From ad42e8870803335a549784888ddda80e4662f441 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 21 Feb 2019 15:16:14 +0100 Subject: Static documentation rebuilt by pkgdown --- docs/articles/FOCUS_D.html | 10 ++--- docs/articles/FOCUS_L.html | 56 ++++++++++++------------ docs/articles/index.html | 2 +- docs/articles/mkin.html | 2 +- docs/articles/twa.html | 2 +- docs/articles/web_only/FOCUS_Z.html | 2 +- docs/articles/web_only/compiled_models.html | 14 +++--- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 2 +- docs/reference/AIC.mmkin.html | 2 +- docs/reference/CAKE_export.html | 2 +- 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/logLik.mkinfit.html | 2 +- docs/reference/logistic.solution.html | 3 +- docs/reference/max_twa_parent.html | 2 +- docs/reference/mccall81_245T.html | 18 ++++---- 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 | 60 +++++++++++++------------- docs/reference/mkinmod.html | 4 +- docs/reference/mkinparplot.html | 2 +- docs/reference/mkinplot.html | 2 +- docs/reference/mkinpredict.html | 6 +-- docs/reference/mkinresplot.html | 2 +- docs/reference/mkinsub.html | 2 +- docs/reference/mmkin.html | 6 +-- docs/reference/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 | 32 +++++++------- 55 files changed, 160 insertions(+), 161 deletions(-) diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 4a080ac1..4dd23fd2 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -30,7 +30,7 @@ mkin - 0.9.47.6 + 0.9.48.1 @@ -161,10 +161,10 @@

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)
-
## mkin version used for fitting:    0.9.47.6 
+
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:58:25 2019 
-## Date of summary: Thu Feb 21 14:58:26 2019 
+## Date of fit:     Thu Feb 21 15:13:35 2019 
+## Date of summary: Thu Feb 21 15:13:35 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -172,7 +172,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.705 s
+## Fitted with method Port using 153 model solutions performed in 0.683 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index b9f72dbe..0820b21a 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -30,7 +30,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -109,17 +109,17 @@
 
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:    0.9.47.6 
+
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:58:27 2019 
-## Date of summary: Thu Feb 21 14:58:27 2019 
+## Date of fit:     Thu Feb 21 15:13:37 2019 
+## Date of summary: Thu Feb 21 15:13:37 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.096 s
+## Fitted with method Port using 37 model solutions performed in 0.101 s
 ## 
 ## Weighting: none
 ## 
@@ -200,17 +200,17 @@
 plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")

 

 
summary(m.L1.FOMC, data = FALSE)

-
## mkin version used for fitting:    0.9.47.6 
+
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:58:29 2019 
-## Date of summary: Thu Feb 21 14:58:29 2019 
+## Date of fit:     Thu Feb 21 15:13:39 2019 
+## Date of summary: Thu Feb 21 15:13:39 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 611 model solutions performed in 1.507 s
+## Fitted with method Port using 611 model solutions performed in 1.545 s
 ## 
 ## Weighting: none
 ## 
@@ -295,10 +295,10 @@
      main = "FOCUS L2 - FOMC")

 

 
summary(m.L2.FOMC, data = FALSE)

-
## mkin version used for fitting:    0.9.47.6 
+
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:58:30 2019 
-## Date of summary: Thu Feb 21 14:58:30 2019 
+## Date of fit:     Thu Feb 21 15:13:39 2019 
+## Date of summary: Thu Feb 21 15:13:39 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -366,10 +366,10 @@
      main = "FOCUS L2 - DFOP")

 

 
summary(m.L2.DFOP, data = FALSE)

-
## mkin version used for fitting:    0.9.47.6 
+
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:58:31 2019 
-## Date of summary: Thu Feb 21 14:58:31 2019 
+## Date of fit:     Thu Feb 21 15:13:40 2019 
+## Date of summary: Thu Feb 21 15:13:40 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -378,7 +378,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.842 s
+## Fitted with method Port using 336 model solutions performed in 0.852 s
 ## 
 ## Weighting: none
 ## 
@@ -458,10 +458,10 @@
 
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.

