From 0b677308e3ffbf742880f05cc54da469f3ecc854 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 9 Mar 2018 23:14:39 +0100 Subject: Another rebuild of the static docs Now with rbenchmark installed, to get results for the compiled_models vignette --- .Rbuildignore | 4 +- .gitignore | 2 + docs/articles/FOCUS_D.html | 13 +++--- docs/articles/FOCUS_D_files/figure-html/plot-1.png | Bin 96321 -> 98934 bytes .../FOCUS_D_files/figure-html/plot_2-1.png | Bin 14047 -> 14308 bytes docs/articles/FOCUS_L.html | 47 ++++++++++----------- .../figure-html/unnamed-chunk-10-1.png | Bin 28683 -> 29157 bytes .../figure-html/unnamed-chunk-12-1.png | Bin 52097 -> 54520 bytes .../figure-html/unnamed-chunk-13-1.png | Bin 21427 -> 21712 bytes .../figure-html/unnamed-chunk-15-1.png | Bin 36600 -> 38347 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 23247 -> 23493 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 14668 -> 14866 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 23624 -> 23973 bytes .../figure-html/unnamed-chunk-8-1.png | Bin 27537 -> 27988 bytes .../figure-html/unnamed-chunk-9-1.png | Bin 27959 -> 28412 bytes docs/articles/FOCUS_Z.html | 7 +-- .../figure-html/FOCUS_2006_Z_fits_1-1.png | Bin 83846 -> 85456 bytes .../figure-html/FOCUS_2006_Z_fits_10-1.png | Bin 123289 -> 128546 bytes .../figure-html/FOCUS_2006_Z_fits_11-1.png | Bin 122641 -> 128162 bytes .../figure-html/FOCUS_2006_Z_fits_11a-1.png | Bin 96633 -> 101891 bytes .../figure-html/FOCUS_2006_Z_fits_11b-1.png | Bin 22186 -> 22697 bytes .../figure-html/FOCUS_2006_Z_fits_2-1.png | Bin 84217 -> 86036 bytes .../figure-html/FOCUS_2006_Z_fits_3-1.png | Bin 83907 -> 85658 bytes .../figure-html/FOCUS_2006_Z_fits_5-1.png | Bin 96969 -> 101516 bytes .../figure-html/FOCUS_2006_Z_fits_6-1.png | Bin 123363 -> 129164 bytes .../figure-html/FOCUS_2006_Z_fits_7-1.png | Bin 123396 -> 128994 bytes .../figure-html/FOCUS_2006_Z_fits_9-1.png | Bin 103846 -> 108244 bytes docs/articles/compiled_models.html | 37 +++++++++------- docs/articles/index.html | 1 - 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- - - @@ -80,7 +77,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2018-03-01

+

2018-03-09

@@ -155,8 +152,8 @@ 
summary(fit)
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:17:55 2018 
-## Date of summary: Thu Mar  1 14:17:55 2018 
+## Date of fit:     Fri Mar  9 23:09:48 2018 
+## Date of summary: Fri Mar  9 23:09:48 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -164,7 +161,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.993 s
+## Fitted with method Port using 153 model solutions performed in 0.99 s
 ## 
 ## Weighting: none
 ## 
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diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 5de06ad5..196a0c4f 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -9,10 +9,7 @@
 
 
 
-
-
-
-
@@ -80,7 +77,7 @@
       
Example evaluation of FOCUS Laboratory Data L1 to L3

                         
Johannes Ranke

             
-            
2018-03-01

+            
2018-03-09

           
 
