From 39b6d8b8569801c2957b22d0973b5ad0c9405e7d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 18 Sep 2018 10:14:40 +0200 Subject: Support maximum twa for HS, test, docs --- DESCRIPTION | 2 +- NEWS.md | 4 +- R/max_twa_parent.R | 18 +++++++- build.log | 2 +- docs/articles/FOCUS_D.html | 4 +- docs/articles/FOCUS_L.html | 46 +++++++++---------- docs/articles/index.html | 2 +- docs/articles/mkin.html | 4 +- docs/articles/twa.html | 4 +- docs/articles/web_only/FOCUS_Z.html | 4 +- docs/articles/web_only/compiled_models.html | 14 +++--- docs/authors.html | 2 +- docs/index.html | 3 +- docs/news/index.html | 14 +++++- docs/reference/DFOP.solution.html | 2 +- docs/reference/Extract.mmkin.html | 16 +++---- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 2 +- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_datasets.html | 2 +- docs/reference/FOMC.solution.html | 2 +- docs/reference/HS.solution.html | 2 +- docs/reference/IORE.solution.html | 2 +- docs/reference/SFO.solution.html | 2 +- docs/reference/SFORB.solution.html | 2 +- docs/reference/add_err.html | 2 +- docs/reference/endpoints.html | 2 +- docs/reference/geometric_mean.html | 2 +- docs/reference/ilr.html | 2 +- docs/reference/index.html | 2 +- docs/reference/max_twa_parent.html | 6 +-- docs/reference/mccall81_245T.html | 18 ++++---- docs/reference/mkin_long_to_wide.html | 2 +- docs/reference/mkin_wide_to_long.html | 2 +- docs/reference/mkinds.html | 2 +- docs/reference/mkinerrmin.html | 2 +- docs/reference/mkinfit.html | 62 +++++++++++++------------- docs/reference/mkinmod.html | 4 +- docs/reference/mkinparplot.html | 2 +- docs/reference/mkinplot.html | 2 +- docs/reference/mkinpredict.html | 8 ++-- docs/reference/mkinresplot.html | 2 +- docs/reference/mkinsub.html | 2 +- docs/reference/mmkin.html | 6 +-- docs/reference/plot.mkinfit.html | 2 +- docs/reference/plot.mmkin.html | 2 +- docs/reference/print.mkinds.html | 2 +- docs/reference/print.mkinmod.html | 2 +- docs/reference/schaefer07_complex_case.html | 2 +- docs/reference/sigma_twocomp.html | 2 +- docs/reference/summary.mkinfit.html | 10 ++--- docs/reference/synthetic_data_for_UBA.html | 2 +- docs/reference/test_data_from_UBA_2014.html | 2 +- docs/reference/transform_odeparms.html | 34 +++++++------- man/max_twa_parent.Rd | 2 +- test.log | 20 +++++---- tests/testthat/test_twa.R | 42 +++++++++-------- 58 files changed, 225 insertions(+), 190 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1b5b399d..53285036 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: 2018-09-14 +Date: 2018-09-18 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 43146df9..780ee5ac 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,9 @@ -# mkin 0.9.47.6 (2018-09-15) +# mkin 0.9.47.6 (2018-09-18) - '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 + # mkin 0.9.47.5 (2018-09-14) - Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows diff --git a/R/max_twa_parent.R b/R/max_twa_parent.R index 8d8b77f8..946a9b3d 100644 --- a/R/max_twa_parent.R +++ b/R/max_twa_parent.R @@ -1,4 +1,4 @@ -# Copyright (C) 2016,2017 Johannes Ranke +# Copyright (C) 2016,2017,2018 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package mkin @@ -55,7 +55,21 @@ max_twa_parent <- function(fit, windows) { M0/t * ((g/k1) * (1 - exp(- k1 * t)) + ((1 - g)/k2) * (1 - exp(- k2 * t))) } } - if (type %in% c("HS", "IORE", "SFORB")) { + if (type == "HS") { + k1 <- parms.all["k1"] + k2 <- parms.all["k2"] + tb <- parms.all["tb"] + twafunc <- function(t) { + ifelse(t <= tb, + M0 * (1 - exp(- k1 * t)) / (k1 * t), + (M0 / t) * ( + (1/k1) * (1 - exp(- k1 * tb)) + + (exp(- k1 * tb) / k2) * (1 - exp(- k2 * (t - tb))) + ) + ) + } + } + if (type %in% c("IORE", "SFORB")) { stop("Calculation of maximum time weighted average concentrations is currently ", "not implemented for the ", type, " model.") } diff --git a/build.log b/build.log index ca1c6f50..79c00855 100644 --- a/build.log +++ b/build.log @@ -6,5 +6,5 @@ * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added -* building ‘mkin_0.9.47.5.tar.gz’ +* building ‘mkin_0.9.47.6.tar.gz’ diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index a90cb7fb..b44462aa 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -29,7 +29,7 @@ mkin - 0.9.47.5 + 0.9.47.6 @@ -84,7 +84,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2018-09-14