 
summary(mm.L3[["DFOP", 1]])

-
## mkin version used for fitting:    0.9.47.6 
+
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:58:32 2019 
-## Date of summary: Thu Feb 21 14:58:32 2019 
+## Date of fit:     Thu Feb 21 15:13:41 2019 
+## Date of summary: Thu Feb 21 15:13:41 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -470,7 +470,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.346 s
+## Fitted with method Port using 137 model solutions performed in 0.345 s
 ## 
 ## Weighting: none
 ## 
@@ -559,17 +559,17 @@
 

 
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.

 
summary(mm.L4[["SFO", 1]], data = FALSE)

-
## mkin version used for fitting:    0.9.47.6 
+
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:58:32 2019 
-## Date of summary: Thu Feb 21 14:58:33 2019 
+## Date of fit:     Thu Feb 21 15:13:42 2019 
+## Date of summary: Thu Feb 21 15:13:42 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.111 s
+## Fitted with method Port using 46 model solutions performed in 0.112 s
 ## 
 ## Weighting: none
 ## 
@@ -619,17 +619,17 @@
 ##        DT50 DT90
 ## parent  106  352

 
summary(mm.L4[["FOMC", 1]], data = FALSE)

-
## mkin version used for fitting:    0.9.47.6 
+
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:58:33 2019 
-## Date of summary: Thu Feb 21 14:58:33 2019 
+## Date of fit:     Thu Feb 21 15:13:42 2019 
+## Date of summary: Thu Feb 21 15:13:42 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.165 s
+## Fitted with method Port using 66 model solutions performed in 0.169 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 2da6c874..b2b11a3f 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -60,7 +60,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index c5b0d9c1..8f770680 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -30,7 +30,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 8a1f82a8..2dbe2a32 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -30,7 +30,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index c55abdbc..b4fa25ac 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -30,7 +30,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index e1149c67..b00fda46 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -30,7 +30,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -126,9 +126,9 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.329    1.000     2.327        0
-## 1 deSolve, not compiled            3  17.556    7.538    17.549        0
-## 2      Eigenvalue based            3   2.863    1.229     2.860        0
+## 3     deSolve, compiled            3   2.340    1.000     2.338        0
+## 1 deSolve, not compiled            3  17.729    7.576    17.720        0
+## 2      Eigenvalue based            3   2.889    1.235     2.888        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -157,13 +157,13 @@
 }

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

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.105    1.000     4.101        0
-## 1 deSolve, not compiled            3  37.400    9.111    37.381        0
+## 2     deSolve, compiled            3   4.122     1.00     4.120        0
+## 1 deSolve, not compiled            3  37.471     9.09    37.452        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 0.9.47.6 on

