From 95178837d3f91e84837628446b5fd468179af2b9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 4 Jun 2019 15:09:28 +0200 Subject: Additional algorithm "d_c", more tests, docs The new algorithm tries direct optimization of the likelihood, as well as a three step procedure. In this way, we consistently get the model with the highest likelihood for SFO, DFOP and HS for all 12 new test datasets. --- docs/articles/FOCUS_L.html | 60 +++++++++++++++++++++++----------------------- 1 file changed, 30 insertions(+), 30 deletions(-) (limited to 'docs/articles/FOCUS_L.html') diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 6771bf63..75b2cf10 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -30,7 +30,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -88,7 +88,7 @@

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2019-05-08

+

2019-06-04

@@ -112,17 +112,17 @@

Since mkin version 0.9-32 (July 2014), we can use shorthand notation like "SFO" for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.

m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
-
## mkin version used for fitting:    0.9.49.4 
+
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:29 2019 
-## Date of summary: Wed May  8 20:52:29 2019 
+## Date of fit:     Tue Jun  4 15:03:20 2019 
+## Date of summary: Tue Jun  4 15:03:20 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.276 s
+## Fitted using 133 model solutions performed in 0.28 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -213,10 +213,10 @@
 
## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt

 
## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
 ## finite result is doubtful

-
## mkin version used for fitting:    0.9.49.4 
+
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:31 2019 
-## Date of summary: Wed May  8 20:52:31 2019 
+## Date of fit:     Tue Jun  4 15:03:22 2019 
+## Date of summary: Tue Jun  4 15:03:22 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -317,17 +317,17 @@
      main = "FOCUS L2 - FOMC")

 

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

-
## mkin version used for fitting:    0.9.49.4 
+
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:32 2019 
-## Date of summary: Wed May  8 20:52:32 2019 
+## Date of fit:     Tue Jun  4 15:03:23 2019 
+## Date of summary: Tue Jun  4 15:03:23 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.483 s
+## Fitted using 239 model solutions performed in 0.484 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -392,10 +392,10 @@
      main = "FOCUS L2 - DFOP")

 

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

-
## mkin version used for fitting:    0.9.49.4 
+
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:33 2019 
-## Date of summary: Wed May  8 20:52:33 2019 
+## Date of fit:     Tue Jun  4 15:03:25 2019 
+## Date of summary: Tue Jun  4 15:03:25 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -404,7 +404,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 572 model solutions performed in 1.185 s
+## Fitted using 572 model solutions performed in 1.193 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -491,10 +491,10 @@
 
The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.

 
We can extract the summary and plot for e.g. the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.

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

-
## mkin version used for fitting:    0.9.49.4 
+
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:35 2019 
-## Date of summary: Wed May  8 20:52:35 2019 
+## Date of fit:     Tue Jun  4 15:03:26 2019 
+## Date of summary: Tue Jun  4 15:03:27 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -503,7 +503,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 373 model solutions performed in 0.768 s
+## Fitted using 373 model solutions performed in 0.767 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -596,17 +596,17 @@
 

 
The \(\chi^2\) error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the \(\chi^2\) test passes is slightly lower for the FOMC model. However, the difference appears negligible.

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

-
## mkin version used for fitting:    0.9.49.4 
+
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:36 2019 
-## Date of summary: Wed May  8 20:52:37 2019 
+## Date of fit:     Tue Jun  4 15:03:27 2019 
+## Date of summary: Tue Jun  4 15:03:28 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.289 s
+## Fitted using 142 model solutions performed in 0.288 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -660,17 +660,17 @@
 ##        DT50 DT90
 ## parent  106  352

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

-
## mkin version used for fitting:    0.9.49.4 
+
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:36 2019 
-## Date of summary: Wed May  8 20:52:37 2019 
+## Date of fit:     Tue Jun  4 15:03:28 2019 
+## Date of summary: Tue Jun  4 15:03:28 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.45 s
+## Fitted using 224 model solutions performed in 0.449 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -769,7 +769,7 @@
 
 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
 
-- 
cgit v1.2.3


From b6027bbd157734e1c7f8c3ba6373451f5c85fc38 Mon Sep 17 00:00:00 2001
From: Johannes Ranke 
Date: Wed, 5 Jun 2019 15:16:59 +0200
Subject: Add error model algorithm to output

