitted with method Port using 153 model solutions performed in 0.645 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 1087c0ed..8b06f072 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -110,15 +110,15 @@
 summary(m.L1.SFO)
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 16:54:49 2018 
-## Date of summary: Fri Sep 14 16:54:49 2018 
+## Date of fit:     Fri Sep 14 17:43:07 2018 
+## Date of summary: Fri Sep 14 17:43:07 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.088 s
+## Fitted with method Port using 37 model solutions performed in 0.091 s
 ## 
 ## Weighting: none
 ## 
@@ -201,15 +201,15 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 16:54:51 2018 
-## Date of summary: Fri Sep 14 16:54:51 2018 
+## Date of fit:     Fri Sep 14 17:43:09 2018 
+## Date of summary: Fri Sep 14 17:43:09 2018 
 ## 
 ## 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 1.349 s
+## Fitted with method Port using 611 model solutions performed in 1.398 s
 ## 
 ## Weighting: none
 ## 
@@ -296,8 +296,8 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 16:54:51 2018 
-## Date of summary: Fri Sep 14 16:54:51 2018 
+## Date of fit:     Fri Sep 14 17:43:10 2018 
+## Date of summary: Fri Sep 14 17:43:10 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -367,8 +367,8 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 16:54:52 2018 
-## Date of summary: Fri Sep 14 16:54:52 2018 
+## Date of fit:     Fri Sep 14 17:43:11 2018 
+## Date of summary: Fri Sep 14 17:43:11 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -377,7 +377,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.754 s
+## Fitted with method Port using 336 model solutions performed in 0.782 s
 ## 
 ## Weighting: none
 ## 
@@ -459,8 +459,8 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 16:54:53 2018 
-## Date of summary: Fri Sep 14 16:54:53 2018 
+## Date of fit:     Fri Sep 14 17:43:12 2018 
+## Date of summary: Fri Sep 14 17:43:12 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -560,15 +560,15 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 16:54:54 2018 
-## Date of summary: Fri Sep 14 16:54:54 2018 
+## Date of fit:     Fri Sep 14 17:43:12 2018 
+## Date of summary: Fri Sep 14 17:43:12 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.098 s
+## Fitted with method Port using 46 model solutions performed in 0.106 s
 ## 
 ## Weighting: none
 ## 
@@ -620,15 +620,15 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 16:54:54 2018 
-## Date of summary: Fri Sep 14 16:54:54 2018 
+## Date of fit:     Fri Sep 14 17:43:12 2018 
+## Date of summary: Fri Sep 14 17:43:12 2018 
 ## 
 ## 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 0.153 s
+## Fitted with method Port using 66 model solutions performed in 0.15 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index e941bea3..0d91a50c 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -125,9 +125,9 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.120    1.000     2.118    0.000
-## 1 deSolve, not compiled            3  17.195    8.111    17.187    0.000
-## 2      Eigenvalue based            3   2.589    1.221     2.582    0.004
+## 3     deSolve, compiled            3   2.174    1.000     2.172        0
+## 1 deSolve, not compiled            3  16.745    7.702    16.737        0
+## 2      Eigenvalue based            3   2.652    1.220     2.650        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -156,12 +156,12 @@
 }

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

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   3.761    1.000     3.758    0.000
-## 1 deSolve, not compiled            3  36.462    9.695    36.441    0.004
+## 2     deSolve, compiled            3   4.012    1.000     4.010        0
+## 1 deSolve, not compiled            3  35.620    8.878    35.604        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

-
Here we get a performance benefit of a factor of 10 using the version of the differential equation model compiled from C code!

+
Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!

 
This vignette was built with mkin 0.9.47.5 on

 
## R version 3.5.1 (2018-07-02)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/news/index.html b/docs/news/index.html
index 4bd93964..cbfcdde0 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -117,17 +117,26 @@
       
     
 
-    

+    

 

-mkin 0.9.47.4 (2018-09-14) Unreleased 
+mkin 0.9.47.5 (2018-09-14) Unreleased 
+

+
    
+
  • Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows
    • 
+
  • Move two vignettes to a location where they will not be built on CRAN (to avoid more NOTES from long execution times)
    • 
+

+

+    

+

+mkin 0.9.47.4 Unreleased 
 

 
    
 
  • Exclude more example code from testing on CRAN to avoid NOTES from long execution times
    • 
 

 

-    

+    

 

-mkin 0.9.47.3 (not released to CRAN) Unreleased 
+mkin 0.9.47.3 Unreleased 
 

 
    