     
@@ -103,15 +100,15 @@ FOCUS_2006_L1_mkin <- summary(m.L1.SFO)
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:31:57 2018 
-## Date of summary: Thu Mar  1 14:31:57 2018 
+## Date of fit:     Fri Mar  9 23:09:50 2018 
+## Date of summary: Fri Mar  9 23:09:50 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 0.24 s
+## Fitted with method Port using 37 model solutions performed in 0.264 s
 ## 
 ## Weighting: none
 ## 
@@ -194,15 +191,15 @@ FOCUS_2006_L1_mkin <- 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:31:59 2018 
-## Date of summary: Thu Mar  1 14:32:00 2018 
+## Date of fit:     Fri Mar  9 23:09:52 2018 
+## Date of summary: Fri Mar  9 23:09:52 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 1.375 s
+## Fitted with method Port using 611 model solutions performed in 1.451 s
 ## 
 ## Weighting: none
 ## 
@@ -289,15 +286,15 @@ FOCUS_2006_L2_mkin <- 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:32:00 2018 
-## Date of summary: Thu Mar  1 14:32:00 2018 
+## Date of fit:     Fri Mar  9 23:09:53 2018 
+## Date of summary: Fri Mar  9 23:09:53 2018 
 ## 
 ## 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 0.158 s
+## Fitted with method Port using 81 model solutions performed in 0.175 s
 ## 
 ## Weighting: none
 ## 
@@ -360,8 +357,8 @@ FOCUS_2006_L2_mkin <- 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:32:01 2018 
-## Date of summary: Thu Mar  1 14:32:01 2018 
+## Date of fit:     Fri Mar  9 23:09:54 2018 
+## Date of summary: Fri Mar  9 23:09:54 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -370,7 +367,7 @@ FOCUS_2006_L2_mkin <-  
summary(mm.L3[["DFOP", 1]])

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:32:02 2018 
-## Date of summary: Thu Mar  1 14:32:02 2018 
+## Date of fit:     Fri Mar  9 23:09:55 2018 
+## Date of summary: Fri Mar  9 23:09:55 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -462,7 +459,7 @@ mm.L3 <-  
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:32:03 2018 
-## Date of summary: Thu Mar  1 14:32:03 2018 
+## Date of fit:     Fri Mar  9 23:09:55 2018 
+## Date of summary: Fri Mar  9 23:09:56 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 0.089 s
+## Fitted with method Port using 46 model solutions performed in 0.09 s
 ## 
 ## Weighting: none
 ## 
@@ -613,8 +610,8 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Thu Mar  1 14:32:03 2018 
-## Date of summary: Thu Mar  1 14:32:03 2018 
+## Date of fit:     Fri Mar  9 23:09:56 2018 
+## Date of summary: Fri Mar  9 23:09:56 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
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index 52a1db77..606121ff 100644
--- a/docs/articles/FOCUS_Z.html
+++ b/docs/articles/FOCUS_Z.html
@@ -9,10 +9,7 @@
 
 
 
-
-
-
-
@@ -80,7 +77,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2018-03-01

+            
2018-03-09

           
 
     
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diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 9f0b5708..915e5474 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -9,10 +9,7 @@
 
 
 
-
-
-
-
@@ -80,7 +77,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2018-03-01

+            
2018-03-09

           
 
     
@@ -101,7 +98,7 @@ SFO_SFO <- 
if (require(rbenchmark)) {
-  b.1 <- benchmark(
+  b.1 <- benchmark(
     "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
                                       solution_type = "deSolve",
                                       use_compiled = FALSE, quiet = TRUE),
@@ -117,10 +114,15 @@ SFO_SFO <- print("R package benchmark is not available")
 }

 
## Lade nötiges Paket: rbenchmark

-
## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'

-
## [1] "R package benchmark is not available"

-
We see that using the compiled model is by a factor of around NA 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.

+
##                    test replications elapsed relative user.self sys.self
+## 3     deSolve, compiled            3   2.044    1.000     2.042        0
+## 1 deSolve, not compiled            3  14.198    6.946    14.185        0
+## 2      Eigenvalue based            3   2.751    1.346     2.747        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.

 
 

 

@@ -131,7 +133,7 @@ SFO_SFO <- parent = mkinsub("FOMC", "m1"),
     m1 = mkinsub( "SFO"))
 
-  b.2 <- benchmark(
+  b.2 <- benchmark(
     "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D,
                                       use_compiled = FALSE, quiet = TRUE),
     "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
@@ -142,11 +144,14 @@ SFO_SFO <-  NA
   print("R package benchmark is not available")
 }

-
## Lade nötiges Paket: rbenchmark

-
## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'

-
## [1] "R package benchmark is not available"

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

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

+
##                    test replications elapsed relative user.self sys.self
+## 2     deSolve, compiled            3   3.695    1.000     3.692        0
+## 1 deSolve, not compiled            3  31.143    8.428    31.114        0
+##   user.child sys.child
+## 2          0         0
+## 1          0         0

+
Here we get a performance benefit of a factor of 8 using the version of the differential equation model compiled from C code!