---
 R/mkinfit.R                                   |  27 ++++++---
 docs/articles/FOCUS_D.html                    |  13 +++--
 docs/articles/FOCUS_L.html                    |  77 ++++++++++++++------------
 docs/articles/mkin.html                       |   2 +-
 docs/articles/twa.html                        |   2 +-
 docs/articles/web_only/FOCUS_Z.html           |   2 +-
 docs/articles/web_only/NAFTA_examples.html    |   2 +-
 docs/articles/web_only/benchmarks.html        |  24 ++++----
 docs/articles/web_only/compiled_models.html   |  12 ++--
 docs/reference/Extract.mmkin.html             |   8 +--
 docs/reference/experimental_data_for_UBA.html |  66 +++++++++++++++++++++-
 docs/reference/mkinfit.html                   |  50 +++++++++--------
 docs/reference/mkinmod.html                   |   2 +-
 docs/reference/mkinpredict.html               |   6 +-
 docs/reference/mmkin.html                     |   4 +-
 docs/reference/summary.mkinfit.html           |  11 ++--
 vignettes/mkin_benchmarks.rda                 | Bin 874 -> 876 bytes
 17 files changed, 198 insertions(+), 110 deletions(-)

(limited to 'docs/articles/FOCUS_L.html')

diff --git a/R/mkinfit.R b/R/mkinfit.R
index 60697cb1..2af4e493 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -506,18 +506,23 @@ mkinfit <- function(mkinmod, observed,
           control = control, ...)
         fit$logLik <- - nlogLik.current
 
+        d_3_messages = c(
+           same = "Direct fitting and three-step fitting yield approximately the same likelihood",
+           threestep = "Three-step fitting yielded a higher likelihood than direct fitting",
+           direct = "Direct fitting yielded a higher likelihood than three-step fitting")
         if (error_model_algorithm == "d_3") {
           rel_diff <- abs((fit_direct$logLik - fit$logLik))/-mean(c(fit_direct$logLik, fit$logLik))
           if (rel_diff < 0.0001) {
-            if (!quiet) {
-              message("Direct fitting and three-step fitting yield approximately the same likelihood")
-            }
+            if (!quiet) message(d_3_messages["same"])
+            fit$d_3_message <- d_3_messages["same"]
           } else {
             if (fit$logLik > fit_direct$logLik) {
-              if (!quiet) message("Three-step fitting yielded a higher likelihood than direct fitting")
+              if (!quiet) message(d_3_messages["threestep"])
+              fit$d_3_message <- d_3_messages["threestep"]
             } else {
-              if (!quiet) message("Direct fitting yielded a higher likelihood than three-step fitting")
+              if (!quiet) message(d_3_messages["direct"])
               fit <- fit_direct
+              fit$d_3_message <- d_3_messages["direct"]
             }
           }
         }
@@ -553,6 +558,7 @@ mkinfit <- function(mkinmod, observed,
         }
       }
     }
+    fit$error_model_algorithm <- error_model_algorithm
 
     # We include the error model in the parameter uncertainty analysis, also
     # for constant variance, to get a confidence interval for it
@@ -725,6 +731,7 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05,
     solution_type = object$solution_type,
     warning = object$warning,
     use_of_ff = object$mkinmod$use_of_ff,
+    error_model_algorithm = object$error_model_algorithm,
     df = c(p, rdf),
     cov.unscaled = covar,
     err_mod = object$err_mod,
@@ -763,8 +770,9 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05,
   ep <- endpoints(object)
   if (length(ep$ff) != 0)
     ans$ff <- ep$ff
-  if(distimes) ans$distimes <- ep$distimes
-  if(length(ep$SFORB) != 0) ans$SFORB <- ep$SFORB
+  if (distimes) ans$distimes <- ep$distimes
+  if (length(ep$SFORB) != 0) ans$SFORB <- ep$SFORB
+  if (!is.null(object$d_3_message)) ans$d_3_message <- object$d_3_message
   class(ans) <- c("summary.mkinfit", "summary.modFit")
   return(ans)
 }
@@ -794,12 +802,15 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
 
   cat("\nFitted using", x$calls, "model solutions performed in", x$time[["elapsed"]],  "s\n")
 
-  cat("\nError model:\n")
+  cat("\nError model: ")
   cat(switch(x$err_mod,
              const = "Constant variance",
              obs = "Variance unique to each observed variable",
              tc = "Two-component variance function"), "\n")
 
