From 587662437bce06ea202551048226b86cff0db187 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 14 Sep 2018 21:02:46 +0200 Subject: Skip more tests on CRAN Static documentation rebuilt by pkgdown --- NEWS.md | 2 - docs/articles/FOCUS_L.html | 40 ++++++------- docs/articles/web_only/compiled_models.html | 10 ++-- docs/news/index.html | 10 +--- docs/reference/Extract.mmkin.html | 12 ++-- docs/reference/mccall81_245T.html | 12 ++-- docs/reference/mkinfit.html | 46 +++++++-------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 6 +- docs/reference/mmkin.html | 4 +- docs/reference/summary.mkinfit.html | 6 +- docs/reference/transform_odeparms.html | 24 ++++---- test.log | 13 ++--- tests/testthat/test_FOCUS_D_UBA_expertise.R | 70 ++++++++++------------- tests/testthat/test_mkinpredict_SFO_SFO.R | 4 +- tests/testthat/test_parent_only.R | 3 + tests/testthat/test_synthetic_data_for_UBA_2014.R | 1 + tests/testthat/test_twa.R | 8 ++- 18 files changed, 128 insertions(+), 145 deletions(-) diff --git a/NEWS.md b/NEWS.md index 4710801b..d265dc6f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,8 +4,6 @@ - Move two vignettes to a location where they will not be built on CRAN (to avoid more NOTES from long execution times) -# mkin 0.9.47.4 - - Exclude more example code from testing on CRAN to avoid NOTES from long execution times # mkin 0.9.47.3 diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index f1a91c04..2a99a609 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -110,15 +110,15 @@ summary(m.L1.SFO) 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 18:22:23 2018 
-## Date of summary: Fri Sep 14 18:22:23 2018 
+## Date of fit:     Fri Sep 14 21:00:22 2018 
+## Date of summary: Fri Sep 14 21:00:22 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 0.092 s
+## Fitted with method Port using 37 model solutions performed in 0.087 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 18:22:25 2018 
-## Date of summary: Fri Sep 14 18:22:25 2018 
+## Date of fit:     Fri Sep 14 21:00:23 2018 
+## Date of summary: Fri Sep 14 21:00:23 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 1.355 s
+## Fitted with method Port using 611 model solutions performed in 1.352 s
 ## 
 ## Weighting: none
 ## 
@@ -296,8 +296,8 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 18:22:25 2018 
-## Date of summary: Fri Sep 14 18:22:25 2018 
+## Date of fit:     Fri Sep 14 21:00:24 2018 
+## Date of summary: Fri Sep 14 21:00:24 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -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 18:22:26 2018 
-## Date of summary: Fri Sep 14 18:22:26 2018 
+## Date of fit:     Fri Sep 14 21:00:25 2018 
+## Date of summary: Fri Sep 14 21:00:25 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 0.756 s
+## Fitted with method Port using 336 model solutions performed in 0.758 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 18:22:27 2018 
-## Date of summary: Fri Sep 14 18:22:28 2018 
+## Date of fit:     Fri Sep 14 21:00:26 2018 
+## Date of summary: Fri Sep 14 21:00:26 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 0.322 s
+## Fitted with method Port using 137 model solutions performed in 0.31 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 18:22:28 2018 
-## Date of summary: Fri Sep 14 18:22:28 2018 
+## Date of fit:     Fri Sep 14 21:00:26 2018 
+## Date of summary: Fri Sep 14 21:00:27 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 0.101 s
+## Fitted with method Port using 46 model solutions performed in 0.102 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 18:22:28 2018 
-## Date of summary: Fri Sep 14 18:22:28 2018 
+## Date of fit:     Fri Sep 14 21:00:26 2018 
+## Date of summary: Fri Sep 14 21:00:27 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 0.16 s
+## Fitted with method Port using 66 model solutions performed in 0.151 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 12c192f0..9aac1ab2 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -125,9 +125,9 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.115    1.000     2.114        0
-## 1 deSolve, not compiled            3  16.235    7.676    16.228        0
-## 2      Eigenvalue based            3   2.589    1.224     2.587        0
+## 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
 ##   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   3.887    1.000     3.885        0
-## 1 deSolve, not compiled            3  35.492    9.131    35.474        0
+## 2     deSolve, compiled            3   3.717    1.000     3.715        0
+## 1 deSolve, not compiled            3  34.646    9.321    34.630        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/news/index.html b/docs/news/index.html
index cbfcdde0..73eb7aa2 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -124,14 +124,7 @@
 