 
  • ‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’. Add ‘manual’ to possible arguments for ‘weight’
    • 
@@ -656,8 +665,9 @@
     
    
       
    Contents
    
       
      
-        
    • 0.9.47.4
      • 
-        
    • 0.9.47.3
      • 
+        
    • 0.9.47.5
      • 
+        
    • 0.9.47.4
      • 
+        
    • 0.9.47.3
      • 
         
    • 0.9.47.2
      • 
         
    • 0.9.47.1
      • 
         
    • 0.9.46.3
      • 
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 9d49313c..8cf55860 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -278,7 +278,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.169       0.000       0.169 
+#>       0.174       0.000       0.173 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -467,8 +467,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555bd4a710>
-#> <environment: 0x55555bd3c748>
+#> <bytecode: 0x55555bd78ed0>
+#> <environment: 0x55555bc7eda8>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -490,8 +490,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555c9b4488>
-#> <environment: 0x55555bd3c748>
+#> <bytecode: 0x55555ca99e50>
+#> <environment: 0x55555bc7eda8>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -558,7 +558,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Fri Sep 14 16:53:13 2018"
+#> [1] "Fri Sep 14 17:41:26 2018"
 #> 
 #> $version
 #> [1] "0.9.47.5"
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 86f3c07e..902f1224 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -158,8 +158,8 @@
                          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:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 16:53:25 2018 
-#> Date of summary: Fri Sep 14 16:53:25 2018 
+#> Date of fit:     Fri Sep 14 17:41:38 2018 
+#> Date of summary: Fri Sep 14 17:41:38 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -169,7 +169,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 574 model solutions performed in 3.403 s
+#> Fitted with method Port using 574 model solutions performed in 3.566 s
 #> 
 #> Weighting: none
 #> 
@@ -247,8 +247,8 @@
                    fixed_parms = "k_phenol_sink", quiet = TRUE)
     summary(fit.2, data = FALSE)
    #> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 16:53:27 2018 
-#> Date of summary: Fri Sep 14 16:53:27 2018 
+#> Date of fit:     Fri Sep 14 17:41:39 2018 
+#> Date of summary: Fri Sep 14 17:41:40 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -258,7 +258,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.46 s
+#> Fitted with method Port using 246 model solutions performed in 1.577 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 0f2bb875..2d5ed97f 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -434,15 +434,15 @@
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
    #> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 16:53:29 2018 
-#> Date of summary: Fri Sep 14 16:53:29 2018 
+#> Date of fit:     Fri Sep 14 17:41:42 2018 
+#> Date of summary: Fri Sep 14 17:41:42 2018 
 #> 
 #> 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 0.158 s
+#> Fitted with method Port using 64 model solutions performed in 0.153 s
 #> 
 #> Weighting: none
 #> 
@@ -511,7 +511,7 @@
   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 
-#>       0.909       0.000       0.910 
    coef(fit)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.946       0.000       0.947 
    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 
@@ -586,7 +586,7 @@
 #> Model cost at call  146 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>        User      System verstrichen 
-#>       0.749       0.000       0.749 
    coef(fit.deSolve)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.762       0.000       0.763 
    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 
@@ -624,8 +624,8 @@
                       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:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 16:53:40 2018 
-#> Date of summary: Fri Sep 14 16:53:40 2018 
+#> Date of fit:     Fri Sep 14 17:41:54 2018 
+#> Date of summary: Fri Sep 14 17:41:54 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -633,7 +633,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.79 s
+#> Fitted with method Port using 186 model solutions performed in 0.874 s
 #> 
 #> Weighting: none
 #> 
@@ -741,8 +741,8 @@
 #>   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:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 16:53:43 2018 
-#> Date of summary: Fri Sep 14 16:53:43 2018 
+#> Date of fit:     Fri Sep 14 17:41:56 2018 
+#> Date of summary: Fri Sep 14 17:41:56 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -750,7 +750,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 551 model solutions performed in 2.278 s
+#> Fitted with method Port using 551 model solutions performed in 2.493 s
 #> 
 #> Weighting: none
 #> 
@@ -863,8 +863,8 @@
 #>   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:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 16:53:43 2018 
-#> Date of summary: Fri Sep 14 16:53:43 2018 
+#> Date of fit:     Fri Sep 14 17:41:57 2018 
+#> Date of summary: Fri Sep 14 17:41:57 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -872,7 +872,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 155 model solutions performed in 0.643 s
+#> Fitted with method Port using 155 model solutions performed in 0.692 s
 #> 
 #> Weighting: mean
 #> 
@@ -981,8 +981,8 @@
                      quiet = TRUE)
 summary(f.w.value)
    #> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 16:53:44 2018 
-#> Date of summary: Fri Sep 14 16:53:44 2018 
+#> Date of fit:     Fri Sep 14 17:41:58 2018 
+#> Date of summary: Fri Sep 14 17:41:58 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -990,7 +990,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 174 model solutions performed in 0.722 s
+#> Fitted with method Port using 174 model solutions performed in 0.749 s
 #> 
 #> Weighting: manual
 #> 
@@ -1101,8 +1101,8 @@
 f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
 summary(f.w.man)
    #> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 16:53:45 2018 
-#> Date of summary: Fri Sep 14 16:53:45 2018 
+#> Date of fit:     Fri Sep 14 17:41:59 2018 
+#> Date of summary: Fri Sep 14 17:41:59 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1110,7 +1110,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 270 model solutions performed in 1.11 s
+#> Fitted with method Port using 270 model solutions performed in 1.155 s
 #> 
 #> Weighting: manual
 #> 
@@ -1219,8 +1219,8 @@
                        reweight.method = "obs")
 summary(f.w.man.irls)
    #> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 16:53:49 2018 
-#> Date of summary: Fri Sep 14 16:53:49 2018 
+#> Date of fit:     Fri Sep 14 17:42:03 2018 
+#> Date of summary: Fri Sep 14 17:42:03 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1228,7 +1228,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 692 model solutions performed in 2.945 s
+#> Fitted with method Port using 692 model solutions performed in 3.154 s
 #> 
 #> Weighting: manual
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 3633686e..fa2880ec 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -229,7 +229,7 @@ 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 file7b505448f8a5.c 2> file7b505448f8a5.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file2cf4aedfaf6.c 2> file2cf4aedfaf6.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 6c30d7a8..fc90757d 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -331,7 +331,7 @@
                 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 
-#>       0.035       0.000       0.035 

