From dd65f3503e9d091c82aedcf91635fcf40f778bf9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 14 Sep 2018 06:41:44 +0200 Subject: Static documentation rebuilt by pkgdown Also update test log --- docs/articles/FOCUS_D.html | 4 +- docs/articles/FOCUS_L.html | 60 +++++++++++++------------- docs/articles/FOCUS_Z.html | 4 +- docs/articles/compiled_models.html | 16 +++---- docs/articles/index.html | 2 +- docs/articles/mkin.html | 4 +- docs/articles/twa.html | 4 +- docs/authors.html | 2 +- docs/index.html | 4 +- docs/news/index.html | 14 +++++- docs/reference/DFOP.solution.html | 2 +- docs/reference/Extract.mmkin.html | 16 +++---- 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/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/max_twa_parent.html | 2 +- docs/reference/mccall81_245T.html | 10 ++--- 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 | 17 ++++---- docs/reference/mkinmod.html | 2 +- docs/reference/mkinparplot.html | 2 +- docs/reference/mkinplot.html | 2 +- docs/reference/mkinpredict.html | 8 ++-- docs/reference/mkinresplot.html | 2 +- docs/reference/mkinsub.html | 2 +- docs/reference/mmkin.html | 2 +- docs/reference/plot.mkinfit.html | 2 +- docs/reference/plot.mmkin.html | 2 +- docs/reference/print.mkinds.html | 2 +- docs/reference/print.mkinmod.html | 2 +- docs/reference/schaefer07_complex_case.html | 2 +- docs/reference/sigma_twocomp.html | 2 +- docs/reference/summary.mkinfit.html | 10 ++--- docs/reference/synthetic_data_for_UBA.html | 2 +- docs/reference/test_data_from_UBA_2014.html | 2 +- docs/reference/transform_odeparms.html | 10 ++--- test.log | 27 +++++++----- 52 files changed, 150 insertions(+), 132 deletions(-) diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 0afabe7f..195570b1 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -29,7 +29,7 @@ mkin - 0.9.47.2 + 0.9.47.3 @@ -84,7 +84,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2018-09-06

+

2018-09-14

diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index a42c6e38..f7bbf961 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -29,7 +29,7 @@ mkin - 0.9.47.2 + 0.9.47.3 @@ -84,7 +84,7 @@

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2018-09-06

+

2018-09-14

@@ -108,17 +108,17 @@

Since mkin version 0.9-32 (July 2014), we can use shorthand notation like "SFO" for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.

m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
-
## mkin version used for fitting:    0.9.47.2 
+
## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 13:35:50 2018 
-## Date of summary: Thu Sep  6 13:35:50 2018 
+## Date of fit:     Fri Sep 14 06:39:28 2018 
+## Date of summary: Fri Sep 14 06:39:28 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 0.086 s
+## Fitted with method Port using 37 model solutions performed in 0.091 s
 ## 
 ## Weighting: none
 ## 
@@ -199,17 +199,17 @@
 plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")

 

 
-
## mkin version used for fitting:    0.9.47.2 
+
## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 13:35:52 2018 
-## Date of summary: Thu Sep  6 13:35:52 2018 
+## Date of fit:     Fri Sep 14 06:39:30 2018 
+## Date of summary: Fri Sep 14 06:39:30 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 1.35 s
+## Fitted with method Port using 611 model solutions performed in 1.333 s
 ## 
 ## Weighting: none
 ## 
@@ -294,17 +294,17 @@
      main = "FOCUS L2 - FOMC")

 

 
-
## mkin version used for fitting:    0.9.47.2 
+
## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 13:35:52 2018 
-## Date of summary: Thu Sep  6 13:35:53 2018 
+## Date of fit:     Fri Sep 14 06:39:30 2018 
+## Date of summary: Fri Sep 14 06:39:30 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 0.175 s
+## Fitted with method Port using 81 model solutions performed in 0.172 s
 ## 
 ## Weighting: none
 ## 
@@ -365,10 +365,10 @@
      main = "FOCUS L2 - DFOP")

 

 
-
## mkin version used for fitting:    0.9.47.2 
+
## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 13:35:53 2018 
-## Date of summary: Thu Sep  6 13:35:53 2018 
+## Date of fit:     Fri Sep 14 06:39:31 2018 
+## Date of summary: Fri Sep 14 06:39:31 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 0.746 s
+## Fitted with method Port using 336 model solutions performed in 0.742 s
 ## 
 ## Weighting: none
 ## 
@@ -457,10 +457,10 @@
 
The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.