+

2018-09-18

diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 2a99a609..8ef55b81 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -29,7 +29,7 @@ mkin - 0.9.47.5 + 0.9.47.6 @@ -84,7 +84,7 @@

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2018-09-14

+

2018-09-18

@@ -110,15 +110,15 @@ summary(m.L1.SFO) 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 21:00:22 2018 
-## Date of summary: Fri Sep 14 21:00:22 2018 
+## Date of fit:     Tue Sep 18 09:50:45 2018 
+## Date of summary: Tue Sep 18 09:50:45 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 0.087 s
+## Fitted with method Port using 37 model solutions performed in 0.081 s
 ## 
 ## Weighting: none
 ## 
@@ -201,15 +201,15 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 21:00:23 2018 
-## Date of summary: Fri Sep 14 21:00:23 2018 
+## Date of fit:     Tue Sep 18 09:50:47 2018 
+## Date of summary: Tue Sep 18 09:50:47 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 1.352 s
+## Fitted with method Port using 611 model solutions performed in 1.294 s
 ## 
 ## Weighting: none
 ## 
@@ -296,15 +296,15 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 21:00:24 2018 
-## Date of summary: Fri Sep 14 21:00:24 2018 
+## Date of fit:     Tue Sep 18 09:50:47 2018 
+## Date of summary: Tue Sep 18 09:50:47 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 0.175 s
+## Fitted with method Port using 81 model solutions performed in 0.166 s
 ## 
 ## Weighting: none
 ## 
@@ -367,8 +367,8 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 21:00:25 2018 
-## Date of summary: Fri Sep 14 21:00:25 2018 
+## Date of fit:     Tue Sep 18 09:50:48 2018 
+## Date of summary: Tue Sep 18 09:50:48 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 0.758 s
+## Fitted with method Port using 336 model solutions performed in 0.714 s
 ## 
 ## Weighting: none
 ## 
@@ -459,8 +459,8 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 21:00:26 2018 
-## Date of summary: Fri Sep 14 21:00:26 2018 
+## Date of fit:     Tue Sep 18 09:50:49 2018 
+## Date of summary: Tue Sep 18 09:50:49 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 0.31 s
+## Fitted with method Port using 137 model solutions performed in 0.299 s
 ## 
 ## Weighting: none
 ## 
@@ -560,15 +560,15 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 21:00:26 2018 
-## Date of summary: Fri Sep 14 21:00:27 2018 
+## Date of fit:     Tue Sep 18 09:50:50 2018 
+## Date of summary: Tue Sep 18 09:50:50 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 0.102 s
+## Fitted with method Port using 46 model solutions performed in 0.093 s
 ## 
 ## Weighting: none
 ## 
@@ -620,15 +620,15 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 21:00:26 2018 
-## Date of summary: Fri Sep 14 21:00:27 2018 
+## Date of fit:     Tue Sep 18 09:50:50 2018 
+## Date of summary: Tue Sep 18 09:50:50 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 0.151 s
+## Fitted with method Port using 66 model solutions performed in 0.138 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/index.html b/docs/articles/index.html
index ad0ab46e..c48dfec7 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -58,7 +58,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 3ae09165..e483043b 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -29,7 +29,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
@@ -84,7 +84,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2018-09-14

+            
2018-09-18

       
       