 
This vignette was built with mkin 0.9.46.3 on

 
## R version 3.4.3 (2017-11-30)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 2b16580a..c0c5864b 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -27,7 +27,6 @@
 
   
   
-
 
 
 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index a91da0a4..f668b500 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -9,10 +9,7 @@
 
 
 
-
-
-
-
@@ -80,7 +77,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2018-03-01

+            
2018-03-09

           
 
     
diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
index 5a3e3b6c..fafe8afd 100644
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diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 400b1383..e5b68cfe 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -9,10 +9,7 @@
 
 
 
-
-
-
-
@@ -80,7 +77,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2018-03-01

+            
2018-03-09

           
 
     
diff --git a/docs/authors.html b/docs/authors.html
index 7abb53de..af022eab 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -27,7 +27,6 @@
 
   
   
-
 
 
 
@@ -107,19 +106,19 @@
 
     
    
       
  • 
-        
    Johannes Ranke. Author, maintainer, copyright holder. 
-        
    
+        
    Johannes Ranke. Author, maintainer, copyright holder.
+        
    0000-0003-4371-6538
    
       
    • 
       
  • 
-        
    Katrin Lindenberger. Contributor. 
+        
    Katrin Lindenberger. Contributor.
         
    
       
    • 
       
  • 
-        
    René Lehmann. Contributor. 
+        
    René Lehmann. Contributor.
         
    
       
    • 
       
  • 
-        
    Eurofins Regulatory AG. Copyright holder. 
+        
    Eurofins Regulatory AG. Copyright holder.
         
    
       
    • 
     

diff --git a/docs/index.html b/docs/index.html
index c20d124b..88fd4f6d 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -9,17 +9,7 @@
 
 
 
-
-
-
-
@@ -102,7 +92,7 @@
 

 

 Usage

-
For a start, have a look a the code examples provided for plot.mkinfit and plot.mmkin, and at the package vignettes FOCUS L and FOCUS D.

+
For a start, have a look a the code examples provided for plot.mkinfit and plot.mmkin, and at the package vignettes FOCUS L and FOCUS D.

 

 

 

@@ -113,17 +103,17 @@
 

 Features

 
    
-
  • Highly flexible model specification using mkinmod, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.
    • 
-
  • As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example plot.mmkin.
    • 
-
  • Model solution (forward modelling) in the function mkinpredict is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the deSolve package (default is lsoda).
    • 
-
  • If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see vignette compiled_models. The autogeneration of C code was inspired by the ccSolve package. Thanks to Karline Soetaert for her work on that.
    • 
-
  • By default, kinetic rate constants and kinetic formation fractions are transformed internally using transform_odeparms so their estimators can more reasonably be expected to follow a normal distribution. This has the side effect that no constraints are needed in the optimisation. Thanks to René Lehmann for the nice cooperation on this, especially the isometric logration transformation that is now used for the formation fractions.
    • 
+
  • Highly flexible model specification using mkinmod, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.
    • 
+
  • As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example plot.mmkin.
    • 
+
  • Model solution (forward modelling) in the function mkinpredict is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the deSolve package (default is lsoda).
    • 
+
  • If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see vignette compiled_models. The autogeneration of C code was inspired by the ccSolve package. Thanks to Karline Soetaert for her work on that.
    • 
+
  • By default, kinetic rate constants and kinetic formation fractions are transformed internally using transform_odeparms so their estimators can more reasonably be expected to follow a normal distribution. This has the side effect that no constraints are needed in the optimisation. Thanks to René Lehmann for the nice cooperation on this, especially the isometric logration transformation that is now used for the formation fractions.
    • 
 
  • A side effect of this is that when parameter estimates are backtransformed to match the model definition, confidence intervals calculated from standard errors are also backtransformed to the correct scale, and will not include meaningless values like negative rate constants or formation fractions adding up to more than 1, which can not occur in a single experiment with a single defined radiolabel position.
    • 
 
  • The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.
    • 
 
  • Summary and plotting functions. The summary of an mkinfit object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.
    • 
 