+  cat("\nError model algorithm:", x$error_model_algorithm, "\n")
+  if (!is.null(x$d_3_message)) cat(x$d_3_message, "\n")
+
   cat("\nStarting values for parameters to be optimised:\n")
   print(x$start)
 
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 698ccebc..be1f40f5 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -88,7 +88,7 @@
       
Example evaluation of FOCUS Example Dataset D

                         
Johannes Ranke

             
-            
2019-06-04

+            
2019-06-05

       
       
       
@@ -168,8 +168,8 @@
 
summary(fit)

 
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jun  4 15:03:18 2019 
-## Date of summary: Tue Jun  4 15:03:18 2019 
+## Date of fit:     Wed Jun  5 15:10:49 2019 
+## Date of summary: Wed Jun  5 15:10:50 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -177,10 +177,11 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 389 model solutions performed in 0.978 s
+## Fitted using 389 model solutions performed in 0.984 s
 ## 
-## Error model:
-## Constant variance 
+## Error model: Constant variance 
+## 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##                    value   type
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 75b2cf10..4388edd2 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -88,7 +88,7 @@
       
Example evaluation of FOCUS Laboratory Data L1 to L3

                         
Johannes Ranke

             
-            
2019-06-04

+            
2019-06-05

       
       
       
@@ -114,18 +114,19 @@
 summary(m.L1.SFO)

 
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jun  4 15:03:20 2019 
-## Date of summary: Tue Jun  4 15:03:20 2019 
+## Date of fit:     Wed Jun  5 15:10:52 2019 
+## Date of summary: Wed Jun  5 15:10:52 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.28 s
+## Fitted using 133 model solutions performed in 0.277 s
 ## 
-## Error model:
-## Constant variance 
+## Error model: Constant variance 
+## 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##                   value   type
@@ -215,8 +216,8 @@
 ## finite result is doubtful

 
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jun  4 15:03:22 2019 
-## Date of summary: Tue Jun  4 15:03:22 2019 
+## Date of fit:     Wed Jun  5 15:10:54 2019 
+## Date of summary: Wed Jun  5 15:10:54 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -228,10 +229,11 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 899 model solutions performed in 1.868 s
+## Fitted using 899 model solutions performed in 1.877 s
+## 
+## Error model: Constant variance 
 ## 
-## Error model:
-## Constant variance 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##              value   type
@@ -319,18 +321,19 @@
 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jun  4 15:03:23 2019 
-## Date of summary: Tue Jun  4 15:03:23 2019 
+## Date of fit:     Wed Jun  5 15:10:55 2019 
+## Date of summary: Wed Jun  5 15:10:55 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.484 s
+## Fitted using 239 model solutions performed in 0.492 s
 ## 
-## Error model:
-## Constant variance 
+## Error model: Constant variance 
+## 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##              value   type
@@ -394,8 +397,8 @@
 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jun  4 15:03:25 2019 
-## Date of summary: Tue Jun  4 15:03:25 2019 
+## Date of fit:     Wed Jun  5 15:10:56 2019 
+## Date of summary: Wed Jun  5 15:10:56 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -404,10 +407,11 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 572 model solutions performed in 1.193 s
+## Fitted using 572 model solutions performed in 1.183 s
+## 
+## Error model: Constant variance 
 ## 
-## Error model:
-## Constant variance 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##              value   type
@@ -493,8 +497,8 @@
 
summary(mm.L3[["DFOP", 1]])

 
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jun  4 15:03:26 2019 
-## Date of summary: Tue Jun  4 15:03:27 2019 
+## Date of fit:     Wed Jun  5 15:10:58 2019 
+## Date of summary: Wed Jun  5 15:10:58 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -503,10 +507,11 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 373 model solutions performed in 0.767 s
+## Fitted using 373 model solutions performed in 0.773 s
 ## 
-## Error model:
-## Constant variance 
+## Error model: Constant variance 
+## 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##              value   type
@@ -598,8 +603,8 @@
 
