From 62e66eb483aef4edcfd839e475354ef1ddb9e49f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 26 Nov 2018 09:32:07 +0100 Subject: Static documentation rebuilt by pkgdown --- docs/articles/FOCUS_L.html | 36 +++++++++++------------ docs/articles/web_only/compiled_models.html | 12 ++++---- docs/reference/Extract.mmkin.html | 12 ++++---- docs/reference/logLik.mkinfit.html | 32 +++++++++++++++++++-- docs/reference/mccall81_245T.html | 12 ++++---- docs/reference/mkinfit.html | 44 ++++++++++++++--------------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 6 ++-- docs/reference/mmkin.html | 4 +-- docs/reference/summary.mkinfit.html | 4 +-- docs/reference/transform_odeparms.html | 24 ++++++++-------- 11 files changed, 108 insertions(+), 80 deletions(-) (limited to 'docs') diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index dc562002..02b3f60e 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -110,8 +110,8 @@ summary(m.L1.SFO) 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Mon Nov 26 09:07:07 2018 
-## Date of summary: Mon Nov 26 09:07:07 2018 
+## Date of fit:     Mon Nov 26 09:29:29 2018 
+## Date of summary: Mon Nov 26 09:29:29 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -201,15 +201,15 @@
 
 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Mon Nov 26 09:07:09 2018 
-## Date of summary: Mon Nov 26 09:07:09 2018 
+## Date of fit:     Mon Nov 26 09:29:30 2018 
+## Date of summary: Mon Nov 26 09:29:30 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 1.481 s
+## Fitted with method Port using 611 model solutions performed in 1.467 s
 ## 
 ## Weighting: none
 ## 
@@ -296,8 +296,8 @@
 
 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Mon Nov 26 09:07:10 2018 
-## Date of summary: Mon Nov 26 09:07:10 2018 
+## Date of fit:     Mon Nov 26 09:29:31 2018 
+## Date of summary: Mon Nov 26 09:29:31 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -367,8 +367,8 @@
 
 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Mon Nov 26 09:07:11 2018 
-## Date of summary: Mon Nov 26 09:07:11 2018 
+## Date of fit:     Mon Nov 26 09:29:32 2018 
+## Date of summary: Mon Nov 26 09:29:32 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 0.86 s
+## Fitted with method Port using 336 model solutions performed in 0.828 s
 ## 
 ## Weighting: none
 ## 
@@ -459,8 +459,8 @@
 
 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Mon Nov 26 09:07:12 2018 
-## Date of summary: Mon Nov 26 09:07:12 2018 
+## Date of fit:     Mon Nov 26 09:29:33 2018 
+## Date of summary: Mon Nov 26 09:29:33 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 0.339 s
+## Fitted with method Port using 137 model solutions performed in 0.334 s
 ## 
 ## Weighting: none
 ## 
@@ -560,8 +560,8 @@
 
 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Mon Nov 26 09:07:12 2018 
-## Date of summary: Mon Nov 26 09:07:13 2018 
+## Date of fit:     Mon Nov 26 09:29:34 2018 
+## Date of summary: Mon Nov 26 09:29:34 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -620,15 +620,15 @@
 
 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Mon Nov 26 09:07:13 2018 
-## Date of summary: Mon Nov 26 09:07:13 2018 
+## Date of fit:     Mon Nov 26 09:29:34 2018 
+## Date of summary: Mon Nov 26 09:29:34 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 0.159 s
+## Fitted with method Port using 66 model solutions performed in 0.158 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 25a3a62e..93c800bf 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -125,9 +125,9 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.296    1.000     2.295        0
-## 1 deSolve, not compiled            3  17.937    7.812    17.928        0
-## 2      Eigenvalue based            3   2.861    1.246     2.859        0
+## 3     deSolve, compiled            3   2.268    1.000     2.267        0
+## 1 deSolve, not compiled            3  18.698    8.244    18.690        0
+## 2      Eigenvalue based            3   2.812    1.240     2.811        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -156,12 +156,12 @@
 }

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

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.020    1.000     4.017        0
-## 1 deSolve, not compiled            3  37.721    9.383    37.704        0
+## 2     deSolve, compiled            3   4.032    1.000     4.028        0
+## 1 deSolve, not compiled            3  39.759    9.861    39.741        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!