  • The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.
    • 
 
  • Iteratively reweighted least squares fitting is implemented in a similar way as in KinGUII and CAKE (see below). Simply add the argument reweight.method = "obs" to your call to mkinfit and a separate variance componenent for each of the observed variables will be optimised in a second stage after the primary optimisation algorithm has converged.
    • 
-
  • Iterative reweighting is also possible using the two-component error model for analytical data of Rocke and Lorenzato using the argument reweight.method = "tc".
    • 
+
  • Iterative reweighting is also possible using the two-component error model for analytical data of Rocke and Lorenzato using the argument reweight.method = "tc".
    • 
 
  • When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite.
    • 
 

 

@@ -169,7 +159,8 @@
 
GPL

 
Developers

 
    
-
  • Johannes Ranke 
     Author, maintainer, copyright holder   
    • 
+
  • Johannes Ranke 
     Author, maintainer, copyright holder  
    (0000-0003-4371-6538)
+
    • 
 
  • All authors...
    • 
 

 
Dev status

diff --git a/docs/news/index.html b/docs/news/index.html
index dfb70875..39b21d12 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -27,7 +27,6 @@
 
   
   
-
 
 
 
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index 181fe639..59b659f2 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -100,11 +100,6 @@ a.anchor {
   margin-bottom: 0.5em;
 }
 
-.orcid {
-  height: 16px;
-  vertical-align: middle;
-}
-
 /* Reference index & topics ----------------------------------------------- */
 
 .ref-index th {font-weight: normal;}
@@ -142,12 +137,6 @@ pre, code {
   color: #333;
 }
 
-pre code {
-  overflow: auto;
-  word-wrap: normal;
-  white-space: pre;
-}
-
 pre .img {
   margin: 5px 0;
 }
@@ -162,10 +151,6 @@ code a, pre a {
   color: #375f84;
 }
 
-a.sourceLine:hover {
-  text-decoration: none;
-}
-
 .fl      {color: #1514b5;}
 .fu      {color: #000000;} /* function */
 .ch,.st  {color: #036a07;} /* string */
diff --git a/docs/reference/DFOP.solution-1.png b/docs/reference/DFOP.solution-1.png
index 1549a73b..e9268f94 100644
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diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index ff1ad823..f89a66e2 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -27,11 +27,6 @@
 
   
   
-
-
-
-
 
 
 
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 11738484..3b96f9ae 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -27,10 +27,6 @@
 
   
   
-
-
-
-
 
 
 
@@ -263,7 +259,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>   0.058   0.000   0.057 
+#>    0.06    0.00    0.06 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -452,8 +448,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555ad80908>
-#> <environment: 0x55555b1b4b90>
+#> <bytecode: 0x5555599fd348>
+#> <environment: 0x555557684190>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -475,8 +471,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555b174428>
-#> <environment: 0x55555b1b4b90>
+#> <bytecode: 0x555559feb960>
+#> <environment: 0x555557684190>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -543,7 +539,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Thu Mar  1 14:26:09 2018"
+#> [1] "Fri Mar  9 23:08:11 2018"
 #> 
 #> $version
 #> [1] "0.9.47.1"
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 5fb3ccfe..de986f3f 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -27,14 +27,6 @@
 
   
   
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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 c1665dee..4bc0fd4b 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -27,14 +27,6 @@
 
   
   
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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 db3d228d..bf0331cc 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -27,14 +27,6 @@
 
   
   
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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 cc4fcb1d..6f05cbb9 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -27,14 +27,6 @@
 
   
   
-
-
-
-
 
 
 
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 4548c983..9ea69f23 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -27,10 +27,6 @@
 
   
   
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diff --git a/docs/reference/FOMC.solution-1.png b/docs/reference/FOMC.solution-1.png
index 58178df5..f10cff4e 100644
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index 810b0eba..b5b4c87c 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -27,14 +27,6 @@
 
   
   
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diff --git a/docs/reference/HS.solution-1.png b/docs/reference/HS.solution-1.png
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index 79358efb..0dc432ef 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -27,11 +27,6 @@
 
   
   
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diff --git a/docs/reference/IORE.solution-1.png b/docs/reference/IORE.solution-1.png
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index f705ab2f..b055534a 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -27,11 +27,6 @@
 
   
   
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diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index a7934a35..eda43e4d 100644
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+++ b/docs/reference/SFO.solution.html
@@ -27,10 +27,6 @@
 
   
   