+
This vignette was built with mkin 0.9.48.1 on

 
## R version 3.5.2 (2018-12-20)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 9 (stretch)

diff --git a/docs/authors.html b/docs/authors.html
index dfea8ffd..78296059 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -60,7 +60,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/index.html b/docs/index.html
index 21d9164c..d7908ca2 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -37,7 +37,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/news/index.html b/docs/news/index.html
index 4a4d71fe..2e62819c 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -60,7 +60,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html
index d90b325f..3d10d36e 100644
--- a/docs/reference/AIC.mmkin.html
+++ b/docs/reference/AIC.mmkin.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html
index 21dd46a9..886c1922 100644
--- a/docs/reference/CAKE_export.html
+++ b/docs/reference/CAKE_export.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index 7f17e421..9bc215f0 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index fe6fc125..39228ba7 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -280,7 +280,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.199       0.000       0.200 
+#>       0.197       0.000       0.197 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -469,8 +469,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x555559227548>
-#> <environment: 0x555556ee4048>
+#> <bytecode: 0x55555920c328>
+#> <environment: 0x555555b0eb48>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -492,8 +492,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555a34ddf0>
-#> <environment: 0x555556ee4048>
+#> <bytecode: 0x55555a39faa0>
+#> <environment: 0x555555b0eb48>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -560,10 +560,10 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Thu Feb 21 14:56:32 2019"
+#> [1] "Thu Feb 21 15:11:41 2019"
 #> 
 #> $version
-#> [1] "0.9.47.6"
+#> [1] "0.9.48.1"
 #> 
 #> $Rversion
 #> [1] "3.5.2"
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 8565c1e6..9a43e010 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -67,7 +67,7 @@ in this fit." />
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
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 96329ca3..663600dd 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -67,7 +67,7 @@ in this fit." />
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
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 e1f9ae2b..58cab325 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -67,7 +67,7 @@ in this fit." />
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
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 1d039652..f9cf0e11 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -67,7 +67,7 @@ in this fit." />
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index e3c366b5..56f58d03 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 3ece2c08..fe6944d3 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -67,7 +67,7 @@ The form given here differs slightly from the original reference by Gustafson
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 0d8751e1..6997ebae 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 2ad38a16..103a1ae3 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 55ff216c..325a4285 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index 81ed61aa..f22b3af5 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -67,7 +67,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index c8024d66..c2db5b52 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index 9952f7ad..e241c7b9 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -66,7 +66,7 @@ with the advantage that the SFORB model can also be used for metabolites." />
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index ca3d8808..e52ac866 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 760dd3aa..4c8af606 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 78eb0337..f31a72fe 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -60,7 +60,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index a23ea52b..1e3b5702 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -80,7 +80,7 @@ In the case of iterative reweighting, the variances obtained by this
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index 310f1c5a..1894ed0e 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -194,7 +194,6 @@
 
   sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
   parms_logistic <- c(kmax = 0.08, k0 = 0.0001, r = 0.2)
-  parms_logistic_optim <- c(parent_0 = 100, parms_logistic)
   d_logistic <- mkinpredict(logistic,
     parms_logistic, c(parent = 100),
     sampling_times)
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 320bdd46..2c10b624 100644
--- a/docs/reference/max_twa_parent.html
+++ b/docs/reference/max_twa_parent.html
@@ -67,7 +67,7 @@ guidance." />
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index bed8ed8e..ce1c88e9 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -158,10 +158,10 @@
     
  SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
                          phenol = list(type = "SFO", to = "anisole"),
                          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:    0.9.47.6 
+    summary(fit.1, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:56:53 2019 
-#> Date of summary: Thu Feb 21 14:56:53 2019 
+#> Date of fit:     Thu Feb 21 15:12:02 2019 
+#> Date of summary: Thu Feb 21 15:12:02 2019 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -171,7 +171,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 574 model solutions performed in 3.873 s
+#> Fitted with method Port using 574 model solutions performed in 3.856 s
 #> 
 #> Weighting: none
 #> 
@@ -247,10 +247,10 @@
     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:    0.9.47.6 
+    summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:56:55 2019 
-#> Date of summary: Thu Feb 21 14:56:55 2019 
+#> Date of fit:     Thu Feb 21 15:12:04 2019 
+#> Date of summary: Thu Feb 21 15:12:04 2019 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -260,7 +260,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.633 s
+#> Fitted with method Port using 246 model solutions performed in 1.607 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index 290d3e76..f8849a3e 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     

 
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index d7438fcf..04eaff8b 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index bf90726d..7a87c11e 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 35086a61..c155a838 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -64,7 +64,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." />
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 4f071574..369d7bbe 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -73,7 +73,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -436,17 +436,17 @@
     
Examples

     
# Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.47.6 
+summary(fit)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:56:58 2019 
-#> Date of summary: Thu Feb 21 14:56:58 2019 
+#> Date of fit:     Thu Feb 21 15:12:07 2019 
+#> Date of summary: Thu Feb 21 15:12:07 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 64 model solutions performed in 0.16 s
+#> Fitted with method Port using 64 model solutions performed in 0.164 s
 #> 
 #> Weighting: none
 #> 
@@ -515,7 +515,7 @@
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#>        User      System verstrichen 
-#>       1.036       0.000       1.036 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       1.045       0.000       1.046 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -590,7 +590,7 @@
 #> Model cost at call  146 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>        User      System verstrichen 
-#>       0.830       0.000       0.832 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.835       0.000       0.835 
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 
@@ -626,10 +626,10 @@
 
# Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
                       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:    0.9.47.6 
+summary(f.noweight)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:57:10 2019 
-#> Date of summary: Thu Feb 21 14:57:10 2019 
+#> Date of fit:     Thu Feb 21 15:12:19 2019 
+#> Date of summary: Thu Feb 21 15:12:19 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -637,7 +637,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.86 s
+#> Fitted with method Port using 186 model solutions performed in 0.853 s
 #> 
 #> Weighting: none
 #> 
@@ -743,10 +743,10 @@
 #>   100       m1    33.13  31.98163  1.148e+00
 #>   120       m1    25.15  28.78984 -3.640e+00
 #>   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:    0.9.47.6 
+summary(f.irls)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:57:13 2019 
-#> Date of summary: Thu Feb 21 14:57:13 2019 
+#> Date of fit:     Thu Feb 21 15:12:22 2019 
+#> Date of summary: Thu Feb 21 15:12:22 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -754,7 +754,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 551 model solutions performed in 2.543 s
+#> Fitted with method Port using 551 model solutions performed in 2.573 s
 #> 
 #> Weighting: none
 #> 
@@ -865,10 +865,10 @@
 #>   100       m1    33.13  31.98971  1.140e+00 2.722
 #>   120       m1    25.15  28.80898 -3.659e+00 2.722
 #>   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:    0.9.47.6 
+summary(f.w.mean)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:57:14 2019 
-#> Date of summary: Thu Feb 21 14:57:14 2019 
+#> Date of fit:     Thu Feb 21 15:12:22 2019 
+#> Date of summary: Thu Feb 21 15:12:22 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -983,10 +983,10 @@
 #>   120       m1    25.15  28.82413  -3.674128
 #>   120       m1    33.31  28.82413   4.485872
f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value",
                      quiet = TRUE)
-summary(f.w.value)
#> mkin version used for fitting:    0.9.47.6 
+summary(f.w.value)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:57:15 2019 
-#> Date of summary: Thu Feb 21 14:57:15 2019 
+#> Date of fit:     Thu Feb 21 15:12:23 2019 
+#> Date of summary: Thu Feb 21 15:12:23 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -994,7 +994,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 174 model solutions performed in 0.8 s
+#> Fitted with method Port using 174 model solutions performed in 0.802 s
 #> 
 #> Weighting: manual
 #> 
@@ -1103,10 +1103,10 @@
 errors <- c(parent = 2, m1 = 1)
 dw$err.man <- errors[FOCUS_2006_D$name]
 f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
-summary(f.w.man)
#> mkin version used for fitting:    0.9.47.6 
+summary(f.w.man)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:57:16 2019 
-#> Date of summary: Thu Feb 21 14:57:16 2019 
+#> Date of fit:     Thu Feb 21 15:12:25 2019 
+#> Date of summary: Thu Feb 21 15:12:25 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1114,7 +1114,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 270 model solutions performed in 1.248 s
+#> Fitted with method Port using 270 model solutions performed in 1.251 s
 #> 
 #> Weighting: manual
 #> 
@@ -1221,10 +1221,10 @@
 #>   120       m1    25.15  28.76062  -3.610621   2
 #>   120       m1    33.31  28.76062   4.549379   2
f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE,
                        reweight.method = "obs")
-summary(f.w.man.irls)
#> mkin version used for fitting:    0.9.47.6 
+summary(f.w.man.irls)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:57:19 2019 
-#> Date of summary: Thu Feb 21 14:57:19 2019 
+#> Date of fit:     Thu Feb 21 15:12:28 2019 
+#> Date of summary: Thu Feb 21 15:12:28 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1232,7 +1232,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 692 model solutions performed in 3.287 s
+#> Fitted with method Port using 692 model solutions performed in 3.31 s
 #> 
 #> Weighting: manual
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 17d8400d..e4509e8a 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -68,7 +68,7 @@ For the definition of model types and their parameters, the equations given
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     

 
@@ -231,7 +231,7 @@ For the definition of model types and their parameters, the equations given
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file522976635fac.c 2> file522976635fac.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file6490632228a0.c 2> file6490632228a0.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 93aa4b41..7438e0e0 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     