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jun  4 15:03:27 2019 
-## Date of summary: Tue Jun  4 15:03:28 2019 
+## Date of fit:     Wed Jun  5 15:10:59 2019 
+## Date of summary: Wed Jun  5 15:10:59 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -608,8 +613,9 @@
 ## 
 ## Fitted using 142 model solutions performed in 0.288 s
 ## 
-## Error model:
-## Constant variance 
+## Error model: Constant variance 
+## 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##                  value   type
@@ -662,18 +668,19 @@
 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jun  4 15:03:28 2019 
-## Date of summary: Tue Jun  4 15:03:28 2019 
+## Date of fit:     Wed Jun  5 15:10:59 2019 
+## Date of summary: Wed Jun  5 15:10:59 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.449 s
+## Fitted using 224 model solutions performed in 0.453 s
+## 
+## Error model: Constant variance 
 ## 
-## Error model:
-## Constant variance 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##              value   type
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 09b1b8ea..5977d642 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -88,7 +88,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2019-06-04

+            
2019-06-05

       
       
       
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index ede27942..f98026e7 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -88,7 +88,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2019-06-04

+            
2019-06-05

       
       
       
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 555400df..542deb14 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -88,7 +88,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2019-06-04

+            
2019-06-05

       
       
       
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index 7f3cc76b..4cd16437 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -88,7 +88,7 @@
       
Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance

                         
Johannes Ranke

             
-            
2019-06-04

+            
2019-06-05

       
       
       
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 43f8d238..507bdb61 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -88,7 +88,7 @@
       
Benchmark timings for mkin on various systems

                         
Johannes Ranke

             
-            
2019-06-04

+            
2019-06-05

       
       
       
@@ -202,77 +202,77 @@
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.805
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.828
 ##                                                                         t2
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.748
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.869
 ##                                                                        t3
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.403
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.412
 ##                                                                         t4
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  8.461
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.613
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.497
 ##                                                                         t5
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1  9.495
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  6.395
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.675
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.386
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  6.002
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.309
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.329
 ##                                                                        t6
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.546
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.548
 ##                                                                        t7
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.214
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.192
 ##                                                                        t8
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.02
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.871
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.827
 ##                                                                         t9
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  8.171
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  7.618
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  7.763
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.738
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.653
 ##                                                                       t10
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.763
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.762
 ##                                                                        t11
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  5.636
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.574
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.365
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  5.626
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.527

+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.512

 
save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")

 
   
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index f3062c66..5f0301fc 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -88,7 +88,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2019-06-04

+            
2019-06-05

       
       
       
@@ -163,9 +163,9 @@
 ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
 ## = TRUE): Observations with value of zero were removed from the data

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   3.053    1.000     3.052        0
-## 1 deSolve, not compiled            3  28.457    9.321    28.442        0
-## 2      Eigenvalue based            3   4.296    1.407     4.293        0
+## 3     deSolve, compiled            3   3.041    1.000     3.039        0
+## 1 deSolve, not compiled            3  28.429    9.349    28.415        0
+## 2      Eigenvalue based            3   4.291    1.411     4.288        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -214,8 +214,8 @@
 ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
 ## value of zero were removed from the data

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.828    1.000     4.825        0
-## 1 deSolve, not compiled            3  53.153   11.009    53.125        0
+## 2     deSolve, compiled            3   4.927    1.000     4.924        0
+## 1 deSolve, not compiled            3  53.138   10.785    53.108        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 1d1da50e..37c0b361 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -172,16 +172,16 @@
                 cores = 1, quiet = TRUE)
   fits["FOMC", ]
#>       dataset
 #> model  B       C      
-#>   FOMC List,36 List,36
+#>   FOMC List,37 List,37
 #> attr(,"class")
 #> [1] "mmkin"
  fits[, "B"]
#>       dataset
 #> model  B      
-#>   SFO  List,36
-#>   FOMC List,36
+#>   SFO  List,37
+#>   FOMC List,37
 #> attr(,"class")
 #> [1] "mmkin"
  fits["SFO", "B"]
#>      dataset
 #> model B      
-#>   SFO List,36
+#>   SFO List,37
 #> attr(,"class")
 #> [1] "mmkin"