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diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index aaae7cdd..2b6b2bc6 100644
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+++ b/docs/reference/SFORB.solution.html
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index 42bec993..407e1a3e 100644
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diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
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index 2c51001f..7ed15db5 100644
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diff --git a/docs/reference/index.html b/docs/reference/index.html
index 218194ad..84bc1dfc 100644
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diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 5d6baf6a..9e1e3974 100644
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diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index ec7f8ccd..30aa894e 100644
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+++ b/docs/reference/mccall81_245T.html
@@ -27,12 +27,6 @@
 
   
   
-
-
-
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@@ -151,8 +145,8 @@
                  fixed_parms = "k_phenol_sink", quiet = TRUE)
   summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.1 
 #> R version used for fitting:       3.4.3 
-#> Date of fit:     Thu Mar  1 14:26:15 2018 
-#> Date of summary: Thu Mar  1 14:26:15 2018 
+#> Date of fit:     Fri Mar  9 23:08:18 2018 
+#> Date of summary: Fri Mar  9 23:08:18 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index a5432dac..dc781aaf 100644
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diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
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diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
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diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
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@@ -414,15 +400,15 @@
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
#> mkin version used for fitting:    0.9.47.1 
 #> R version used for fitting:       3.4.3 
-#> Date of fit:     Thu Mar  1 14:26:18 2018 
-#> Date of summary: Thu Mar  1 14:26:18 2018 
+#> Date of fit:     Fri Mar  9 23:08:20 2018 
+#> Date of summary: Fri Mar  9 23:08:20 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 0.135 s
+#> Fitted with method Port using 64 model solutions performed in 0.148 s
 #> 
 #> Weighting: none
 #> 
@@ -491,7 +477,7 @@
   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 elapsed 
-#>    0.84    0.00    0.84 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   0.839   0.000   0.840 
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 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index c1287905..032fcbb6 100644
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--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -27,12 +27,6 @@
 
   
   
-
-
-
-
 
 
 
@@ -311,7 +305,7 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>    user  system elapsed 
-#>   0.002   0.000   0.001 
  system.time(
+#>   0.002   0.000   0.002 
  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", use_compiled = FALSE)[201,]))
#>     time   parent       m1
diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png
index 8636baf2..5b201616 100644
Binary files a/docs/reference/mkinresplot-1.png and b/docs/reference/mkinresplot-1.png differ
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index 036917f1..b4b6b116 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -27,13 +27,6 @@
 
   
   
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diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 7724220f..b4915112 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -27,11 +27,6 @@
 
   
   
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diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index e97e3f81..78033dd2 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -27,11 +27,6 @@
 
   
   
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diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png
index 2bb8f5dd..0d54d2fe 100644
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diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png
index 22a3f8b0..377d63b6 100644
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diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png
index 93e859c7..b23ddfe7 100644
Binary files a/docs/reference/plot.mkinfit-3.png and b/docs/reference/plot.mkinfit-3.png differ
diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png
index 27edd6f3..0dd9f4d6 100644
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diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 4bdad93f..b6dd1525 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -27,15 +27,6 @@
 
   
   
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diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png
index 2554b68b..c2c25e90 100644
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diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png
index 9a66294f..b40ae0d5 100644
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diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png
index b0f7fa21..dfbe014f 100644
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diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 11da6685..8b80273c 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -27,14 +27,6 @@
 
   
   
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diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 8e0d18b2..02882776 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -27,10 +27,6 @@
 
   
   
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diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index db15cc60..cd6678a6 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -27,10 +27,6 @@
 
   
   
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diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 6c53f805..04c72edd 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -27,12 +27,6 @@
 
   
   
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diff --git a/docs/reference/sigma_rl.html b/docs/reference/sigma_rl.html
index 868c0d4f..4b287e55 100644
--- a/docs/reference/sigma_rl.html
+++ b/docs/reference/sigma_rl.html
@@ -27,12 +27,6 @@
 
   
   
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diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 977ff8d8..f34736b3 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -27,13 +27,6 @@
 
   
   