 
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 7e832f97..2f386d45 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 414d97a8..deb1335a 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -330,12 +330,12 @@
                 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 
-#>       0.001       0.000       0.002 
  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
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.039       0.000       0.040 

+#>       0.039       0.000       0.039 

   
    # Predict from a fitted model
     f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Model cost at call  1 :  552.5739 
 #> Model cost at call  3 :  552.5739 
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index d088cfc9..702e50eb 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -66,7 +66,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     

 
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 135c0325..95689f48 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 7352fb74..af52e38a 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -191,8 +191,8 @@
 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.044       0.036       7.245 
time_1
#>        User      System verstrichen 
-#>      22.796       0.004      22.814 

+#>       0.036       0.050       7.160 
time_1
#>        User      System verstrichen 
+#>      22.888       0.000      22.902 

 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/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index ab94d61b..b46da2f1 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -68,7 +68,7 @@ If the current plot device is a tikz device,
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     

 
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 689fd488..acea2def 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -67,7 +67,7 @@ If the current plot device is a tikz device,
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 0cab1051..e4e142d7 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index 0c78b6fb..d5e128a7 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index d1c89770..410c95d8 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index 00b463e8..01b0d542 100644
--- a/docs/reference/sigma_twocomp.html
+++ b/docs/reference/sigma_twocomp.html
@@ -68,7 +68,7 @@ This is the error model used for example by Werner et al. (1978). The model
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 53b94948..80298bb4 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -66,7 +66,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -206,17 +206,17 @@
     
 
     
Examples

-    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.6 
+    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:58:11 2019 
-#> Date of summary: Thu Feb 21 14:58:11 2019 
+#> Date of fit:     Thu Feb 21 15:13:20 2019 
+#> Date of summary: Thu Feb 21 15:13:20 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.085 s
+#> Fitted with method Port using 35 model solutions performed in 0.087 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 14db4358..b2b55805 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -78,7 +78,7 @@ Compare also the code in the example section to see the degradation models." />
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     

 
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 1999de8d..39f6d364 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     

 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 3dbacbe8..088ea9d0 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -71,7 +71,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -200,10 +200,10 @@ 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:    0.9.47.6 
+summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:58:19 2019 
-#> Date of summary: Thu Feb 21 14:58:19 2019 
+#> Date of fit:     Thu Feb 21 15:13:29 2019 
+#> Date of summary: Thu Feb 21 15:13:29 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -211,7 +211,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.765 s
+#> Fitted with method Port using 153 model solutions performed in 0.84 s
 #> 
 #> Weighting: none
 #> 
@@ -276,10 +276,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> parent   7.023  23.33
 #> m1     131.761 437.70

 
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
-summary(fit.2, data=FALSE)
#> mkin version used for fitting:    0.9.47.6 
+summary(fit.2, data=FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:58:21 2019 
-#> Date of summary: Thu Feb 21 14:58:21 2019 
+#> Date of fit:     Thu Feb 21 15:13:30 2019 
+#> Date of summary: Thu Feb 21 15:13:30 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -287,7 +287,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 350 model solutions performed in 1.58 s
+#> Fitted with method Port using 350 model solutions performed in 1.631 s
 #> 
 #> Weighting: none
 #> 
@@ -364,10 +364,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
   m1 = list(type = "SFO"),
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-summary(fit.ff, data = FALSE)
#> mkin version used for fitting:    0.9.47.6 
+summary(fit.ff, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:58:22 2019 
-#> Date of summary: Thu Feb 21 14:58:22 2019 
+#> Date of fit:     Thu Feb 21 15:13:32 2019 
+#> Date of summary: Thu Feb 21 15:13:32 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -375,7 +375,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.872 s
+#> Fitted with method Port using 186 model solutions performed in 0.852 s
 #> 
 #> Weighting: none
 #> 
@@ -448,10 +448,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
-summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.6 
+summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:58:23 2019 
-#> Date of summary: Thu Feb 21 14:58:23 2019 
+#> Date of fit:     Thu Feb 21 15:13:32 2019 
+#> Date of summary: Thu Feb 21 15:13:32 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
-- 
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