   head(
diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html
index 3e8d20ef..bb94fd11 100644
--- a/docs/reference/experimental_data_for_UBA.html
+++ b/docs/reference/experimental_data_for_UBA.html
@@ -37,7 +37,30 @@
  and advance error model specifications. The fact that these data and some
  results are shown here do not imply a license to use them in the context of
  pesticide registrations, as the use of the data may be constrained by
- data protection regulations." />
+ data protection regulations.
+Preprocessing of data was performed based on the recommendations of the FOCUS
+ kinetics workgroup (FOCUS, 2014) as described below.
+Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox
+ (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1
+ was assumed. Metabolite residues reported for day zero were added to the
+ parent compound residues.
+Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid
+ (Belgium, 2014, p. 8) and show the data for two different radiolabels. For
+ dataset 4, the value given for the metabolite in the day zero sampling
+ in replicate B was added to the parent compound, following the respective
+ FOCUS recommendation.
+Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate
+ (Austria, 2015, p. 16).
+Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate
+ (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling,
+ the residues given for the metabolite were added to the parent
+ value, following the recommendation of the FOCUS kinetics workgroup.
+Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D
+ (Germany, 2013b, p. 644). Values reported as zero were set to NA, with
+ the exception of the day three sampling of metabolite A2, which was set
+ to one half of the LOD reported to be 1% AR.
+Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
+ (United Kingdom, 2014, p. 81)." />
 
 
 
@@ -139,6 +162,29 @@
  results are shown here do not imply a license to use them in the context of
  pesticide registrations, as the use of the data may be constrained by
  data protection regulations.

+
Preprocessing of data was performed based on the recommendations of the FOCUS
+ kinetics workgroup (FOCUS, 2014) as described below.

+
Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox
+ (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1
+ was assumed. Metabolite residues reported for day zero were added to the
+ parent compound residues.

+
Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid
+ (Belgium, 2014, p. 8) and show the data for two different radiolabels. For
+ dataset 4, the value given for the metabolite in the day zero sampling
+ in replicate B was added to the parent compound, following the respective
+ FOCUS recommendation.

+
Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate
+ (Austria, 2015, p. 16).

+
Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate
+ (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling,
+ the residues given for the metabolite were added to the parent
+ value, following the recommendation of the FOCUS kinetics workgroup.

+
Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D
+ (Germany, 2013b, p. 644). Values reported as zero were set to NA, with
+ the exception of the day three sampling of metabolite A2, which was set
+ to one half of the LOD reported to be 1% AR.

+
Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
+ (United Kingdom, 2014, p. 81).

     
     

 
@@ -154,8 +200,24 @@
     
     
Source

 
-    
Ranke (2019) Documentation of results obtained for the error model expertise
+    
+    
Austria (2015). Ethofumesate Renewal Assessment Report Volume 3 Annex B.8 (AS)

+
Belgium (2014). Isofetamid (IKF-5411) Draft Assessment Report Volume 3 Annex B.8 (AS)

+
France (2015). Imazamox Draft Renewal Assessment Report Volume 3 Annex B.8 (AS)

+
FOCUS (2014) “Generic guidance for Estimating Persistence and
+  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+  Registration” Report of the FOCUS Work Group on Degradation Kinetics,
+  Version 1.1, 18 December 2014
+  http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

+
Germany (2013a). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate
+  and Behaviour

+
Germany (2013b). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the
+  environment

+
Ranke (2019) Documentation of results obtained for the error model expertise
   written for the German Umweltbundesamt.

+
United Kingdom (2014). Thifensulfuron-methyl - Annex B.8 (Volume 3) to the Report and Proposed
+  Decision of the United Kingdom made to the European Commission under Regulation (EC) No.
+  1141/2010 for renewal of an active substance

     
 