 
We can extract the summary and plot for e.g. the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.

 
-
## mkin version used for fitting:    0.9.47.2 
+
## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 13:35:54 2018 
-## Date of summary: Thu Sep  6 13:35:55 2018 
+## Date of fit:     Fri Sep 14 06:39:32 2018 
+## Date of summary: Fri Sep 14 06:39:32 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -469,7 +469,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.324 s
+## Fitted with method Port using 137 model solutions performed in 0.312 s
 ## 
 ## Weighting: none
 ## 
@@ -558,17 +558,17 @@
 

 
The \(\chi^2\) error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the \(\chi^2\) test passes is slightly lower for the FOMC model. However, the difference appears negligible.

 
-
## mkin version used for fitting:    0.9.47.2 
+
## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 13:35:55 2018 
-## Date of summary: Thu Sep  6 13:35:55 2018 
+## Date of fit:     Fri Sep 14 06:39:33 2018 
+## Date of summary: Fri Sep 14 06:39:33 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 0.107 s
+## Fitted with method Port using 46 model solutions performed in 0.097 s
 ## 
 ## Weighting: none
 ## 
@@ -618,17 +618,17 @@
 ##        DT50 DT90
 ## parent  106  352

 
-
## mkin version used for fitting:    0.9.47.2 
+
## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 13:35:55 2018 
-## Date of summary: Thu Sep  6 13:35:55 2018 
+## Date of fit:     Fri Sep 14 06:39:33 2018 
+## Date of summary: Fri Sep 14 06:39:33 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 0.161 s
+## Fitted with method Port using 66 model solutions performed in 0.143 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html
index 6e7707f8..9753abd6 100644
--- a/docs/articles/FOCUS_Z.html
+++ b/docs/articles/FOCUS_Z.html
@@ -29,7 +29,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
@@ -84,7 +84,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2018-09-06

+            
2018-09-14

       
       
       
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 16059fcb..d93fe9e1 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -29,7 +29,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
@@ -84,7 +84,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2018-09-06

+            
2018-09-14

       
       
       
@@ -125,9 +125,9 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.218    1.000     2.217        0
-## 1 deSolve, not compiled            3  16.654    7.509    16.646        0
-## 2      Eigenvalue based            3   2.724    1.228     2.722        0
+## 3     deSolve, compiled            3   2.110    1.000     2.108        0
+## 1 deSolve, not compiled            3  16.442    7.792    16.433        0
+## 2      Eigenvalue based            3   2.593    1.229     2.592        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -156,13 +156,13 @@
 }

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

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   3.780    1.000     3.777        0
-## 1 deSolve, not compiled            3  35.169    9.304    35.152        0
+## 2     deSolve, compiled            3   3.781    1.000     3.778        0
+## 1 deSolve, not compiled            3  34.742    9.189    34.725        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

 
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 0.9.47.2 on

+
This vignette was built with mkin 0.9.47.3 on

 
## R version 3.5.1 (2018-07-02)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 9 (stretch)

diff --git a/docs/articles/index.html b/docs/articles/index.html
index 7902c611..dcaf33b8 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -58,7 +58,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 234c6885..4d62b50d 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -29,7 +29,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
@@ -84,7 +84,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2018-09-06

+            
2018-09-14

       
       
       
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 1a8a7eb2..2952e887 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -29,7 +29,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
@@ -84,7 +84,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2018-09-06

+            
2018-09-14

       
       
       
diff --git a/docs/authors.html b/docs/authors.html
index b60e270c..20849b4a 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -58,7 +58,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/index.html b/docs/index.html
index 11a699ff..ba838a39 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -36,7 +36,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
@@ -139,7 +139,7 @@
 

 

 News

-
There is a ChangeLog, for the latest CRAN release and one for the github master branch.

+
There is a ChangeLog, for the latest CRAN release and one for the github master branch.