    
 
  • Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows
    • 
 
  • Move two vignettes to a location where they will not be built on CRAN (to avoid more NOTES from long execution times)
    • 
-

-
-    

-

-mkin 0.9.47.4 Unreleased 
-

-
    
-
  • Exclude more example code from testing on CRAN to avoid NOTES from long execution times
    • 
+
  • Exclude more example code from testing on CRAN to avoid NOTES from long execution times
    • 
 

 

     

@@ -666,7 +659,6 @@
       
Contents

       
    
         
  • 0.9.47.5
    • 
-        
  • 0.9.47.4
    • 
         
  • 0.9.47.3
    • 
         
  • 0.9.47.2
    • 
         
  • 0.9.47.1
    • 
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 91226e69..97562d44 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -278,7 +278,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.166       0.000       0.166 
+#>       0.177       0.000       0.176 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -467,8 +467,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555bd812a0>
-#> <environment: 0x55555bc871e8>
+#> <bytecode: 0x55555bd7f230>
+#> <environment: 0x55555bc85178>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -490,8 +490,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555caa1d18>
-#> <environment: 0x55555bc871e8>
+#> <bytecode: 0x55555ca9fca8>
+#> <environment: 0x55555bc85178>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -558,7 +558,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Fri Sep 14 18:20:46 2018"
+#> [1] "Fri Sep 14 20:58:46 2018"
 #> 
 #> $version
 #> [1] "0.9.47.5"
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index d91431f3..52c09969 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -158,8 +158,8 @@
                          anisole = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  
    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
     summary(fit.1, data = FALSE)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:20:57 2018 
-#> Date of summary: Fri Sep 14 18:20:57 2018 
+#> Date of fit:     Fri Sep 14 20:58:58 2018 
+#> Date of summary: Fri Sep 14 20:58:58 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 3.418 s
+#> Fitted with method Port using 574 model solutions performed in 3.393 s
 #> 
 #> Weighting: none
 #> 
@@ -247,8 +247,8 @@
                    fixed_parms = "k_phenol_sink", quiet = TRUE)
     summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:20:59 2018 
-#> Date of summary: Fri Sep 14 18:20:59 2018 
+#> Date of fit:     Fri Sep 14 20:58:59 2018 
+#> Date of summary: Fri Sep 14 20:59:00 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 1.458 s
+#> Fitted with method Port using 246 model solutions performed in 1.451 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 261d48fb..f3c6d595 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -434,15 +434,15 @@
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:21:02 2018 
-#> Date of summary: Fri Sep 14 18:21:02 2018 
+#> Date of fit:     Fri Sep 14 20:59:02 2018 
+#> Date of summary: Fri Sep 14 20:59:02 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 0.143 s
+#> Fitted with method Port using 64 model solutions performed in 0.141 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 
-#>       0.918       0.000       0.919 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.895       0.000       0.897 
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 
-#>       0.757       0.000       0.757 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.726       0.000       0.726 
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 
@@ -624,8 +624,8 @@
                       m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(f.noweight)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:21:13 2018 
-#> Date of summary: Fri Sep 14 18:21:13 2018 
+#> Date of fit:     Fri Sep 14 20:59:13 2018 
+#> Date of summary: Fri Sep 14 20:59:13 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 0.775 s
+#> Fitted with method Port using 186 model solutions performed in 0.757 s
 #> 
 #> Weighting: none
 #> 
@@ -741,8 +741,8 @@
 #>   120       m1    33.31  28.78984  4.520e+00
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
 summary(f.irls)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:21:15 2018 
-#> Date of summary: Fri Sep 14 18:21:15 2018 
+#> Date of fit:     Fri Sep 14 20:59:15 2018 
+#> Date of summary: Fri Sep 14 20:59:16 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 2.282 s
+#> Fitted with method Port using 551 model solutions performed in 2.329 s
 #> 
 #> Weighting: none
 #> 
@@ -863,8 +863,8 @@
 #>   120       m1    33.31  28.80898  4.501e+00 2.722
f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE)
 summary(f.w.mean)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:21:16 2018 
-#> Date of summary: Fri Sep 14 18:21:16 2018 
+#> Date of fit:     Fri Sep 14 20:59:16 2018 
+#> Date of summary: Fri Sep 14 20:59:16 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 0.653 s
+#> Fitted with method Port using 155 model solutions performed in 0.628 s
 #> 
 #> Weighting: mean
 #> 
@@ -981,8 +981,8 @@
                      quiet = TRUE)
 summary(f.w.value)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:21:17 2018 
-#> Date of summary: Fri Sep 14 18:21:17 2018 
+#> Date of fit:     Fri Sep 14 20:59:17 2018 
+#> Date of summary: Fri Sep 14 20:59:17 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 0.721 s
+#> Fitted with method Port using 174 model solutions performed in 0.713 s
 #> 
 #> Weighting: manual
 #> 
@@ -1101,8 +1101,8 @@
 f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
 summary(f.w.man)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:21:18 2018 
-#> Date of summary: Fri Sep 14 18:21:18 2018 
+#> Date of fit:     Fri Sep 14 20:59:18 2018 
+#> Date of summary: Fri Sep 14 20:59:18 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 1.215 s
+#> Fitted with method Port using 270 model solutions performed in 1.119 s
 #> 
 #> Weighting: manual
 #> 
@@ -1219,8 +1219,8 @@
                        reweight.method = "obs")
 summary(f.w.man.irls)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:21:22 2018 
-#> Date of summary: Fri Sep 14 18:21:22 2018 
+#> Date of fit:     Fri Sep 14 20:59:21 2018 
+#> Date of summary: Fri Sep 14 20:59:21 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 3.114 s
+#> Fitted with method Port using 692 model solutions performed in 2.955 s
 #> 
 #> Weighting: manual
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 9048c1b1..464178bc 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -229,7 +229,7 @@ For the definition of model types and their parameters, the equations given
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file49ec17c0788e.c 2> file49ec17c0788e.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file7aee6cc2a6d.c 2> file7aee6cc2a6d.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 6c30d7a8..dfcd08a8 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -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 
-#>       0.003       0.000       0.003 
  system.time(
+#>       0.004       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 
-#>       0.002       0.000       0.002 
  system.time(
+#>       0.001       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 
-#>       0.035       0.000       0.035 