       
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 4d516ff1..d9249f9d 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -29,7 +29,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
@@ -84,7 +84,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2018-09-14

+            
2018-09-18

       
       
       
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 381c9e4f..a3e743d1 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -29,7 +29,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
@@ -84,7 +84,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2018-09-14

+            
2018-09-18

       
       
       
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 9aac1ab2..3b3e9150 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -29,7 +29,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
@@ -84,7 +84,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2018-09-14

+            
2018-09-18

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

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.134    1.000     2.132        0
-## 1 deSolve, not compiled            3  16.165    7.575    16.157        0
-## 2      Eigenvalue based            3   2.597    1.217     2.595        0
+## 3     deSolve, compiled            3   2.001    1.000     1.999        0
+## 1 deSolve, not compiled            3  15.374    7.683    15.368        0
+## 2      Eigenvalue based            3   2.439    1.219     2.438        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   3.717    1.000     3.715        0
-## 1 deSolve, not compiled            3  34.646    9.321    34.630        0
+## 2     deSolve, compiled            3   3.608    1.000     3.607        0
+## 1 deSolve, not compiled            3  33.150    9.188    33.135        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/authors.html b/docs/authors.html
index fddc66c9..d80afb2e 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -58,7 +58,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/index.html b/docs/index.html
index 60787c81..10b75279 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -36,7 +36,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
@@ -189,6 +189,7 @@
 
Dev status

 
    
 
    • 
+
  • Build Status
    • 
 

 
 
diff --git a/docs/news/index.html b/docs/news/index.html
index 73eb7aa2..2636b8b0 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -58,7 +58,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
@@ -117,9 +117,18 @@
       
     
 
+    

+

+mkin 0.9.47.6 (2018-09-18) Unreleased 
+

+
    
+
  • ‘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
    • 
+

+

     

 

-mkin 0.9.47.5 (2018-09-14) Unreleased 
+mkin 0.9.47.5 (2018-09-14) 2018-09-14 
 

 
    
 
  • Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows
    • 
@@ -658,6 +667,7 @@
     
    
       
    Contents
    
       
      
+        
    • 0.9.47.6
      • 
         
    • 0.9.47.5
      • 
         
    • 0.9.47.3
      • 
         
    • 0.9.47.2
      • 
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index f3ee0099..ad0ff22a 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
    
 
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 97562d44..39a8bb84 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     

 
@@ -278,7 +278,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.177       0.000       0.176 
+#>       0.161       0.000       0.162 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -467,8 +467,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555bd7f230>
-#> <environment: 0x55555bc85178>
+#> <bytecode: 0x55555bd56848>
+#> <environment: 0x55555bd53cb0>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -490,8 +490,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555ca9fca8>
-#> <environment: 0x55555bc85178>
+#> <bytecode: 0x55555c9bc2c0>
+#> <environment: 0x55555bd53cb0>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -558,10 +558,10 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Fri Sep 14 20:58:46 2018"
+#> [1] "Tue Sep 18 09:49:15 2018"
 #> 
 #> $version
-#> [1] "0.9.47.5"
+#> [1] "0.9.47.6"
 #> 
 #> $Rversion
 #> [1] "3.5.1"
diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
index d5354c28..6923f19a 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -65,7 +65,7 @@ in this fit." />
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
index f5c36792..90f6eb49 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -65,7 +65,7 @@ in this fit." />
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
index fb2cd7de..85a72047 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -65,7 +65,7 @@ in this fit." />
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
index dfccea5c..f2fb835b 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -65,7 +65,7 @@ in this fit." />
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 7f89e33e..9023aee0 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index abda4d81..1d3e4dd3 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -65,7 +65,7 @@ The form given here differs slightly from the original reference by Gustafson
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index bb3768ba..99f537cf 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index d86ee0c3..8394cd52 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 17f1920c..e123d358 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index 050d19cf..75449616 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index cea1e03c..db910f82 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index a54fb71e..6a505e9f 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -64,7 +64,7 @@ with the advantage that the SFORB model can also be used for metabolites." />
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index 41ccbbfd..6e154149 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 601ab1a2..722bb0e9 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 615f6777..a7806970 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -58,7 +58,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 3a19c754..c760960f 100644
--- a/docs/reference/max_twa_parent.html
+++ b/docs/reference/max_twa_parent.html
@@ -34,7 +34,7 @@
 
