From fbfffc0e47171cac03797340fde697a75a5afd61 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 26 Nov 2018 11:44:27 +0100 Subject: Add AIC method for mmkin column objects Static documentation rebuilt by pkgdown --- docs/articles/FOCUS_L.html | 40 +++--- docs/articles/web_only/compiled_models.html | 10 +- docs/news/index.html | 3 +- docs/reference/AIC.mmkin.html | 211 ++++++++++++++++++++++++++++ docs/reference/Extract.mmkin.html | 12 +- docs/reference/logLik.mkinfit.html | 19 ++- docs/reference/mccall81_245T.html | 12 +- docs/reference/mkinfit.html | 46 +++--- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 4 +- docs/reference/mmkin.html | 4 +- docs/reference/summary.mkinfit.html | 4 +- docs/reference/transform_odeparms.html | 24 ++-- 13 files changed, 305 insertions(+), 86 deletions(-) create mode 100644 docs/reference/AIC.mmkin.html (limited to 'docs') diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 4d337e72..448a03bb 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -110,15 +110,15 @@ summary(m.L1.SFO) 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Mon Nov 26 09:47:23 2018 
-## Date of summary: Mon Nov 26 09:47:23 2018 
+## Date of fit:     Mon Nov 26 11:41:50 2018 
+## Date of summary: Mon Nov 26 11:41:50 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.093 s
+## Fitted with method Port using 37 model solutions performed in 0.094 s
 ## 
 ## Weighting: none
 ## 
@@ -201,8 +201,8 @@
 
 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Mon Nov 26 09:47:25 2018 
-## Date of summary: Mon Nov 26 09:47:25 2018 
+## Date of fit:     Mon Nov 26 11:41:52 2018 
+## Date of summary: Mon Nov 26 11:41:52 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -296,15 +296,15 @@
 
 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Mon Nov 26 09:47:26 2018 
-## Date of summary: Mon Nov 26 09:47:26 2018 
+## Date of fit:     Mon Nov 26 11:41:53 2018 
+## Date of summary: Mon Nov 26 11:41:53 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.192 s
+## Fitted with method Port using 81 model solutions performed in 0.193 s
 ## 
 ## Weighting: none
 ## 
@@ -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 09:47:27 2018 
-## Date of summary: Mon Nov 26 09:47:27 2018 
+## Date of fit:     Mon Nov 26 11:41:54 2018 
+## Date of summary: Mon Nov 26 11:41:54 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 0.831 s
+## Fitted with method Port using 336 model solutions performed in 0.826 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 09:47:28 2018 
-## Date of summary: Mon Nov 26 09:47:28 2018 
+## Date of fit:     Mon Nov 26 11:41:55 2018 
+## Date of summary: Mon Nov 26 11:41:55 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 0.336 s
+## Fitted with method Port using 137 model solutions performed in 0.337 s
 ## 
 ## Weighting: none
 ## 
@@ -560,15 +560,15 @@
 
 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Mon Nov 26 09:47:28 2018 
-## Date of summary: Mon Nov 26 09:47:29 2018 
+## Date of fit:     Mon Nov 26 11:41:55 2018 
+## Date of summary: Mon Nov 26 11:41:56 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.107 s
+## Fitted with method Port using 46 model solutions performed in 0.108 s
 ## 
 ## Weighting: none
 ## 
@@ -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 09:47:28 2018 
-## Date of summary: Mon Nov 26 09:47:29 2018 
+## Date of fit:     Mon Nov 26 11:41:56 2018 
+## Date of summary: Mon Nov 26 11:41:56 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 0.168 s
+## Fitted with method Port using 66 model solutions performed in 0.16 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 083cdb79..8da95e4d 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   2.264    1.000     2.263        0
-## 1 deSolve, not compiled            3  17.642    7.792    17.634        0
-## 2      Eigenvalue based            3   2.801    1.237     2.799        0
+## 3     deSolve, compiled            3   2.302    1.000     2.301        0
+## 1 deSolve, not compiled            3  17.754    7.712    17.743        0
+## 2      Eigenvalue based            3   2.840    1.234     2.838        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -156,8 +156,8 @@
 }

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

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.012    1.000     4.010        0
-## 1 deSolve, not compiled            3  37.606    9.373    37.589        0
+## 2     deSolve, compiled            3   4.116    1.000     4.114        0
+## 1 deSolve, not compiled            3  37.902    9.208    37.884        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/news/index.html b/docs/news/index.html
index 9f658dad..1b2455a8 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -122,7 +122,8 @@
 mkin 0.9.47.6 (2018-11-26) Unreleased 
 
 
    
-
  • Add the function ‘logLik.mkinfit.R’ which makes it possible to calculate an AIC for mkinfit objects
    • 
+
  • Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects
    • 
+
  • Add the function ‘AIC.mmkin’ to makeqit easy to compare columns of mmkin objects
    • 
 
