From 3621588c04cbaa393ba62c97137f6aec746d114f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 26 Nov 2018 09:09:43 +0100 Subject: Support logLik and AIC for manual weights Static documentation rebuilt by pkgdown --- DESCRIPTION | 2 +- NEWS.md | 4 ++- R/logLik.mkinfit.R | 13 +++++++-- docs/articles/FOCUS_D.html | 2 +- docs/articles/FOCUS_L.html | 38 ++++++++++++------------- 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 | 12 ++++---- docs/news/index.html | 7 +++-- docs/reference/Extract.mmkin.html | 10 +++---- docs/reference/logLik.mkinfit.html | 9 ++++-- 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 | 6 ++-- docs/reference/transform_odeparms.html | 24 ++++++++-------- man/logLik.mkinfit.Rd | 6 ++-- 20 files changed, 111 insertions(+), 94 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4b5fd905..f2f1d6ea 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 0.9.47.6 -Date: 2018-11-23 +Date: 2018-11-26 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", comment = c(ORCID = "0000-0003-4371-6538")), diff --git a/NEWS.md b/NEWS.md index cce1bea6..10211f96 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,6 @@ -# mkin 0.9.47.6 (2018-09-21) +# mkin 0.9.47.6 (2018-11-26) + +- Add the function 'logLik.mkinfit.R' which makes it possible to calculate an AIC for mkinfit objects - 'add_err': Respect the argument giving the number of replicates in the synthetic dataset diff --git a/R/logLik.mkinfit.R b/R/logLik.mkinfit.R index c30cc099..d3f4232d 100644 --- a/R/logLik.mkinfit.R +++ b/R/logLik.mkinfit.R @@ -19,12 +19,21 @@ logLik.mkinfit <- function(object, ...) { y_ij <- object$data$observed yhat_ij <- object$data$predicted if (is.null(object$data$err)) { + # For unweighted fits we estimate a single value for sigma from the residuals err <- sd(object$data$residual) n_var_comp <- 1 # Number of variance components estimated } else { err <- object$data$err - if (object$reweight.method == "obs") n_var_comp <- length(object$var_ms_unweighted) - else n_var_comp <- 2 + # For weighted fits we check for variance models used in IRLS + # If the variance values (err) were given and were not + # reweighted, the number of variance components estimated is zero + if (is.null(object$reweight.method)) { + n_var_comp <- 0 + } else { + n_var_comp <- switch(object$reweight.method, + obs = length(object$var_ms_unweighted), + tc = 2) + } } prob_dens <- dnorm(y_ij, yhat_ij, err) val <- log(prod(prob_dens)) diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index b03e7612..0d463f63 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -84,7 +84,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2018-11-23

+

2018-11-26

diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index e83664bc..dc562002 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -84,7 +84,7 @@

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2018-11-23

+

2018-11-26

@@ -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:     Fri Nov 23 20:47:25 2018 
-## Date of summary: Fri Nov 23 20:47:25 2018 
+## Date of fit:     Mon Nov 26 09:07:07 2018 
+## Date of summary: Mon Nov 26 09:07:07 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:     Fri Nov 23 20:47:26 2018 
-## Date of summary: Fri Nov 23 20:47:26 2018 
+## Date of fit:     Mon Nov 26 09:07:09 2018 
+## Date of summary: Mon Nov 26 09:07:09 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 1.481 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:     Fri Nov 23 20:47:27 2018 
-## Date of summary: Fri Nov 23 20:47:27 2018 
+## Date of fit:     Mon Nov 26 09:07:10 2018 
+## Date of summary: Mon Nov 26 09:07:10 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 0.191 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:     Fri Nov 23 20:47:28 2018 
-## Date of summary: Fri Nov 23 20:47:28 2018 
+## Date of fit:     Mon Nov 26 09:07:11 2018 
+## Date of summary: Mon Nov 26 09:07:11 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 0.822 s
+## Fitted with method Port using 336 model solutions performed in 0.86 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:     Fri Nov 23 20:47:29 2018 
-## Date of summary: Fri Nov 23 20:47:29 2018 
+## Date of fit:     Mon Nov 26 09:07:12 2018 
+## Date of summary: Mon Nov 26 09:07:12 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 0.339 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:     Fri Nov 23 20:47:29 2018 
-## Date of summary: Fri Nov 23 20:47:30 2018 
+## Date of fit:     Mon Nov 26 09:07:12 2018 
+## Date of summary: Mon Nov 26 09:07:13 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -620,8 +620,8 @@
 
 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Nov 23 20:47:30 2018 
-## Date of summary: Fri Nov 23 20:47:30 2018 
+## Date of fit:     Mon Nov 26 09:07:13 2018 
+## Date of summary: Mon Nov 26 09:07:13 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 4ead1062..e73b989a 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -84,7 +84,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2018-11-23

+            
2018-11-26

       
       
       
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 8c053c10..6ba7e1a7 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -84,7 +84,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2018-11-23