 

 

 

diff --git a/docs/news/index.html b/docs/news/index.html
index 71390917..b76ca884 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -58,7 +58,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     

 
@@ -117,6 +117,15 @@
       
     
 
+    

+

+mkin 0.9.47.3 (2018-09-13) Unreleased 
+

+
    
+
  • ‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’
    • 
+
  • Test that FOCUS_2006_C can be evaluated with DFOP and reweight.method = ‘tc’
    • 
+

+

     

 

 mkin 0.9.47.2 (2018-07-19) 2018-07-19 
@@ -131,7 +140,7 @@
 mkin 0.9.47.1 (2018-02-06) 2018-02-06 
 

 
    
-
  • Skip some test on CRAN and winbuilder to avoid timeouts
    • 
+
  • Skip some tests on CRAN and winbuilder to avoid timeouts
    • 
 
  • ‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014
    • 
 
  • ‘mkinfit’: Added the iterative reweighting method ‘tc’ using the two-component error model from Rocke and Lorenzato. NA values in the data are not returned any more.
    • 
 
  • ‘mkinfit’: Work around a bug in the current FME version that prevented the convergence message to be returned in the case of non-convergence.
    • 
@@ -639,6 +648,7 @@
     
    
       
    Contents
    
       
      
+        
    • 0.9.47.3
      • 
         
    • 0.9.47.2
      • 
         
    • 0.9.47.1
      • 
         
    • 0.9.46.3
      • 
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index c1177306..22709123 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
    
 
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 8771b53b..94c4d336 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     

 
@@ -278,7 +278,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.171       0.001       0.171 
+#>       0.165       0.000       0.165 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -467,8 +467,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555bd7f970>
-#> <environment: 0x55555bc8fca8>
+#> <bytecode: 0x55555bd36378>
+#> <environment: 0x55555bd42bc8>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -490,8 +490,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555ca84338>
-#> <environment: 0x55555bc8fca8>
+#> <bytecode: 0x55555c995188>
+#> <environment: 0x55555bd42bc8>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -558,10 +558,10 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Thu Sep  6 13:35:24 2018"
+#> [1] "Fri Sep 14 06:38:57 2018"
 #> 
 #> $version
-#> [1] "0.9.47.2"
+#> [1] "0.9.47.3"
 #> 
 #> $Rversion
 #> [1] "3.5.1"
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 6888c0ba..2b6886ff 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -65,7 +65,7 @@ in this fit." />
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
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 624f3908..73b2450b 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -65,7 +65,7 @@ in this fit." />
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
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 c089e5e7..e5621863 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -65,7 +65,7 @@ in this fit." />
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
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 e6846a38..872d68a9 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -65,7 +65,7 @@ in this fit." />
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 42ff6926..232be6f3 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 9f7db6c1..c4f3158d 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -65,7 +65,7 @@ The form given here differs slightly from the original reference by Gustafson
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 87ee2d20..8f1ff8de 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 18c8a751..ae09fcf7 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index ac26f950..f4e8eb42 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index bb782104..e568bd5a 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index 9d71c18c..99871884 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index 46cb10e1..e39d1c15 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -64,7 +64,7 @@ with the advantage that the SFORB model can also be used for metabolites." />
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index 091e65ea..a5c63aeb 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 34edfc08..ec49468a 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index d9705ce3..af7642e6 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -58,7 +58,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 447d9fda..8d31b0d2 100644
--- a/docs/reference/max_twa_parent.html
+++ b/docs/reference/max_twa_parent.html
@@ -65,7 +65,7 @@ guidance." />
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 9894f8eb..cea92155 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
@@ -164,10 +164,10 @@
   fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),
                  parms.ini = c(k_phenol_sink = 0),
                  fixed_parms = "k_phenol_sink", quiet = TRUE)
-  summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.2 
+  summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.3 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Thu Sep  6 13:35:34 2018 
-#> Date of summary: Thu Sep  6 13:35:34 2018 
+#> Date of fit:     Fri Sep 14 06:39:07 2018 
+#> Date of summary: Fri Sep 14 06:39:07 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -177,7 +177,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.549 s
+#> Fitted with method Port using 246 model solutions performed in 1.423 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index 2bf67d39..8d53bc1b 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     