  • ‘add_err’: Respect the argument giving the number of replicates in the synthetic dataset
    • 
 
  • ‘max_twa_parent’: Support maximum time weighted average concentration calculations for the hockey stick (HS) model
    • 
 
  • ‘mkinpredict’: Make the function generic and create a method for mkinfit objects
    • 
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html
new file mode 100644
index 00000000..a2ce9885
--- /dev/null
+++ b/docs/reference/AIC.mmkin.html
@@ -0,0 +1,211 @@
+
+
+
+  
+  
+
+
+
+Calculated the AIC for a column of an mmkin object — AIC.mmkin • mkin
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+  
+
+  
+    
    
+      
    
+      
+
+      
+      
    
+
+
    
+  
    
+    
    
+    
    Calculated the AIC for a column of an mmkin object
    
+    
+    
+    
    
+
+    
    
+    
+    
    Provides a convenient way to compare different kineti models fitted to the
+  same dataset.
    
+    
+    
    
+
+    
    # S3 method for mmkin
+AIC(object, ..., k = 2)
    
+    
+    
    Arguments
    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
    object
    An object of class mmkin, containing only one column.
    …
    For compatibility with the generic method
    k
    As in the generic method
    
+    
+    
    Value
    
+
+    
    As in the generic method (a numeric value for single fits, or a dataframe if
+  there are several fits in the column).
    
+    
+
+    
    Examples
    
+    
      f <- mmkin(c("SFO", "FOMC", "DFOP"),
+    list("FOCUS A" = FOCUS_2006_A,
+         "FOCUS C" = FOCUS_2006_C))
+  AIC(f[1, "FOCUS A"]) # We get a single number for a single fit
    #> [1] 55.32452
    
+  # For FOCUS A, the models fit almost equally well, so the higher the number
+  # of parameters, the higher (worse) the AIC
+  AIC(f[, "FOCUS A"])
    #>      df      AIC
+#> SFO   3 55.32452
+#> FOMC  4 57.32477
+#> DFOP  5 59.32452
      AIC(f[, "FOCUS A"], k = 0) # If we do not penalize additional parameters, we get nearly the same
    #>      df      AIC
+#> SFO   3 49.32452
+#> FOMC  4 49.32477
+#> DFOP  5 49.32452
    
+  # For FOCUS C, the more complex models fit better
+  AIC(f[, "FOCUS C"])
    #>      df      AIC
+#> SFO   3 59.84675
+#> FOMC  4 44.70584
+#> DFOP  5 29.08369
    
+  
    
+  
+
    
+
+      
    
+      
    
+  
    Developed by Johannes Ranke.
    
+
    
+
+
    
+  
    Site built with pkgdown.
    
+
    
+
+      
    
+   
    
+
+  
+
+  
+
+
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 51da42fc..b304c2fb 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -278,7 +278,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.183       0.000       0.183 
+#>       0.188       0.000       0.188 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -467,8 +467,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555be28e50>
-#> <environment: 0x55555bc4d2b0>
+#> <bytecode: 0x55555bd98970>
+#> <environment: 0x55555d417aa8>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -490,8 +490,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555cd2fbb8>
-#> <environment: 0x55555bc4d2b0>
+#> <bytecode: 0x55555cd14308>
+#> <environment: 0x55555d417aa8>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -558,7 +558,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Mon Nov 26 09:45:35 2018"
+#> [1] "Mon Nov 26 11:40:00 2018"
 #> 
 #> $version
 #> [1] "0.9.47.6"
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index b1901703..33d9eb36 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -34,15 +34,15 @@
 
 See also
+
+    
    Compare the AIC of columns of mmkin objects using
+  AIC.mmkin.
    
+    
 
     
    Examples
    
     
      sfo_sfo <- mkinmod(
@@ -207,6 +212,8 @@ In the case of iterative reweighting, the variances obtained by this
       