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

 
This vignette was built with mkin 0.9.47.6 on

 
## R version 3.5.1 (2018-07-02)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index ec2c7eb7..33d90e5b 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -278,7 +278,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.184       0.000       0.184 
+#>       0.182       0.000       0.183 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -467,8 +467,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555be327a0>
-#> <environment: 0x55555bc27c20>
+#> <bytecode: 0x55555be42410>
+#> <environment: 0x55555bc697f8>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -490,8 +490,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555cd76230>
-#> <environment: 0x55555bc27c20>
+#> <bytecode: 0x55555cd2ca88>
+#> <environment: 0x55555bc697f8>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -558,7 +558,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Mon Nov 26 09:05:19 2018"
+#> [1] "Mon Nov 26 09:27:40 2018"
 #> 
 #> $version
 #> [1] "0.9.47.6"
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index 250bc1d8..5fd6c6d7 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -33,7 +33,21 @@
 
 
 
+  calculated using dnorm, i.e. assuming normal distribution.
+The total number of estimated parameters returned with the value 
+  of the likelihood is calculated as the sum of fitted degradation 
+  model parameters and the fitted error model parameters.
+For the case of unweighted least squares fitting, we calculate one
+  constant standard deviation from the residuals using sd
+  and add one to the number of fitted degradation model parameters.
+For the case of manual weighting, we use the weight given for each
+  observation as standard deviation in calculating its likelihood.
+In the case of iterative reweighting, the variances obtained by this
+  procedure are used in the likelihood calculations, and the number of
+  estimated parameters is obtained by the number of degradation model
+  parameters plus the number of variance model parameters, i.e. the number of
+  observed variables if the reweighting method is "obs", and two if the
+  reweighting method is "tc"." />
 
 
 
@@ -125,7 +139,21 @@
     

     
     
This function simply calculates the product of the likelihood densities
-  calc

+  calculated using dnorm, i.e. assuming normal distribution.

+
The total number of estimated parameters returned with the value 
+  of the likelihood is calculated as the sum of fitted degradation 
+  model parameters and the fitted error model parameters.

+
For the case of unweighted least squares fitting, we calculate one
+  constant standard deviation from the residuals using sd
+  and add one to the number of fitted degradation model parameters.

+
For the case of manual weighting, we use the weight given for each
+  observation as standard deviation in calculating its likelihood.

+
In the case of iterative reweighting, the variances obtained by this
+  procedure are used in the likelihood calculations, and the number of
+  estimated parameters is obtained by the number of degradation model
+  parameters plus the number of variance model parameters, i.e. the number of
+  observed variables if the reweighting method is "obs", and two if the
+  reweighting method is "tc".

     
     

 
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 505da201..2cd933e9 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -158,8 +158,8 @@
                          anisole = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  
    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
     summary(fit.1, data = FALSE)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:05:38 2018 
-#> Date of summary: Mon Nov 26 09:05:38 2018 
+#> Date of fit:     Mon Nov 26 09:27:59 2018 
+#> Date of summary: Mon Nov 26 09:27:59 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -169,7 +169,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 574 model solutions performed in 3.64 s
+#> Fitted with method Port using 574 model solutions performed in 3.635 s
 #> 
 #> Weighting: none
 #> 
@@ -247,8 +247,8 @@
                    fixed_parms = "k_phenol_sink", quiet = TRUE)
     summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:05:40 2018 
-#> Date of summary: Mon Nov 26 09:05:40 2018 
+#> Date of fit:     Mon Nov 26 09:28:01 2018 
+#> Date of summary: Mon Nov 26 09:28:01 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -258,7 +258,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.626 s
+#> Fitted with method Port using 246 model solutions performed in 1.623 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 2017a35c..addd9c30 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -436,8 +436,8 @@
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:05:43 2018 
-#> Date of summary: Mon Nov 26 09:05:43 2018 
+#> Date of fit:     Mon Nov 26 09:28:04 2018 
+#> Date of summary: Mon Nov 26 09:28:04 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -513,7 +513,7 @@
   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 
-#>       0.974       0.000       0.975 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       1.009       0.000       1.009 
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 
@@ -588,7 +588,7 @@
 #> Model cost at call  146 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>        User      System verstrichen 
-#>       0.796       0.000       0.796 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.909       0.000       0.910 
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 
@@ -626,8 +626,8 @@
                       m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(f.noweight)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:05:54 2018 
-#> Date of summary: Mon Nov 26 09:05:54 2018 
+#> Date of fit:     Mon Nov 26 09:28:16 2018 
+#> Date of summary: Mon Nov 26 09:28:16 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -635,7 +635,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.885 s
+#> Fitted with method Port using 186 model solutions performed in 0.927 s
 #> 
 #> Weighting: none
 #> 
@@ -743,8 +743,8 @@
 #>   120       m1    33.31  28.78984  4.520e+00
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
 summary(f.irls)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:05:57 2018 
-#> Date of summary: Mon Nov 26 09:05:57 2018 
+#> Date of fit:     Mon Nov 26 09:28:18 2018 
+#> Date of summary: Mon Nov 26 09:28:18 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -752,7 +752,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 551 model solutions performed in 2.451 s
+#> Fitted with method Port using 551 model solutions performed in 2.509 s
 #> 
 #> Weighting: none
 #> 
@@ -865,8 +865,8 @@
 #>   120       m1    33.31  28.80898  4.501e+00 2.722
f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE)
 summary(f.w.mean)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:05:58 2018 
-#> Date of summary: Mon Nov 26 09:05:58 2018 
+#> Date of fit:     Mon Nov 26 09:28:19 2018 
+#> Date of summary: Mon Nov 26 09:28:19 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -874,7 +874,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 155 model solutions performed in 0.69 s
+#> Fitted with method Port using 155 model solutions performed in 0.68 s
 #> 
 #> Weighting: mean
 #> 
@@ -983,8 +983,8 @@
                      quiet = TRUE)
 summary(f.w.value)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:05:59 2018 
-#> Date of summary: Mon Nov 26 09:05:59 2018 
+#> Date of fit:     Mon Nov 26 09:28:20 2018 
+#> Date of summary: Mon Nov 26 09:28:20 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -992,7 +992,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 174 model solutions performed in 0.772 s
+#> Fitted with method Port using 174 model solutions performed in 0.775 s
 #> 
 #> Weighting: manual
 #> 
@@ -1103,8 +1103,8 @@
 f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
 summary(f.w.man)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:06:00 2018 
-#> Date of summary: Mon Nov 26 09:06:00 2018 
+#> Date of fit:     Mon Nov 26 09:28:22 2018 
+#> Date of summary: Mon Nov 26 09:28:22 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1112,7 +1112,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 270 model solutions performed in 1.201 s
+#> Fitted with method Port using 270 model solutions performed in 1.203 s
 #> 
 #> Weighting: manual
 #> 
@@ -1221,8 +1221,8 @@
                        reweight.method = "obs")
 summary(f.w.man.irls)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:06:03 2018 
-#> Date of summary: Mon Nov 26 09:06:03 2018 
+#> Date of fit:     Mon Nov 26 09:28:25 2018 
+#> Date of summary: Mon Nov 26 09:28:25 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1230,7 +1230,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 692 model solutions performed in 3.087 s
+#> Fitted with method Port using 692 model solutions performed in 3.078 s
 #> 
 #> Weighting: manual
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index a7f26322..448c0e8e 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -229,7 +229,7 @@ For the definition of model types and their parameters, the equations given
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file672328842b40.c 2> file672328842b40.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file775a236112e7.c 2> file775a236112e7.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index f26422a4..84e6591b 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -323,17 +323,17 @@
                 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       0.004 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
 #> 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 
-#>       0.041       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/mmkin.html b/docs/reference/mmkin.html
index eb2e5bcf..a27cf5db 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -189,8 +189,8 @@
 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.043       0.032       6.850 
time_1
#>        User      System verstrichen 
-#>      21.779       0.000      21.791 