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@@ -191,15 +184,15 @@
     
Examples

     
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.1 
 #> R version used for fitting:       3.4.3 
-#> Date of fit:     Thu Mar  1 14:26:27 2018 
-#> Date of summary: Thu Mar  1 14:26:27 2018 
+#> Date of fit:     Fri Mar  9 23:08:29 2018 
+#> Date of summary: Fri Mar  9 23:08:29 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 0.076 s
+#> Fitted with method Port using 35 model solutions performed in 0.075 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 192e8dc2..396a6e2b 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -27,22 +27,6 @@
 
   
   
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diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index c4292d9c..13e072c6 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -27,11 +27,6 @@
 
   
   
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diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 630a5103..266db603 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -27,18 +27,6 @@
 
   
   
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@@ -185,8 +173,8 @@ 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:    0.9.47.1 
 #> R version used for fitting:       3.4.3 
-#> Date of fit:     Thu Mar  1 14:26:28 2018 
-#> Date of summary: Thu Mar  1 14:26:28 2018 
+#> Date of fit:     Fri Mar  9 23:08:30 2018 
+#> Date of summary: Fri Mar  9 23:08:30 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -194,7 +182,7 @@ 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 0.571 s
+#> Fitted with method Port using 153 model solutions performed in 0.657 s
 #> 
 #> Weighting: none
 #> 
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 8aaa70d6..d8c5b19b 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -12,7 +12,7 @@
 
 
 
-
+
 
 Performance benefit by using compiled model definitions in mkin
 
@@ -70,7 +70,7 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
 
 
Performance benefit by using compiled model definitions in mkin

 
Johannes Ranke

-
2018-01-14

+
2018-03-09

 
 
 
@@ -87,27 +87,27 @@ SFO_SFO <- mkinmod(
   m1 = mkinsub("SFO"))

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

 
We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.

-
if (require(rbenchmark)) {
+
if (require(rbenchmark)) {
   b.1 <- benchmark(
-    "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
+    "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
                                       solution_type = "deSolve",
                                       use_compiled = FALSE, quiet = TRUE),
-    "Eigenvalue based" = mkinfit(SFO_SFO, FOCUS_2006_D,
+    "Eigenvalue based" = mkinfit(SFO_SFO, FOCUS_2006_D,
                                  solution_type = "eigen", quiet = TRUE),
-    "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
+    "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
                                   solution_type = "deSolve", quiet = TRUE),
     replications = 3)
   print(b.1)
   factor_SFO_SFO <- round(b.1["1", "relative"])
-} else {
+} else {
   factor_SFO_SFO <- NA
   print("R package benchmark is not available")
 }

 
## Loading required package: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.005    1.000     2.000    0.004
-## 1 deSolve, not compiled            3  14.202    7.083    14.196    0.000
-## 2      Eigenvalue based            3   2.427    1.210     2.428    0.000
+## 3     deSolve, compiled            3   1.980    1.000     1.979        0
+## 1 deSolve, not compiled            3  13.926    7.033    13.914        0
+## 2      Eigenvalue based            3   2.362    1.193     2.360        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -117,35 +117,35 @@ SFO_SFO <- mkinmod(
 

 
Model that can not be solved with Eigenvalues

 
This evaluation is also taken from the example section of mkinfit.

-
if (require(rbenchmark)) {
+
if (require(rbenchmark)) {
   FOMC_SFO <- mkinmod(
     parent = mkinsub("FOMC", "m1"),
     m1 = mkinsub( "SFO"))
 
   b.2 <- benchmark(
-    "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D,
+    "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D,
                                       use_compiled = FALSE, quiet = TRUE),
-    "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
+    "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
     replications = 3)
   print(b.2)
   factor_FOMC_SFO <- round(b.2["1", "relative"])
-} else {
+} else {
   factor_FOMC_SFO <- NA
   print("R package benchmark is not available")
 }

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

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   3.489    1.000     3.488        0
-## 1 deSolve, not compiled            3  28.906    8.285    28.904        0
+## 2     deSolve, compiled            3   3.437    1.000     3.433        0
+## 1 deSolve, not compiled            3  30.406    8.847    30.380        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

-
Here we get a performance benefit of a factor of 8 using the version of the differential equation model compiled from C code!

-
This vignette was built with mkin 0.9.47.1 on

+
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 0.9.46.3 on

 
## R version 3.4.3 (2017-11-30)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 9 (stretch)

-
## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz

+
## CPU model: AMD Ryzen 7 1700 Eight-Core Processor

 

 
 
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