 
 
@@ -65,7 +65,7 @@ guidance." />
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
@@ -129,7 +129,7 @@ guidance." />
     
     
This function calculates maximum moving window time weighted average concentrations
 (TWAs) for kinetic models fitted with mkinfit. Currently, only
-calculations for the parent are implemented for the SFO, FOMC and DFOP models,
+calculations for the parent are implemented for the SFO, FOMC, DFOP and HS models,
 using the analytical formulas given in the PEC soil section of the FOCUS
 guidance.

     
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 52c09969..042073f2 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
@@ -156,10 +156,10 @@
     
  SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
                          phenol = list(type = "SFO", to = "anisole"),
                          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:    0.9.47.5 
+    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 Sep 14 20:58:58 2018 
-#> Date of summary: Fri Sep 14 20:58:58 2018 
+#> Date of fit:     Tue Sep 18 09:49:26 2018 
+#> Date of summary: Tue Sep 18 09:49:26 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 3.393 s
+#> Fitted with method Port using 574 model solutions performed in 3.213 s
 #> 
 #> Weighting: none
 #> 
@@ -245,10 +245,10 @@
     fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),
                    parms.ini = c(k_phenol_sink = 0),
                    fixed_parms = "k_phenol_sink", quiet = TRUE)
-    summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.5 
+    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 Sep 14 20:58:59 2018 
-#> Date of summary: Fri Sep 14 20:59:00 2018 
+#> Date of fit:     Tue Sep 18 09:49:27 2018 
+#> Date of summary: Tue Sep 18 09:49:27 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 1.451 s
+#> Fitted with method Port using 246 model solutions performed in 1.363 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index ea74ff47..36a7e0ae 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     

 
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index 369649e3..f09f5102 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index d356fdab..357370ad 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 4f70a274..dd947e65 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -62,7 +62,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." />
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index f3c6d595..1ae53f8a 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -71,7 +71,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
@@ -432,17 +432,17 @@
     
Examples

     
# Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.47.5 
+summary(fit)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 20:59:02 2018 
-#> Date of summary: Fri Sep 14 20:59:02 2018 
+#> Date of fit:     Tue Sep 18 09:49:30 2018 
+#> Date of summary: Tue Sep 18 09:49:30 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 64 model solutions performed in 0.141 s
+#> Fitted with method Port using 64 model solutions performed in 0.14 s
 #> 
 #> Weighting: none
 #> 
@@ -511,7 +511,7 @@
   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 
-#>       0.895       0.000       0.897 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.872       0.001       0.874 
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 
@@ -586,7 +586,7 @@
 #> Model cost at call  146 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>        User      System verstrichen 
-#>       0.726       0.000       0.726 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.690       0.000       0.689 
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 
@@ -622,10 +622,10 @@
 