 
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index 3e0f10f7..e7342cee 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index 3f4a84ec..16086f3e 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 44fc1e51..c8fd8272 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -62,7 +62,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." />
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index f9c6c117..b1c42168 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -71,7 +71,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
@@ -161,7 +161,7 @@
   transform_rates = TRUE,
   transform_fractions = TRUE,
   plot = FALSE, quiet = FALSE, err = NULL,
-  weight = c("none", "std", "mean", "tc"),
+  weight = c("none", "manual", "std", "mean", "tc"),
   tc = c(sigma_low = 0.5, rsd_high = 0.07),
   scaleVar = FALSE,
   atol = 1e-8, rtol = 1e-10, n.outtimes = 100,
@@ -326,7 +326,8 @@
       weight
       
only if err=NULL: how to weight the residuals, one of "none",
     "std", "mean", see details of modCost, or "tc" for the
-    two component error model.

+    two component error model. The option "manual" is available for 
+    the case that err!=NULL, but it is not necessary to specify it.

     
     
       tc
@@ -431,17 +432,17 @@
     
Examples

     
# Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.47.2 
+summary(fit)
#> mkin version used for fitting:    0.9.47.3 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Thu Sep  6 13:35:36 2018 
-#> Date of summary: Thu Sep  6 13:35:36 2018 
+#> Date of fit:     Fri Sep 14 06:39:09 2018 
+#> Date of summary: Fri Sep 14 06:39:09 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 0.144 s
+#> Fitted with method Port using 64 model solutions performed in 0.157 s
 #> 
 #> Weighting: none
 #> 
@@ -510,7 +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 
-#>       0.919       0.000       0.920 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.892       0.000       0.892 
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 a9c6bb26..a0eade3b 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -66,7 +66,7 @@ For the definition of model types and their parameters, the equations given
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     

 
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 33eeefbd..75d22288 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 71437181..6aa67e5b 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 59b67a5d..6c2ba992 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
@@ -321,17 +321,17 @@
                 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(
+#>       0.004       0.000       0.003 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.002       0.000       0.002 
  system.time(
+#>       0.001       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
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.037       0.000       0.038 

+#>       0.035       0.000       0.036 

   
   
 
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 85345135..65de0664 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 2a060628..557da0d7 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 07fc4854..765f1628 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -66,7 +66,7 @@ If the current plot device is a tikz device,
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 829105bd..0599907d 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -65,7 +65,7 @@ If the current plot device is a tikz device,
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 70c4f768..86bb58e5 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index 141dd1c9..bc4c644a 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 18f3b78f..b212aa53 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index 8bf1d5f6..c8000ae5 100644
--- a/docs/reference/sigma_twocomp.html
+++ b/docs/reference/sigma_twocomp.html
@@ -66,7 +66,7 @@ This is the error model used for example by Werner et al. (1978). The model
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 7b7b0a31..28447e64 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
@@ -204,17 +204,17 @@
     
 
     
Examples

-    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.2 
+    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.3 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Thu Sep  6 13:35:46 2018 
-#> Date of summary: Thu Sep  6 13:35:46 2018 
+#> Date of fit:     Fri Sep 14 06:39:24 2018 
+#> Date of summary: Fri Sep 14 06:39:24 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 0.075 s
+#> Fitted with method Port using 35 model solutions performed in 0.081 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 9d9404e5..dd44a450 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -76,7 +76,7 @@ Compare also the code in the example section to see the degradation models." />
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     

 
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 5b683283..f9032c84 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     

 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 1b94d319..a31b075e 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -69,7 +69,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
       
       
         mkin
-        0.9.47.2
+        0.9.47.3
       
     
 