+            
2018-11-26

       
       
       
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 5215e039..6ebe3c73 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -84,7 +84,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2018-11-23

+            
2018-11-26

       
       
       
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index c47425fb..25a3a62e 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -84,7 +84,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2018-11-23

+            
2018-11-26

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

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.274    1.000     2.273        0
-## 1 deSolve, not compiled            3  17.686    7.777    17.676        0
-## 2      Eigenvalue based            3   2.800    1.231     2.799        0
+## 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
 ##   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   4.038    1.000     4.035        0
-## 1 deSolve, not compiled            3  37.805    9.362    37.788        0
+## 2     deSolve, compiled            3   4.020    1.000     4.017        0
+## 1 deSolve, not compiled            3  37.721    9.383    37.704        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/news/index.html b/docs/news/index.html
index f3e57dd0..9f658dad 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -117,11 +117,12 @@
       
     
 
-    

+    

 

-mkin 0.9.47.6 (2018-09-21) Unreleased 
+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_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
    • 
@@ -670,7 +671,7 @@
     
    
       
    Contents
    
       
      
-        
    • 0.9.47.6
      • 
+        
    • 0.9.47.6
      • 
         
    • 0.9.47.5
      • 
         
    • 0.9.47.3
      • 
         
    • 0.9.47.2
      • 
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index a595dd0d..ec2c7eb7 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -467,8 +467,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555be3c890>
-#> <environment: 0x55555bc2f5a0>
+#> <bytecode: 0x55555be327a0>
+#> <environment: 0x55555bc27c20>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -490,8 +490,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555cd74468>
-#> <environment: 0x55555bc2f5a0>
+#> <bytecode: 0x55555cd76230>
+#> <environment: 0x55555bc27c20>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -558,7 +558,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Fri Nov 23 20:45:37 2018"
+#> [1] "Mon Nov 26 09:05:19 2018"
 #> 
 #> $version
 #> [1] "0.9.47.6"
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index 1dda313f..250bc1d8 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -158,13 +158,16 @@
     m1 = mkinsub("SFO")
   )
    #> Successfully compiled differential equation model from auto-generated C code.
      d_t <- FOCUS_2006_D
   d_t[23:24, "value"] <- c(NA, NA) # can't cope with zero values at the moment
-  f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE)
+  f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE) # no weighting (weights are unity)
   f_obs <- mkinfit(sfo_sfo, d_t, reweight.method = "obs", quiet = TRUE)
   f_tc <- mkinfit(sfo_sfo, d_t, reweight.method = "tc", quiet = TRUE)
-  AIC(f_nw, f_obs, f_tc)
    #>       df      AIC
+  d_t$err <- d_t$value # Manual weighting assuming sigma ~ y
+  f_man <- mkinfit(sfo_sfo, d_t, err = "err", quiet = TRUE)
+  AIC(f_nw, f_obs, f_tc, f_man)
    #>       df      AIC
 #> f_nw   5 204.4619
 #> f_obs  6 205.8727
-#> f_tc   6 143.8773

+#> f_tc   6 143.8773
+#> f_man  4 291.8000

   
   
#> 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:     Fri Nov 23 20:45:55 2018 
-#> Date of summary: Fri Nov 23 20:45:55 2018 
+#> Date of fit:     Mon Nov 26 09:05:38 2018 
+#> Date of summary: Mon Nov 26 09:05:38 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 3.63 s
+#> Fitted with method Port using 574 model solutions performed in 3.64 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:     Fri Nov 23 20:45:57 2018 
-#> Date of summary: Fri Nov 23 20:45:57 2018 
+#> Date of fit:     Mon Nov 26 09:05:40 2018 
+#> Date of summary: Mon Nov 26 09:05:40 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 1.547 s
+#> Fitted with method Port using 246 model solutions performed in 1.626 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index b2e7363d..2017a35c 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:     Fri Nov 23 20:46:00 2018 
-#> Date of summary: Fri Nov 23 20:46:00 2018 
+#> Date of fit:     Mon Nov 26 09:05:43 2018 
+#> Date of summary: Mon Nov 26 09:05:43 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 
-#>       0.978       0.000       0.978 
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 
-#>       0.794       0.000       0.795 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.796       0.000       0.796 
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:     Fri Nov 23 20:46:12 2018 
-#> Date of summary: Fri Nov 23 20:46:12 2018 
+#> Date of fit:     Mon Nov 26 09:05:54 2018 
+#> Date of summary: Mon Nov 26 09:05:54 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 0.816 s
+#> Fitted with method Port using 186 model solutions performed in 0.885 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:     Fri Nov 23 20:46:14 2018 
-#> Date of summary: Fri Nov 23 20:46:14 2018 
+#> Date of fit:     Mon Nov 26 09:05:57 2018 
+#> Date of summary: Mon Nov 26 09:05:57 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 2.451 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:     Fri Nov 23 20:46:15 2018 
-#> Date of summary: Fri Nov 23 20:46:15 2018 
+#> Date of fit:     Mon Nov 26 09:05:58 2018 
+#> Date of summary: Mon Nov 26 09:05:58 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 0.687 s
+#> Fitted with method Port using 155 model solutions performed in 0.69 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:     Fri Nov 23 20:46:16 2018 
-#> Date of summary: Fri Nov 23 20:46:16 2018 
+#> Date of fit:     Mon Nov 26 09:05:59 2018 
+#> Date of summary: Mon Nov 26 09:05:59 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 0.789 s
+#> Fitted with method Port using 174 model solutions performed in 0.772 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:     Fri Nov 23 20:46:17 2018 
-#> Date of summary: Fri Nov 23 20:46:17 2018 
+#> Date of fit:     Mon Nov 26 09:06:00 2018 
+#> Date of summary: Mon Nov 26 09:06:00 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 1.212 s
+#> Fitted with method Port using 270 model solutions performed in 1.201 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:     Fri Nov 23 20:46:21 2018 
-#> Date of summary: Fri Nov 23 20:46:21 2018 
+#> Date of fit:     Mon Nov 26 09:06:03 2018 
+#> Date of summary: Mon Nov 26 09:06:03 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 3.081 s
+#> Fitted with method Port using 692 model solutions performed in 3.087 s
 #> 
 #> Weighting: manual
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index e16a4147..a7f26322 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 file32ab4b1aa093.c 2> file32ab4b1aa093.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file672328842b40.c 2> file672328842b40.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 9b8be306..f26422a4 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 
-#>       0.004       0.000       0.003 
  system.time(
+#>       0.003       0.000       0.003 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
@@ -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 
-#>       0.047       0.000       0.047 