+#>        0.04        0.00        0.04 

   
   
#>        User      System verstrichen 
-#>       0.054       0.029       6.762 
time_1
#>        User      System verstrichen 
-#>      20.495       0.004      20.512 

+#>       0.044       0.034       7.567 
time_1
#>        User      System verstrichen 
+#>      22.374       0.000      22.397 

 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 bb701470..01c0d330 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -206,15 +206,15 @@
     
Examples

     
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 16:54:36 2018 
-#> Date of summary: Fri Sep 14 16:54:36 2018 
+#> Date of fit:     Fri Sep 14 17:42:54 2018 
+#> Date of summary: Fri Sep 14 17:42:54 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.077 s
+#> Fitted with method Port using 35 model solutions performed in 0.078 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 38c3fe9d..55640a7f 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -200,8 +200,8 @@ 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:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 16:54:43 2018 
-#> Date of summary: Fri Sep 14 16:54:43 2018 
+#> Date of fit:     Fri Sep 14 17:43:01 2018 
+#> Date of summary: Fri Sep 14 17:43:01 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -209,7 +209,7 @@ 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 0.629 s
+#> Fitted with method Port using 153 model solutions performed in 0.739 s
 #> 
 #> Weighting: none
 #> 
@@ -276,8 +276,8 @@ 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:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 16:54:45 2018 
-#> Date of summary: Fri Sep 14 16:54:45 2018 
+#> Date of fit:     Fri Sep 14 17:43:03 2018 
+#> Date of summary: Fri Sep 14 17:43:03 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -285,7 +285,7 @@ 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 1.426 s
+#> Fitted with method Port using 350 model solutions performed in 1.457 s
 #> 
 #> Weighting: none
 #> 
@@ -364,8 +364,8 @@ 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:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 16:54:46 2018 
-#> Date of summary: Fri Sep 14 16:54:46 2018 
+#> Date of fit:     Fri Sep 14 17:43:04 2018 
+#> Date of summary: Fri Sep 14 17:43:04 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -373,7 +373,7 @@ 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 0.766 s
+#> Fitted with method Port using 186 model solutions performed in 0.785 s
 #> 
 #> Weighting: none
 #> 
@@ -448,8 +448,8 @@ 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:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 16:54:46 2018 
-#> Date of summary: Fri Sep 14 16:54:46 2018 
+#> Date of fit:     Fri Sep 14 17:43:05 2018 
+#> Date of summary: Fri Sep 14 17:43:05 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -457,7 +457,7 @@ 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 0.42 s
+#> Fitted with method Port using 104 model solutions performed in 0.429 s
 #> 
 #> Weighting: none
 #> 
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