# Weighted fits, including IRLS
 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)
-summary(f.noweight)
#> mkin version used for fitting:    0.9.47.5 
+summary(f.noweight)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 20:59:13 2018 
-#> Date of summary: Fri Sep 14 20:59:13 2018 
+#> Date of fit:     Tue Sep 18 09:49:40 2018 
+#> Date of summary: Tue Sep 18 09:49:40 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -633,7 +633,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.757 s
+#> Fitted with method Port using 186 model solutions performed in 0.725 s
 #> 
 #> Weighting: none
 #> 
@@ -739,10 +739,10 @@
 #>   100       m1    33.13  31.98163  1.148e+00
 #>   120       m1    25.15  28.78984 -3.640e+00
 #>   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:    0.9.47.5 
+summary(f.irls)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 20:59:15 2018 
-#> Date of summary: Fri Sep 14 20:59:16 2018 
+#> Date of fit:     Tue Sep 18 09:49:42 2018 
+#> Date of summary: Tue Sep 18 09:49:42 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -750,7 +750,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 551 model solutions performed in 2.329 s
+#> Fitted with method Port using 551 model solutions performed in 2.147 s
 #> 
 #> Weighting: none
 #> 
@@ -861,10 +861,10 @@
 #>   100       m1    33.13  31.98971  1.140e+00 2.722
 #>   120       m1    25.15  28.80898 -3.659e+00 2.722
 #>   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:    0.9.47.5 
+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 Sep 14 20:59:16 2018 
-#> Date of summary: Fri Sep 14 20:59:16 2018 
+#> Date of fit:     Tue Sep 18 09:49:43 2018 
+#> Date of summary: Tue Sep 18 09:49:43 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -872,7 +872,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 155 model solutions performed in 0.628 s
+#> Fitted with method Port using 155 model solutions performed in 0.603 s
 #> 
 #> Weighting: mean
 #> 
@@ -979,10 +979,10 @@
 #>   120       m1    25.15  28.82413  -3.674128
 #>   120       m1    33.31  28.82413   4.485872
f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value",
                      quiet = TRUE)
-summary(f.w.value)
#> mkin version used for fitting:    0.9.47.5 
+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 Sep 14 20:59:17 2018 
-#> Date of summary: Fri Sep 14 20:59:17 2018 
+#> Date of fit:     Tue Sep 18 09:49:44 2018 
+#> Date of summary: Tue Sep 18 09:49:44 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -990,7 +990,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 174 model solutions performed in 0.713 s
+#> Fitted with method Port using 174 model solutions performed in 0.69 s
 #> 
 #> Weighting: manual
 #> 
@@ -1099,10 +1099,10 @@
 errors <- c(parent = 2, m1 = 1)
 dw$err.man <- errors[FOCUS_2006_D$name]
 f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
-summary(f.w.man)
#> mkin version used for fitting:    0.9.47.5 
+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 Sep 14 20:59:18 2018 
-#> Date of summary: Fri Sep 14 20:59:18 2018 
+#> Date of fit:     Tue Sep 18 09:49:45 2018 
+#> Date of summary: Tue Sep 18 09:49:45 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1110,7 +1110,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 270 model solutions performed in 1.119 s
+#> Fitted with method Port using 270 model solutions performed in 1.133 s
 #> 
 #> Weighting: manual
 #> 
@@ -1217,10 +1217,10 @@
 #>   120       m1    25.15  28.76062  -3.610621   2
 #>   120       m1    33.31  28.76062   4.549379   2
f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE,
                        reweight.method = "obs")
-summary(f.w.man.irls)
#> mkin version used for fitting:    0.9.47.5 
+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 Sep 14 20:59:21 2018 
-#> Date of summary: Fri Sep 14 20:59:21 2018 
+#> Date of fit:     Tue Sep 18 09:49:48 2018 
+#> Date of summary: Tue Sep 18 09:49:48 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1228,7 +1228,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 692 model solutions performed in 2.955 s
+#> Fitted with method Port using 692 model solutions performed in 2.77 s
 #> 
 #> Weighting: manual
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 464178bc..c1e7b840 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -66,7 +66,7 @@ For the definition of model types and their parameters, the equations given
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     

 
@@ -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 file7aee6cc2a6d.c 2> file7aee6cc2a6d.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file73da22034c44.c 2> file73da22034c44.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 6ed32315..a57a439c 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     

 
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 72ff93f6..18da0660 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index dfcd08a8..5fad64de 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
@@ -321,17 +321,17 @@
                 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 
-#>       0.004       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
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.001       0.000       0.002 
  system.time(
+#>       0.002       0.000       0.001 
  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 
-#>       0.036       0.000       0.036 

+#>       0.033       0.000       0.034 

   
   
 
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 0a2bf41a..3f2d2f86 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 383e5928..13cdedff 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
@@ -189,8 +189,8 @@
 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.056       0.024       6.712 
time_1
#>        User      System verstrichen 
-#>      20.446       0.000      20.459 

+#>       0.043       0.040       6.475 
time_1
#>        User      System verstrichen 
+#>      19.165       0.000      19.179 

 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/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index e88c2025..c082f125 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -66,7 +66,7 @@ If the current plot device is a tikz device,
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     