+#>       0.036       0.000       0.036 

   
   
#>        User      System verstrichen 
-#>       0.059       0.027       6.918 
time_1
#>        User      System verstrichen 
-#>      21.127       0.000      21.141 

+#>       0.056       0.024       6.712 
time_1
#>        User      System verstrichen 
+#>      20.446       0.000      20.459 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340480   0.2659520   0.7505686   0.2494314 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index cb6beda2..317c7a87 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -206,15 +206,15 @@
     
Examples

     
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:22:10 2018 
-#> Date of summary: Fri Sep 14 18:22:10 2018 
+#> Date of fit:     Fri Sep 14 21:00:08 2018 
+#> Date of summary: Fri Sep 14 21:00:08 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 0.076 s
+#> Fitted with method Port using 35 model solutions performed in 0.081 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index db92667c..6f7ec4a4 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -200,8 +200,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:22:17 2018 
-#> Date of summary: Fri Sep 14 18:22:17 2018 
+#> Date of fit:     Fri Sep 14 21:00:16 2018 
+#> Date of summary: Fri Sep 14 21:00:16 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 0.701 s
+#> Fitted with method Port using 153 model solutions performed in 0.71 s
 #> 
 #> Weighting: none
 #> 
@@ -276,8 +276,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
 summary(fit.2, data=FALSE)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:22:19 2018 
-#> Date of summary: Fri Sep 14 18:22:19 2018 
+#> Date of fit:     Fri Sep 14 21:00:17 2018 
+#> Date of summary: Fri Sep 14 21:00:17 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 1.431 s
+#> Fitted with method Port using 350 model solutions performed in 1.417 s
 #> 
 #> Weighting: none
 #> 
@@ -364,8 +364,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff, data = FALSE)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:22:20 2018 
-#> Date of summary: Fri Sep 14 18:22:20 2018 
+#> Date of fit:     Fri Sep 14 21:00:18 2018 
+#> Date of summary: Fri Sep 14 21:00:18 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 0.778 s
+#> Fitted with method Port using 186 model solutions performed in 0.755 s
 #> 
 #> Weighting: none
 #> 
@@ -448,8 +448,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:22:20 2018 
-#> Date of summary: Fri Sep 14 18:22:20 2018 
+#> Date of fit:     Fri Sep 14 21:00:19 2018 
+#> Date of summary: Fri Sep 14 21:00:19 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 0.417 s
+#> Fitted with method Port using 104 model solutions performed in 0.416 s
 #> 
 #> Weighting: none
 #> 
diff --git a/test.log b/test.log
index aab7d12b..c4ced344 100644
--- a/test.log
+++ b/test.log
@@ -3,17 +3,16 @@ 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)
✔ |  6       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [2.2 s]
-
⠏ |  0       | The t-test for significant difference from zero
⠋ |  1       | The t-test for significant difference from zero
⠙ |  2       | The t-test for significant difference from zero
✔ |  2       | The t-test for significant difference from zero [4.3 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 [36.3 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       | 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 [21.8 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 [5.4 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) [4.6 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]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 84.0 s
+Duration: 84.2 s
 