  • Arguments
    • 
       
       
  • Value
    • 
+
+      
  • See also
    • 
       
       
  • Examples
    • 
     

diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 981c633a..96082932 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 09:45:54 2018 
-#> Date of summary: Mon Nov 26 09:45:54 2018 
+#> Date of fit:     Mon Nov 26 11:40:20 2018 
+#> Date of summary: Mon Nov 26 11:40:20 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 3.641 s
+#> Fitted with method Port using 574 model solutions performed in 3.702 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 09:45:56 2018 
-#> Date of summary: Mon Nov 26 09:45:56 2018 
+#> Date of fit:     Mon Nov 26 11:40:22 2018 
+#> Date of summary: Mon Nov 26 11:40:22 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 1.627 s
+#> Fitted with method Port using 246 model solutions performed in 1.646 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 883dda22..77c69f4e 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -436,15 +436,15 @@
 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 09:45:59 2018 
-#> Date of summary: Mon Nov 26 09:45:59 2018 
+#> Date of fit:     Mon Nov 26 11:40:24 2018 
+#> Date of summary: Mon Nov 26 11:40:24 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 0.155 s
+#> Fitted with method Port using 64 model solutions performed in 0.156 s
 #> 
 #> Weighting: none
 #> 
@@ -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 
+#>       0.989       0.000       0.990 
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 
-#>        0.79        0.00        0.79 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.799       0.000       0.800 
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 09:46:10 2018 
-#> Date of summary: Mon Nov 26 09:46:10 2018 
+#> Date of fit:     Mon Nov 26 11:40:36 2018 
+#> Date of summary: Mon Nov 26 11:40:36 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 0.889 s
+#> Fitted with method Port using 186 model solutions performed in 0.839 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 09:46:13 2018 
-#> Date of summary: Mon Nov 26 09:46:13 2018 
+#> Date of fit:     Mon Nov 26 11:40:39 2018 
+#> Date of summary: Mon Nov 26 11:40:39 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 2.441 s
+#> Fitted with method Port using 551 model solutions performed in 2.48 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 09:46:14 2018 
-#> Date of summary: Mon Nov 26 09:46:14 2018 
+#> Date of fit:     Mon Nov 26 11:40:40 2018 
+#> Date of summary: Mon Nov 26 11:40:40 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 0.679 s
+#> Fitted with method Port using 155 model solutions performed in 0.694 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 09:46:15 2018 
-#> Date of summary: Mon Nov 26 09:46:15 2018 
+#> Date of fit:     Mon Nov 26 11:40:41 2018 
+#> Date of summary: Mon Nov 26 11:40:41 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 0.771 s
+#> Fitted with method Port using 174 model solutions performed in 0.778 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 09:46:16 2018 
-#> Date of summary: Mon Nov 26 09:46:16 2018 
+#> Date of fit:     Mon Nov 26 11:40:42 2018 
+#> Date of summary: Mon Nov 26 11:40:42 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 1.2 s
+#> Fitted with method Port using 270 model solutions performed in 1.225 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 09:46:19 2018 
-#> Date of summary: Mon Nov 26 09:46:19 2018 
+#> Date of fit:     Mon Nov 26 11:40:45 2018 
+#> Date of summary: Mon Nov 26 11:40:45 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 3.079 s
+#> Fitted with method Port using 692 model solutions performed in 3.119 s
 #> 
 #> Weighting: manual
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index d947aff5..0d644bc4 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 file74b35b9de5b.c 2> file74b35b9de5b.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file4252799a8f5a.c 2> file4252799a8f5a.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 88858539..bfe71be5 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -323,7 +323,7 @@
                 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 
-#>       0.005       0.000       0.005 
  system.time(
+#>       0.003       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
@@ -333,7 +333,7 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.039       0.000       0.039 

+#>       0.039       0.000       0.040 

   
    # 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 49117199..92f12c2a 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 
-#>       0.037       0.036       7.001 
time_1
#>        User      System verstrichen 
-#>      21.838       0.000      21.852 

+#>       0.050       0.037       6.958 
time_1
#>        User      System verstrichen 
+#>      22.101       0.000      22.114 

 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 e63ab87e..554a28e3 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 09:47:09 2018 
-#> Date of summary: Mon Nov 26 09:47:09 2018 
+#> Date of fit:     Mon Nov 26 11:41:36 2018 
+#> Date of summary: Mon Nov 26 11:41:36 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index c0ff16fd..e6a42993 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 09:47:17 2018 
-#> Date of summary: Mon Nov 26 09:47:17 2018 
+#> Date of fit:     Mon Nov 26 11:41:44 2018 
+#> Date of summary: Mon Nov 26 11:41:44 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 0.673 s
+#> Fitted with method Port using 153 model solutions performed in 0.686 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 09:47:18 2018 
-#> Date of summary: Mon Nov 26 09:47:18 2018 
+#> Date of fit:     Mon Nov 26 11:41:45 2018 
+#> Date of summary: Mon Nov 26 11:41:45 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 1.529 s
+#> Fitted with method Port using 350 model solutions performed in 1.558 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 09:47:20 2018 
-#> Date of summary: Mon Nov 26 09:47:20 2018 
+#> Date of fit:     Mon Nov 26 11:41:46 2018 
+#> Date of summary: Mon Nov 26 11:41:46 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 0.847 s
+#> Fitted with method Port using 186 model solutions performed in 0.828 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 09:47:20 2018 
-#> Date of summary: Mon Nov 26 09:47:20 2018 
+#> Date of fit:     Mon Nov 26 11:41:47 2018 
+#> Date of summary: Mon Nov 26 11:41:47 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 0.457 s
+#> Fitted with method Port using 104 model solutions performed in 0.464 s
 #> 
 #> Weighting: none
 #> 
-- 
cgit v1.2.1