+#>       0.038       0.036       6.851 
time_1
#>        User      System verstrichen 
+#>      21.780       0.000      21.791 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340480   0.2659520   0.7505686   0.2494314 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 9cb43d42..7f510c67 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -206,8 +206,8 @@
     
Examples

     
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:06:53 2018 
-#> Date of summary: Mon Nov 26 09:06:53 2018 
+#> Date of fit:     Mon Nov 26 09:29:14 2018 
+#> Date of summary: Mon Nov 26 09:29:14 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 6178527b..24b50890 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -200,8 +200,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:07:01 2018 
-#> Date of summary: Mon Nov 26 09:07:01 2018 
+#> Date of fit:     Mon Nov 26 09:29:22 2018 
+#> Date of summary: Mon Nov 26 09:29:22 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 0.687 s
+#> Fitted with method Port using 153 model solutions performed in 0.683 s
 #> 
 #> Weighting: none
 #> 
@@ -276,8 +276,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
 summary(fit.2, data=FALSE)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:07:03 2018 
-#> Date of summary: Mon Nov 26 09:07:03 2018 
+#> Date of fit:     Mon Nov 26 09:29:24 2018 
+#> Date of summary: Mon Nov 26 09:29:24 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -285,7 +285,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 350 model solutions performed in 1.537 s
+#> Fitted with method Port using 350 model solutions performed in 1.594 s
 #> 
 #> Weighting: none
 #> 
@@ -364,8 +364,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff, data = FALSE)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:07:04 2018 
-#> Date of summary: Mon Nov 26 09:07:04 2018 
+#> Date of fit:     Mon Nov 26 09:29:25 2018 
+#> Date of summary: Mon Nov 26 09:29:25 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -373,7 +373,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.827 s
+#> Fitted with method Port using 186 model solutions performed in 0.819 s
 #> 
 #> Weighting: none
 #> 
@@ -448,8 +448,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:07:04 2018 
-#> Date of summary: Mon Nov 26 09:07:04 2018 
+#> Date of fit:     Mon Nov 26 09:29:26 2018 
+#> Date of summary: Mon Nov 26 09:29:26 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -457,7 +457,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 104 model solutions performed in 0.454 s
+#> Fitted with method Port using 104 model solutions performed in 0.486 s
 #> 
 #> Weighting: none
 #> 
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