     
Examples

diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 8cabcb21..700b6805 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -399,18 +399,19 @@ Per default, parameters in the kinetic models are internally transformed in
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Tue Jun  4 15:01:15 2019 
-#> Date of summary: Tue Jun  4 15:01:15 2019 
+#> Date of fit:     Wed Jun  5 15:08:20 2019 
+#> Date of summary: Wed Jun  5 15:08:20 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.461 s
+#> Fitted using 222 model solutions performed in 0.469 s
 #> 
-#> Error model:
-#> Constant variance 
+#> Error model: Constant variance 
+#> 
+#> Error model algorithm: d_3 
 #> 
 #> Starting values for parameters to be optimised:
 #>              value   type
@@ -480,7 +481,7 @@ Per default, parameters in the kinetic models are internally transformed in
   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)))
#> Warning: Observations with value of zero were removed from the data
#>        User      System verstrichen 
-#>       1.521       0.000       1.526 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.579       0.000       1.581 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -552,7 +553,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> Sum of squared residuals at call 126: 371.2134
 #> Sum of squared residuals at call 135: 371.2134
 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>       1.093       0.000       1.093 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.159       0.000       1.160 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -584,8 +585,8 @@ Per default, parameters in the kinetic models are internally transformed in
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
                       m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Tue Jun  4 15:01:31 2019 
-#> Date of summary: Tue Jun  4 15:01:31 2019 
+#> Date of fit:     Wed Jun  5 15:08:36 2019 
+#> Date of summary: Wed Jun  5 15:08:36 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -593,10 +594,11 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 421 model solutions performed in 1.096 s
+#> Fitted using 421 model solutions performed in 1.181 s
+#> 
+#> Error model: Constant variance 
 #> 
-#> Error model:
-#> Constant variance 
+#> Error model algorithm: d_3 
 #> 
 #> Starting values for parameters to be optimised:
 #>                     value   type
@@ -702,8 +704,8 @@ Per default, parameters in the kinetic models are internally transformed in
 #>   120       m1    25.15  28.78984 -3.640e+00
 #>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Tue Jun  4 15:01:34 2019 
-#> Date of summary: Tue Jun  4 15:01:34 2019 
+#> Date of fit:     Wed Jun  5 15:08:39 2019 
+#> Date of summary: Wed Jun  5 15:08:39 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -711,10 +713,12 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 979 model solutions performed in 2.603 s
+#> Fitted using 979 model solutions performed in 2.672 s
 #> 
-#> Error model:
-#> Variance unique to each observed variable 
+#> Error model: Variance unique to each observed variable 
+#> 
+#> Error model algorithm: d_3 
+#> Direct fitting and three-step fitting yield approximately the same likelihood 
 #> 
 #> Starting values for parameters to be optimised:
 #>                     value   type
@@ -832,8 +836,8 @@ Per default, parameters in the kinetic models are internally transformed in
 #>   120       m1    25.15  28.80429 -3.654e+00
 #>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Tue Jun  4 15:01:43 2019 
-#> Date of summary: Tue Jun  4 15:01:43 2019 
+#> Date of fit:     Wed Jun  5 15:08:50 2019 
+#> Date of summary: Wed Jun  5 15:08:50 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -841,10 +845,12 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 2289 model solutions performed in 9.499 s
+#> Fitted using 2289 model solutions performed in 10.959 s
+#> 
+#> Error model: Two-component variance function 
 #> 
-#> Error model:
-#> Two-component variance function 
+#> Error model algorithm: d_3 
+#> Direct fitting and three-step fitting yield approximately the same likelihood 
 #> 
 #> Starting values for parameters to be optimised:
 #>                       value   type
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 2c5f056e..ddab656c 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -234,7 +234,7 @@ 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 filebbe6b539c4f.c 2> filebbe6b539c4f.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file50a55c3108b2.c 2> file50a55c3108b2.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index f339b26a..7e71ec27 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -328,17 +328,17 @@
                 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(
+#>       0.003       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 
-#>       0.021       0.000       0.022 

+#>       0.022       0.000       0.022 

   
    # Predict from a fitted model
     f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Ordinary least squares optimisation
#> Sum of squared residuals at call 1: 552.5739
 #> Sum of squared residuals at call 3: 552.5739
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index a830646f..61a029fc 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -194,8 +194,8 @@
 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.046       0.032       5.094 
time_1
#>        User      System verstrichen 
-#>      19.798       0.004      19.814 

+#>       0.038       0.050       6.779 
time_1
#>        User      System verstrichen 
+#>      27.209       0.004      27.278 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340481   0.2659519   0.7505684   0.2494316 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index ffe1edb1..68b36542 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -211,18 +211,19 @@
     
Examples

     
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Tue Jun  4 15:03:02 2019 
-#> Date of summary: Tue Jun  4 15:03:02 2019 
+#> Date of fit:     Wed Jun  5 15:10:34 2019 
+#> Date of summary: Wed Jun  5 15:10:34 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.266 s
+#> Fitted using 131 model solutions performed in 0.268 s
 #> 
-#> Error model:
-#> Constant variance 
+#> Error model: Constant variance 
+#> 
+#> Error model algorithm: d_3 
 #> 
 #> Starting values for parameters to be optimised:
 #>                    value   type
diff --git a/vignettes/mkin_benchmarks.rda b/vignettes/mkin_benchmarks.rda
index 3e160a06..17cf86ce 100644
Binary files a/vignettes/mkin_benchmarks.rda and b/vignettes/mkin_benchmarks.rda differ
-- 
cgit v1.2.3