 OK:       46
 Failed:   0
diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R
index 5d5a801a..3b241aa4 100644
--- a/tests/testthat/test_FOCUS_D_UBA_expertise.R
+++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2015 Johannes Ranke
+# Copyright (C) 2015,2018 Johannes Ranke
 # Contact: jranke@uni-bremen.de
 
 # This file is part of the R package mkin
@@ -18,69 +18,59 @@
 
 context("Results for FOCUS D established in expertise for UBA (Ranke 2014)")
 
-SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
-                   m1 = list(type = "SFO"), quiet = TRUE)
-SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
-                      m1 = list(type = "SFO"), 
-                      use_of_ff = "max", quiet = TRUE)
+# Results are from p. 40
 
-fit.default <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
-fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
+test_that("Fits without formation fractions are correct for FOCUS D", {
+  SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
+                     m1 = list(type = "SFO"), quiet = TRUE)
+  fit.default <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 
-# Results are from p. 40
+  expect_equal(round(as.numeric(endpoints(fit.default)$distimes["parent", ]), 2), 
+               c(7.02, 23.33))
+  expect_equal(round(as.numeric(endpoints(fit.default)$distimes["m1", ]), 1), 
+               c(131.8, 437.7))
 
-test_that("Fitted parameters are correct for FOCUS D", {
+  expect_equal(signif(summary(fit.default)$bpar[, "t value"], 5),
+               c(parent_0 = 61.720, k_parent_sink = 12.777, k_parent_m1 = 24.248, k_m1_sink = 7.3486))
+})
+
+test_that("Fits with formation fractions are correct for FOCUS D", {
+  skip_on_cran()
+  SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
+                        m1 = list(type = "SFO"), 
+                        use_of_ff = "max", quiet = TRUE)
+
+  fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
   expect_equivalent(round(fit.ff$bparms.optim, c(2, 4, 4, 4)), 
                     c(99.60, 0.0987, 0.0053, 0.5145))
-})
 
-test_that("FOCUS chi2 error levels are correct for FOCUS D", {
   expect_equivalent(round(100 * mkinerrmin(fit.ff)$err.min, 2), 
                     c(6.40, 6.46, 4.69))
-})
 
-test_that("DT50/90 are correct for FOCUS D when using formation fractions", {
   expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["parent", ]), 2), 
                c(7.02, 23.33))
   expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["m1", ]), 1), 
                c(131.8, 437.7))
 })
 
-test_that("DT50/90 are correct for FOCUS D when not using formation fractions", {
-  expect_equal(round(as.numeric(endpoints(fit.default)$distimes["parent", ]), 2), 
-               c(7.02, 23.33))
-  expect_equal(round(as.numeric(endpoints(fit.default)$distimes["m1", ]), 1), 
-               c(131.8, 437.7))
-})
-
 # References:
 # Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative
 # zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452
 