+#>       0.041       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 fda9ba60..eb2e5bcf 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 
-#>       0.033       0.040       6.952 
time_1
#>        User      System verstrichen 
-#>      21.739       0.000      21.752 

+#>       0.043       0.032       6.850 
time_1
#>        User      System verstrichen 
+#>      21.779       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 a0ef5efe..9cb43d42 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -206,15 +206,15 @@
     
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:     Fri Nov 23 20:47:10 2018 
-#> Date of summary: Fri Nov 23 20:47:10 2018 
+#> Date of fit:     Mon Nov 26 09:06:53 2018 
+#> Date of summary: Mon Nov 26 09:06:53 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.081 s
+#> Fitted with method Port using 35 model solutions performed in 0.083 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index f98580cb..6178527b 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:     Fri Nov 23 20:47:18 2018 
-#> Date of summary: Fri Nov 23 20:47:18 2018 
+#> Date of fit:     Mon Nov 26 09:07:01 2018 
+#> Date of summary: Mon Nov 26 09:07:01 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 0.666 s
+#> Fitted with method Port using 153 model solutions performed in 0.687 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:     Fri Nov 23 20:47:20 2018 
-#> Date of summary: Fri Nov 23 20:47:20 2018 
+#> Date of fit:     Mon Nov 26 09:07:03 2018 
+#> Date of summary: Mon Nov 26 09:07:03 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 1.539 s
+#> Fitted with method Port using 350 model solutions performed in 1.537 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:     Fri Nov 23 20:47:21 2018 
-#> Date of summary: Fri Nov 23 20:47:21 2018 
+#> Date of fit:     Mon Nov 26 09:07:04 2018 
+#> Date of summary: Mon Nov 26 09:07:04 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 0.824 s
+#> Fitted with method Port using 186 model solutions performed in 0.827 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:     Fri Nov 23 20:47:22 2018 
-#> Date of summary: Fri Nov 23 20:47:22 2018 
+#> Date of fit:     Mon Nov 26 09:07:04 2018 
+#> Date of summary: Mon Nov 26 09:07:04 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 0.458 s
+#> Fitted with method Port using 104 model solutions performed in 0.454 s
 #> 
 #> Weighting: none
 #> 
diff --git a/man/logLik.mkinfit.Rd b/man/logLik.mkinfit.Rd
index 2f3e58a1..2f911d5b 100644
--- a/man/logLik.mkinfit.Rd
+++ b/man/logLik.mkinfit.Rd
@@ -30,10 +30,12 @@
   )
   d_t <- FOCUS_2006_D
   d_t[23:24, "value"] <- c(NA, NA) # can't cope with zero values at the moment
-  f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE)
+  f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE) # no weighting (weights are unity)
   f_obs <- mkinfit(sfo_sfo, d_t, reweight.method = "obs", quiet = TRUE)
   f_tc <- mkinfit(sfo_sfo, d_t, reweight.method = "tc", quiet = TRUE)
-  AIC(f_nw, f_obs, f_tc)
+  d_t$err <- d_t$value # Manual weighting assuming sigma ~ y
+  f_man <- mkinfit(sfo_sfo, d_t, err = "err", quiet = TRUE)
+  AIC(f_nw, f_obs, f_tc, f_man)
 }
 \author{
   Johannes Ranke
-- 
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