From 282f88f9e28e683f524d5e05d65d8b18ab856a8d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 26 Nov 2018 09:49:58 +0100 Subject: Further improvement of the logLik.mkinfit help Static documentation rebuilt by pkgdown --- docs/articles/FOCUS_L.html | 42 +++++++++++++-------------- docs/articles/web_only/compiled_models.html | 12 ++++---- docs/reference/Extract.mmkin.html | 12 ++++---- docs/reference/logLik.mkinfit.html | 8 ++++-- docs/reference/mccall81_245T.html | 12 ++++---- docs/reference/mkinfit.html | 44 ++++++++++++++--------------- 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 ++++++++-------- man/logLik.mkinfit.Rd | 4 ++- 12 files changed, 89 insertions(+), 83 deletions(-) diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 02b3f60e..4d337e72 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 09:29:29 2018 
-## Date of summary: Mon Nov 26 09:29:29 2018 
+## Date of fit:     Mon Nov 26 09:47:23 2018 
+## Date of summary: Mon Nov 26 09:47:23 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 0.094 s
+## Fitted with method Port using 37 model solutions performed in 0.093 s
 ## 
 ## Weighting: none
 ## 
@@ -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 09:29:30 2018 
-## Date of summary: Mon Nov 26 09:29:30 2018 
+## Date of fit:     Mon Nov 26 09:47:25 2018 
+## Date of summary: Mon Nov 26 09:47:25 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 1.467 s
+## Fitted with method Port using 611 model solutions performed in 1.475 s
 ## 
 ## Weighting: none
 ## 
@@ -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 09:29:31 2018 
-## Date of summary: Mon Nov 26 09:29:31 2018 
+## Date of fit:     Mon Nov 26 09:47:26 2018 
+## Date of summary: Mon Nov 26 09:47:26 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 0.191 s
+## Fitted with method Port using 81 model solutions performed in 0.192 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 09:29:32 2018 
-## Date of summary: Mon Nov 26 09:29:32 2018 
+## Date of fit:     Mon Nov 26 09:47:27 2018 
+## Date of summary: Mon Nov 26 09:47:27 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 0.828 s
+## Fitted with method Port using 336 model solutions performed in 0.831 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 09:29:33 2018 
-## Date of summary: Mon Nov 26 09:29:33 2018 
+## Date of fit:     Mon Nov 26 09:47:28 2018 
+## Date of summary: Mon Nov 26 09:47:28 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 0.334 s
+## Fitted with method Port using 137 model solutions performed in 0.336 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 09:29:34 2018 
-## Date of summary: Mon Nov 26 09:29:34 2018 
+## Date of fit:     Mon Nov 26 09:47:28 2018 
+## Date of summary: Mon Nov 26 09:47:29 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 0.108 s
+## Fitted with method Port using 46 model solutions performed in 0.107 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 09:29:34 2018 
-## Date of summary: Mon Nov 26 09:29:34 2018 
+## Date of fit:     Mon Nov 26 09:47:28 2018 
+## Date of summary: Mon Nov 26 09:47:29 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 0.158 s
+## Fitted with method Port using 66 model solutions performed in 0.168 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 93c800bf..083cdb79 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   2.268    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
+## 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
 ##   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   4.032    1.000     4.028        0
-## 1 deSolve, not compiled            3  39.759    9.861    39.741        0
+## 2     deSolve, compiled            3   4.012    1.000     4.010        0
+## 1 deSolve, not compiled            3  37.606    9.373    37.589        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

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

+
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

 
## 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 33d90e5b..51da42fc 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -278,7 +278,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.182       0.000       0.183 
+#>       0.183       0.000       0.183 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -467,8 +467,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555be42410>
-#> <environment: 0x55555bc697f8>
+#> <bytecode: 0x55555be28e50>
+#> <environment: 0x55555bc4d2b0>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -490,8 +490,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555cd2ca88>
-#> <environment: 0x55555bc697f8>
+#> <bytecode: 0x55555cd2fbb8>
+#> <environment: 0x55555bc4d2b0>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -558,7 +558,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Mon Nov 26 09:27:40 2018"
+#> [1] "Mon Nov 26 09:45:35 2018"
 #> 
 #> $version
 #> [1] "0.9.47.6"
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index 5fd6c6d7..b1901703 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -41,7 +41,9 @@ 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.
+  observation as standard deviation in calculating its likelihood
+  and the total number of estimated parameters is equal to the 
+  number of fitted degradation model parameters.
 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
@@ -147,7 +149,9 @@ In the case of iterative reweighting, the variances obtained by this
   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.

+  observation as standard deviation in calculating its likelihood
+  and the total number of estimated parameters is equal to the 
+  number of fitted degradation model parameters.