-context("The t-test for significant difference from zero")
-
-test_that("The t-value for fits using internal transformations corresponds with result from FME", {
-
-  expect_equal(signif(summary(fit.default)$bpar[, "t value"], 5),
-               c(parent_0 = 61.720, k_parent_sink = 12.777, k_parent_m1 = 24.248, k_m1_sink = 7.3486))
-
-})
-
-m_synth_DFOP_par.minff <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
-                           M1 = mkinsub("SFO"),
-                           M2 = mkinsub("SFO"),
-                           use_of_ff = "min", quiet = TRUE)
-
-fit_DFOP_par_c_2 <- mkinfit(m_synth_DFOP_par.minff, 
-                          synthetic_data_for_UBA_2014[[12]]$data,
-                          quiet = TRUE)
-
 test_that("The t-value for fits using internal transformations corresponds with results from FME, synthetic data", {
+  skip_on_cran()
+  m_synth_DFOP_par.minff <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+                             M1 = mkinsub("SFO"),
+                             M2 = mkinsub("SFO"),
+                             use_of_ff = "min", quiet = TRUE)
+
+  fit_DFOP_par_c_2 <- mkinfit(m_synth_DFOP_par.minff, 
+                            synthetic_data_for_UBA_2014[[12]]$data,
+                            quiet = TRUE)
 
   # Note that the k1 and k2 are exchanged in the untransformed fit evaluated with FME for this test
   expect_equal(signif(summary(fit_DFOP_par_c_2)$bpar[1:7, "t value"], 5),
                c(parent_0 = 80.054, k_M1_sink = 12.291, k_M2_sink = 10.588, 
                  f_parent_to_M1 = 21.4960, f_parent_to_M2 = 24.0890,
                  k1 = 16.1450, k2 = 8.1747))
-
 })
diff --git a/tests/testthat/test_mkinpredict_SFO_SFO.R b/tests/testthat/test_mkinpredict_SFO_SFO.R
index b7004f64..3fcdb3a2 100644
--- a/tests/testthat/test_mkinpredict_SFO_SFO.R
+++ b/tests/testthat/test_mkinpredict_SFO_SFO.R
@@ -1,6 +1,4 @@
-# $Id: jranke $
-
-# Copyright (C) 2012-2015 Johannes Ranke
+# Copyright (C) 2012-2015,2018 Johannes Ranke
 # Contact: jranke@uni-bremen.de
 
 # This file is part of the R package mkin
diff --git a/tests/testthat/test_parent_only.R b/tests/testthat/test_parent_only.R
index ee0cc144..7521e145 100644
--- a/tests/testthat/test_parent_only.R
+++ b/tests/testthat/test_parent_only.R
@@ -165,6 +165,7 @@ test_that("Fits for FOCUS C deviate less than 0.1% from median of values from FO
 })
 
 test_that("SFO fits give approximately (0.001%) equal results with different solution methods", {
+  skip_on_cran()
   fit.A.SFO.default <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE)$bparms.optim
 
   fits.A.SFO <- list()
@@ -179,6 +180,7 @@ test_that("SFO fits give approximately (0.001%) equal results with different sol
 })
 
 test_that("FOMC fits give approximately (0.001%) equal results with different solution methods", {
+  skip_on_cran()
   fit.C.FOMC.default <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)$bparms.optim
 
   fits.C.FOMC <- list()
@@ -191,6 +193,7 @@ test_that("FOMC fits give approximately (0.001%) equal results with different so
 })
 
 test_that("DFOP fits give approximately (0.001%) equal results with different solution methods", {
+  skip_on_cran()
   fit.C.DFOP.default <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE)$bparms.optim
 
   fits.C.DFOP <- list()
diff --git a/tests/testthat/test_synthetic_data_for_UBA_2014.R b/tests/testthat/test_synthetic_data_for_UBA_2014.R
index fd3e8bba..6856a9a3 100644
--- a/tests/testthat/test_synthetic_data_for_UBA_2014.R
+++ b/tests/testthat/test_synthetic_data_for_UBA_2014.R
@@ -20,6 +20,7 @@ context("Results for synthetic data established in expertise for UBA (Ranke 2014
 
 
 test_that("Results are correct for SFO_lin_a", {
+  skip_on_cran()
   m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
                              M1 = mkinsub("SFO", "M2"),
                              M2 = mkinsub("SFO"),
diff --git a/tests/testthat/test_twa.R b/tests/testthat/test_twa.R
index d5c0b98b..a84b2c4e 100644
--- a/tests/testthat/test_twa.R
+++ b/tests/testthat/test_twa.R
@@ -18,11 +18,13 @@
 
 context("Calculation of maximum time weighted average concentrations (TWAs)")
 
-twa_models <- c("SFO", "FOMC", "DFOP")
-fits <- mmkin(twa_models, list(FOCUS_D = FOCUS_2006_D), 
-              quiet = TRUE, cores = 1)
 
 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]]
-- 
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