 
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index d67d87d9..3f155473 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -65,7 +65,7 @@ If the current plot device is a tikz device,
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 2489269c..022efe67 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index b6cbad61..efa3272e 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 4ceba867..b22c67fa 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index e74707ff..36612f18 100644
--- a/docs/reference/sigma_twocomp.html
+++ b/docs/reference/sigma_twocomp.html
@@ -66,7 +66,7 @@ This is the error model used for example by Werner et al. (1978). The model
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 317c7a87..0af65ed8 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
@@ -204,17 +204,17 @@
     
 
     
Examples

-    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.5 
+    
  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 Sep 14 21:00:08 2018 
-#> Date of summary: Fri Sep 14 21:00:08 2018 
+#> Date of fit:     Tue Sep 18 09:50:32 2018 
+#> Date of summary: Tue Sep 18 09:50:32 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 0.071 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 384d628d..94397ddf 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -76,7 +76,7 @@ Compare also the code in the example section to see the degradation models." />
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     

 
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 094e003d..b8c4a76b 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     

 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 6f7ec4a4..ce6f6c8d 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -69,7 +69,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
       
       
         mkin
-        0.9.47.5
+        0.9.47.6
       
     
 
@@ -198,10 +198,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
   parent = list(type = "SFO", to = "m1", sink = TRUE),
   m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
-summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.47.5 
+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 Sep 14 21:00:16 2018 
-#> Date of summary: Fri Sep 14 21:00:16 2018 
+#> Date of fit:     Tue Sep 18 09:50:39 2018 
+#> Date of summary: Tue Sep 18 09:50:39 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 0.71 s
+#> Fitted with method Port using 153 model solutions performed in 0.586 s
 #> 
 #> Weighting: none
 #> 
@@ -274,10 +274,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> parent   7.023  23.33
 #> m1     131.761 437.70

 
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
-summary(fit.2, data=FALSE)
#> mkin version used for fitting:    0.9.47.5 
+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 Sep 14 21:00:17 2018 
-#> Date of summary: Fri Sep 14 21:00:17 2018 
+#> Date of fit:     Tue Sep 18 09:50:41 2018 
+#> Date of summary: Tue Sep 18 09:50:41 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 1.417 s
+#> Fitted with method Port using 350 model solutions performed in 1.341 s
 #> 
 #> Weighting: none
 #> 
@@ -362,10 +362,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
   m1 = list(type = "SFO"),
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-summary(fit.ff, data = FALSE)
#> mkin version used for fitting:    0.9.47.5 
+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 Sep 14 21:00:18 2018 
-#> Date of summary: Fri Sep 14 21:00:18 2018 
+#> Date of fit:     Tue Sep 18 09:50:42 2018 
+#> Date of summary: Tue Sep 18 09:50:42 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 0.755 s
+#> Fitted with method Port using 186 model solutions performed in 0.73 s
 #> 
 #> Weighting: none
 #> 
@@ -446,10 +446,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
-summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.5 
+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 Sep 14 21:00:19 2018 
-#> Date of summary: Fri Sep 14 21:00:19 2018 
+#> Date of fit:     Tue Sep 18 09:50:42 2018 
+#> Date of summary: Tue Sep 18 09:50:42 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 0.416 s
+#> Fitted with method Port using 104 model solutions performed in 0.401 s
 #> 
 #> Weighting: none
 #> 
diff --git a/man/max_twa_parent.Rd b/man/max_twa_parent.Rd
index b8c820bc..f599eb1c 100644
--- a/man/max_twa_parent.Rd
+++ b/man/max_twa_parent.Rd
@@ -6,7 +6,7 @@
 \description{
 This function calculates maximum moving window time weighted average concentrations
 (TWAs) for kinetic models fitted with \code{\link{mkinfit}}. Currently, only
-calculations for the parent are implemented for the SFO, FOMC and DFOP models,
+calculations for the parent are implemented for the SFO, FOMC, DFOP and HS models,
 using the analytical formulas given in the PEC soil section of the FOCUS
 guidance.}
 \usage{
diff --git a/test.log b/test.log
index c4ced344..cd3ffc7c 100644
--- a/test.log
+++ b/test.log
@@ -2,19 +2,21 @@ Loading mkin
 Loading required package: testthat
 Testing mkin
 ✔ | OK F W S | Context
-
⠏ |  0       | Calculation of FOCUS chi2 error levels
⠋ |  1       | Calculation of FOCUS chi2 error levels
⠙ |  2       | Calculation of FOCUS chi2 error levels
✔ |  2       | Calculation of FOCUS chi2 error levels [2.2 s]
-
⠏ |  0       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠼ |  5       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠴ |  6       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠦ |  7       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠧ |  8       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ |  8       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [6.5 s]
-
⠏ |  0       | Iteratively reweighted least squares (IRLS) fitting
⠋ |  1       | Iteratively reweighted least squares (IRLS) fitting
⠙ |  2       | Iteratively reweighted least squares (IRLS) fitting
⠹ |  3       | Iteratively reweighted least squares (IRLS) fitting
✔ |  3       | Iteratively reweighted least squares (IRLS) fitting [36.6 s]
+
⠏ |  0       | Calculation of FOCUS chi2 error levels
⠋ |  1       | Calculation of FOCUS chi2 error levels
⠙ |  2       | Calculation of FOCUS chi2 error levels
✔ |  2       | Calculation of FOCUS chi2 error levels [2.1 s]
+
⠏ |  0       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠼ |  5       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠴ |  6       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠦ |  7       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠧ |  8       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ |  8       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [6.1 s]
+
⠏ |  0       | Iteratively reweighted least squares (IRLS) fitting
⠋ |  1       | Iteratively reweighted least squares (IRLS) fitting
⠙ |  2       | Iteratively reweighted least squares (IRLS) fitting
⠹ |  3       | Iteratively reweighted least squares (IRLS) fitting
✔ |  3       | Iteratively reweighted least squares (IRLS) fitting [35.8 s]
 