 
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
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 2cd933e9..981c633a 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 09:27:59 2018 
-#> Date of summary: Mon Nov 26 09:27:59 2018 
+#> Date of fit:     Mon Nov 26 09:45:54 2018 
+#> Date of summary: Mon Nov 26 09:45:54 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 3.635 s
+#> Fitted with method Port using 574 model solutions performed in 3.641 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 09:28:01 2018 
-#> Date of summary: Mon Nov 26 09:28:01 2018 
+#> Date of fit:     Mon Nov 26 09:45:56 2018 
+#> Date of summary: Mon Nov 26 09:45:56 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 1.623 s
+#> Fitted with method Port using 246 model solutions performed in 1.627 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index addd9c30..883dda22 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 09:28:04 2018 
-#> Date of summary: Mon Nov 26 09:28:04 2018 
+#> Date of fit:     Mon Nov 26 09:45:59 2018 
+#> Date of summary: Mon Nov 26 09:45:59 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 
-#>       1.009       0.000       1.009 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.974       0.000       0.975 
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 
-#>       0.909       0.000       0.910 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>        0.79        0.00        0.79 
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 09:28:16 2018 
-#> Date of summary: Mon Nov 26 09:28:16 2018 
+#> Date of fit:     Mon Nov 26 09:46:10 2018 
+#> Date of summary: Mon Nov 26 09:46:10 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 0.927 s
+#> Fitted with method Port using 186 model solutions performed in 0.889 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 09:28:18 2018 
-#> Date of summary: Mon Nov 26 09:28:18 2018 
+#> Date of fit:     Mon Nov 26 09:46:13 2018 
+#> Date of summary: Mon Nov 26 09:46:13 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 2.509 s
+#> Fitted with method Port using 551 model solutions performed in 2.441 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 09:28:19 2018 
-#> Date of summary: Mon Nov 26 09:28:19 2018 
+#> Date of fit:     Mon Nov 26 09:46:14 2018 
+#> Date of summary: Mon Nov 26 09:46:14 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 0.68 s
+#> Fitted with method Port using 155 model solutions performed in 0.679 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 09:28:20 2018 
-#> Date of summary: Mon Nov 26 09:28:20 2018 
+#> Date of fit:     Mon Nov 26 09:46:15 2018 
+#> Date of summary: Mon Nov 26 09:46:15 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 0.775 s
+#> Fitted with method Port using 174 model solutions performed in 0.771 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 09:28:22 2018 
-#> Date of summary: Mon Nov 26 09:28:22 2018 
+#> Date of fit:     Mon Nov 26 09:46:16 2018 
+#> Date of summary: Mon Nov 26 09:46:16 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 1.203 s
+#> Fitted with method Port using 270 model solutions performed in 1.2 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 09:28:25 2018 
-#> Date of summary: Mon Nov 26 09:28:25 2018 
+#> Date of fit:     Mon Nov 26 09:46:19 2018 
+#> Date of summary: Mon Nov 26 09:46:19 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 3.078 s
+#> Fitted with method Port using 692 model solutions performed in 3.079 s
 #> 
 #> Weighting: manual
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 448c0e8e..d947aff5 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 file775a236112e7.c 2> file775a236112e7.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file74b35b9de5b.c 2> file74b35b9de5b.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 84e6591b..88858539 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -323,12 +323,12 @@
                 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 
-#>       0.004       0.000       0.004 
  system.time(
+#>       0.005       0.000       0.005 
  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 
-#>       0.001       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
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index a27cf5db..49117199 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 
-#>       0.038       0.036       6.851 
time_1
#>        User      System verstrichen 
-#>      21.780       0.000      21.791 

+#>       0.037       0.036       7.001 
time_1
#>        User      System verstrichen 
+#>      21.838       0.000      21.852 

 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 7f510c67..e63ab87e 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 09:29:14 2018 
-#> Date of summary: Mon Nov 26 09:29:14 2018 
+#> Date of fit:     Mon Nov 26 09:47:09 2018 
+#> Date of summary: Mon Nov 26 09:47:09 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 24b50890..c0ff16fd 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 09:29:22 2018 
-#> Date of summary: Mon Nov 26 09:29:22 2018 
+#> Date of fit:     Mon Nov 26 09:47:17 2018 
+#> Date of summary: Mon Nov 26 09:47:17 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 0.683 s
+#> Fitted with method Port using 153 model solutions performed in 0.673 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 09:29:24 2018 
-#> Date of summary: Mon Nov 26 09:29:24 2018 
+#> Date of fit:     Mon Nov 26 09:47:18 2018 
+#> Date of summary: Mon Nov 26 09:47:18 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 1.594 s
+#> Fitted with method Port using 350 model solutions performed in 1.529 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 09:29:25 2018 
-#> Date of summary: Mon Nov 26 09:29:25 2018 
+#> Date of fit:     Mon Nov 26 09:47:20 2018 
+#> Date of summary: Mon Nov 26 09:47:20 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 0.819 s
+#> Fitted with method Port using 186 model solutions performed in 0.847 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 09:29:26 2018 
-#> Date of summary: Mon Nov 26 09:29:26 2018 
+#> Date of fit:     Mon Nov 26 09:47:20 2018 
+#> Date of summary: Mon Nov 26 09:47:20 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 0.486 s
+#> Fitted with method Port using 104 model solutions performed in 0.457 s
 #> 
 #> Weighting: none
 #> 
diff --git a/man/logLik.mkinfit.Rd b/man/logLik.mkinfit.Rd
index 78c4e4c2..8080f3db 100644
--- a/man/logLik.mkinfit.Rd
+++ b/man/logLik.mkinfit.Rd
@@ -16,7 +16,9 @@
   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.
+  observation as standard deviation in calculating its likelihood
+  and the total number of estimated parameters is equal to the 
+  number of fitted degradation model parameters.
 
   In the case of iterative reweighting, the variances obtained by this
   procedure are used in the likelihood calculations, and the number of
-- 
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