@@ -198,10 +198,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
   parent = list(type = "SFO", to = "m1", sink = TRUE),
   m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
-summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.47.2 
+summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.47.3 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Thu Sep  6 13:35:48 2018 
-#> Date of summary: Thu Sep  6 13:35:48 2018 
+#> Date of fit:     Fri Sep 14 06:39:25 2018 
+#> Date of summary: Fri Sep 14 06:39:25 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 0.619 s
+#> Fitted with method Port using 153 model solutions performed in 0.642 s
 #> 
 #> Weighting: none
 #> 
diff --git a/test.log b/test.log
index c74df1b7..25afc5a1 100644
--- a/test.log
+++ b/test.log
@@ -1,14 +1,21 @@
 Loading mkin
 Loading required package: testthat
 Testing mkin
-Calculation of FOCUS chi2 error levels: ..
-Results for FOCUS D established in expertise for UBA (Ranke 2014): ......
-The t-test for significant difference from zero: ..
-Iteratively reweighed least squares (IRLS) fitting: ..
-Model predictions with mkinpredict: ...
-Fitting of parent only models: .....................
-Complex test case from Schaefer et al. (2007) Piacenza paper: ..
-Results for synthetic data established in expertise for UBA (Ranke 2014): ....
-Calculation of maximum time weighted average concentrations (TWAs): ...
+✔ | OK F W S | Context
+
⠏ |  0       | Calculation of FOCUS chi2 error levels
⠋ |  1       | Calculation of FOCUS chi2 error levels
⠙ |  2       | Calculation of FOCUS chi2 error levels
✔ |  2       | Calculation of FOCUS chi2 error levels [2.4 s]
+
⠏ |  0       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠼ |  5       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠴ |  6       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ |  6       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [2.3 s]
+
⠏ |  0       | The t-test for significant difference from zero
⠋ |  1       | The t-test for significant difference from zero
⠙ |  2       | The t-test for significant difference from zero
✔ |  2       | The t-test for significant difference from zero [4.2 s]
+
⠏ |  0       | Iteratively reweighed least squares (IRLS) fitting
⠋ |  1       | Iteratively reweighed least squares (IRLS) fitting
⠙ |  2       | Iteratively reweighed least squares (IRLS) fitting
⠹ |  3       | Iteratively reweighed least squares (IRLS) fitting
✔ |  3       | Iteratively reweighed least squares (IRLS) fitting [36.3 s]
+
⠏ |  0       | Model predictions with mkinpredict
⠋ |  1       | Model predictions with mkinpredict
⠙ |  2       | Model predictions with mkinpredict
⠹ |  3       | Model predictions with mkinpredict
✔ |  3       | Model predictions with mkinpredict [0.3 s]
+
⠏ |  0       | Fitting of parent only models
⠋ |  1       | Fitting of parent only models
⠙ |  2       | Fitting of parent only models
⠹ |  3       | Fitting of parent only models
⠸ |  4       | Fitting of parent only models
⠼ |  5       | Fitting of parent only models
⠴ |  6       | Fitting of parent only models
⠦ |  7       | Fitting of parent only models
⠧ |  8       | Fitting of parent only models
⠇ |  9       | Fitting of parent only models
⠏ | 10       | Fitting of parent only models
⠋ | 11       | Fitting of parent only models
⠙ | 12       | Fitting of parent only models
⠹ | 13       | Fitting of parent only models
⠸ | 14       | Fitting of parent only models
⠼ | 15       | Fitting of parent only models
⠴ | 16       | Fitting of parent only models
⠦ | 17       | Fitting of parent only models
⠧ | 18       | Fitting of parent only models
⠇ | 19       | Fitting of parent only models
⠏ | 20       | Fitting of parent only models
⠋ | 21       | Fitting of parent only models
✔ | 21       | Fitting of parent only models [21.6 s]
+
⠏ |  0       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠋ |  1       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠙ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s]
+
⠏ |  0       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ |  4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [6.7 s]
+
⠏ |  0       | Calculation of maximum time weighted average concentrations (TWAs)
⠋ |  1       | Calculation of maximum time weighted average concentrations (TWAs)
⠙ |  2       | Calculation of maximum time weighted average concentrations (TWAs)
⠹ |  3       | Calculation of maximum time weighted average concentrations (TWAs)
✔ |  3       | Calculation of maximum time weighted average concentrations (TWAs) [4.6 s]
 
-DONE ===========================================================================
+══ Results ═════════════════════════════════════════════════════════════════════
+Duration: 83.9 s
+
+OK:       46
+Failed:   0
+Warnings: 0
+Skipped:  0
-- 
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