⠏ |  0       | Model predictions with mkinpredict
⠋ |  1       | Model predictions with mkinpredict
⠙ |  2       | Model predictions with mkinpredict
⠹ |  3       | Model predictions with mkinpredict
✔ |  3       | Model predictions with mkinpredict [0.3 s]
-
⠏ |  0       | Fitting of parent only models
⠋ |  1       | Fitting of parent only models
⠙ |  2       | Fitting of parent only models
⠹ |  3       | Fitting of parent only models
⠸ |  4       | Fitting of parent only models
⠼ |  5       | Fitting of parent only models
⠴ |  6       | Fitting of parent only models
⠦ |  7       | Fitting of parent only models
⠧ |  8       | Fitting of parent only models
⠇ |  9       | Fitting of parent only models
⠏ | 10       | Fitting of parent only models
⠋ | 11       | Fitting of parent only models
⠙ | 12       | Fitting of parent only models
⠹ | 13       | Fitting of parent only models
⠸ | 14       | Fitting of parent only models
⠼ | 15       | Fitting of parent only models
⠴ | 16       | Fitting of parent only models
⠦ | 17       | Fitting of parent only models
⠧ | 18       | Fitting of parent only models
⠇ | 19       | Fitting of parent only models
⠏ | 20       | Fitting of parent only models
⠋ | 21       | Fitting of parent only models
✔ | 21       | Fitting of parent only models [22.6 s]
-
⠏ |  0       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠋ |  1       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠙ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.5 s]
-
⠏ |  0       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ |  4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [6.7 s]
-
⠏ |  0       | Calculation of maximum time weighted average concentrations (TWAs)
⠋ |  1       | Calculation of maximum time weighted average concentrations (TWAs)
⠙ |  2       | Calculation of maximum time weighted average concentrations (TWAs)
⠹ |  3       | Calculation of maximum time weighted average concentrations (TWAs)
✔ |  3       | Calculation of maximum time weighted average concentrations (TWAs) [3.8 s]
+
⠏ |  0       | Fitting of parent only models
⠋ |  1       | Fitting of parent only models
⠙ |  2       | Fitting of parent only models
⠹ |  3       | Fitting of parent only models
⠸ |  4       | Fitting of parent only models
⠼ |  5       | Fitting of parent only models
⠴ |  6       | Fitting of parent only models
⠦ |  7       | Fitting of parent only models
⠧ |  8       | Fitting of parent only models
⠇ |  9       | Fitting of parent only models
⠏ | 10       | Fitting of parent only models
⠋ | 11       | Fitting of parent only models
⠙ | 12       | Fitting of parent only models
⠹ | 13       | Fitting of parent only models
⠸ | 14       | Fitting of parent only models
⠼ | 15       | Fitting of parent only models
⠴ | 16       | Fitting of parent only models
⠦ | 17       | Fitting of parent only models
⠧ | 18       | Fitting of parent only models
⠇ | 19       | Fitting of parent only models
⠏ | 20       | Fitting of parent only models
⠋ | 21       | Fitting of parent only models
✔ | 21       | Fitting of parent only models [22.0 s]
+
⠏ |  0       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠋ |  1       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠙ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.1 s]
+
⠏ |  0       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ |  4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [6.4 s]
+
⠏ |  0       | Calculation of maximum time weighted average concentrations (TWAs)
⠋ |  1       | Calculation of maximum time weighted average concentrations (TWAs)
⠙ |  2       | Calculation of maximum time weighted average concentrations (TWAs)
⠹ |  3       | Calculation of maximum time weighted average concentrations (TWAs)
⠸ |  4       | Calculation of maximum time weighted average concentrations (TWAs)
⠼ |  5       | Calculation of maximum time weighted average concentrations (TWAs)
⠴ |  6       | Calculation of maximum time weighted average concentrations (TWAs)
⠦ |  7       | Calculation of maximum time weighted average concentrations (TWAs)
⠧ |  8       | Calculation of maximum time weighted average concentrations (TWAs)
✔ |  8       | Calculation of maximum time weighted average concentrations (TWAs) [7.5 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 84.2 s
+Duration: 85.3 s
 
-OK:       46
+OK:       51
 Failed:   0
 Warnings: 0
 Skipped:  0
+
+Keep up the good work.
diff --git a/tests/testthat/test_twa.R b/tests/testthat/test_twa.R
index a84b2c4e..758c42c3 100644
--- a/tests/testthat/test_twa.R
+++ b/tests/testthat/test_twa.R
@@ -21,23 +21,29 @@ context("Calculation of maximum time weighted average concentrations (TWAs)")
 
 test_that("Time weighted average concentrations are correct", {
   skip_on_cran()
-  twa_models <- c("SFO", "FOMC", "DFOP")
-  fits <- mmkin(twa_models, list(FOCUS_D = FOCUS_2006_D), 
-                quiet = TRUE, cores = 1)
-
-  outtimes_7 <- seq(0, 7, length.out = 10000)
-  for (model in twa_models) {
-    fit <- fits[[model, 1]]
-    bpar <- summary(fit)$bpar[, "Estimate"]
-    pred_7 <- mkinpredict(fit$mkinmod,
-                odeparms = bpar[2:length(bpar)],
-                odeini = c(parent = bpar[[1]]),
-                outtimes = outtimes_7)
-    twa_num <- mean(pred_7$parent)
-    names(twa_num) <- 7
-    twa_ana <- max_twa_parent(fit, 7)
-
-    # Test for absolute difference (scale = 1)
-    expect_equal(twa_num, twa_ana, tolerance = 0.001, scale = 1)
+  twa_models <- c("SFO", "FOMC", "DFOP", "HS")
+  fits <- mmkin(twa_models,
+                list(FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
+                quiet = TRUE, cores = 8)
+
+  outtimes_10 <- seq(0, 10, length.out = 10000)
+
+  for (ds in c("FOCUS_C", "FOCUS_D")) {
+    for (model in twa_models) {
+      fit <- fits[[model, ds]]
+      bpar <- summary(fit)$bpar[, "Estimate"]
+      pred_10 <- mkinpredict(fit$mkinmod,
+                  odeparms = bpar[2:length(bpar)],
+                  odeini = c(parent = bpar[[1]]),
+                  outtimes = outtimes_10)
+      twa_num <- mean(pred_10$parent)
+      names(twa_num) <- 10
+      twa_ana <- max_twa_parent(fit, 10)
+
+      # Test for absolute difference (scale = 1)
+      # The tolerance can be reduced if the length of outtimes is increased,
+      # but this needs more computing time so we stay with lenght.out = 10k
+      expect_equal(twa_num, twa_ana, tolerance = 0.003, scale = 1)
+    }
   }
 })
-- 
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