From c4a35c0e141a4bb05ba508914bebdc2884109e76 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 14 Sep 2018 11:38:43 +0200 Subject: Exclude more example code from CRAN checks to avoid NOTES about long execution times. Static documentation rebuilt by pkgdown with run_dont_run = TRUE --- DESCRIPTION | 4 +- GNUmakefile | 2 +- NEWS.md | 8 +- build.log | 2 +- docs/articles/FOCUS_D.html | 2 +- docs/articles/FOCUS_L.html | 44 +- docs/articles/FOCUS_Z.html | 2 +- docs/articles/compiled_models.html | 12 +- docs/articles/index.html | 2 +- docs/articles/mkin.html | 2 +- docs/articles/twa.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 19 +- 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-1.png | Bin 0 -> 18757 bytes docs/reference/SFO.solution.html | 6 +- docs/reference/SFORB.solution-1.png | Bin 0 -> 20255 bytes docs/reference/SFORB.solution.html | 6 +- 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 | 2 +- docs/reference/mccall81_245T.html | 111 +++- 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 | 6 +- docs/reference/mkinfit.html | 836 +++++++++++++++++++++++-- docs/reference/mkinmod.html | 35 +- 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-1.png | Bin 0 -> 97714 bytes docs/reference/mmkin-2.png | Bin 0 -> 88254 bytes docs/reference/mmkin-3.png | Bin 0 -> 85755 bytes docs/reference/mmkin-4.png | Bin 0 -> 63345 bytes docs/reference/mmkin-5.png | Bin 0 -> 57629 bytes docs/reference/mmkin.html | 43 +- 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-1.png | Bin 0 -> 55656 bytes docs/reference/schaefer07_complex_case.html | 24 +- docs/reference/sigma_twocomp.html | 2 +- docs/reference/summary.mkinfit.html | 10 +- docs/reference/synthetic_data_for_UBA.html | 11 +- docs/reference/test_data_from_UBA_2014-1.png | Bin 0 -> 53543 bytes docs/reference/test_data_from_UBA_2014-2.png | Bin 0 -> 69982 bytes docs/reference/test_data_from_UBA_2014.html | 62 +- docs/reference/transform_odeparms.html | 245 +++++++- man/mccall81_245T.Rd | 12 +- man/mkinerrmin.Rd | 6 +- man/mkinparplot.Rd | 3 +- 68 files changed, 1357 insertions(+), 242 deletions(-) create mode 100644 docs/reference/SFO.solution-1.png create mode 100644 docs/reference/SFORB.solution-1.png create mode 100644 docs/reference/mmkin-1.png create mode 100644 docs/reference/mmkin-2.png create mode 100644 docs/reference/mmkin-3.png create mode 100644 docs/reference/mmkin-4.png create mode 100644 docs/reference/mmkin-5.png create mode 100644 docs/reference/schaefer07_complex_case-1.png create mode 100644 docs/reference/test_data_from_UBA_2014-1.png create mode 100644 docs/reference/test_data_from_UBA_2014-2.png diff --git a/DESCRIPTION b/DESCRIPTION index eda66f9e..11fb4a9d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 0.9.47.3 -Date: 2018-09-07 +Version: 0.9.47.4 +Date: 2018-09-14 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/GNUmakefile b/GNUmakefile index 2ad613c4..be2e6675 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -74,7 +74,7 @@ vignettes/%.html: vignettes/mkin_vignettes.css vignettes/references.bib vignette vignettes: vignettes/mkin.html vignettes/FOCUS_D.html vignettes/FOCUS_L.html vignettes/FOCUS_Z.html vignettes/compiled_models.html pd: - "$(RBIN)/Rscript" -e "pkgdown::build_site()" + "$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE)" git add -A git commit -m 'Static documentation rebuilt by pkgdown' -e diff --git a/NEWS.md b/NEWS.md index 55755862..00bebd7a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,10 @@ -# mkin 0.9.47.3 (2018-09-13) +# mkin 0.9.47.4 (2018-09-14) -- 'mkinfit': Improve fitting the error model for reweight.method = 'tc' +- Exclude more example code from testing on CRAN to avoid NOTES from long execution times + +# mkin 0.9.47.3 (not released to CRAN) + +- 'mkinfit': Improve fitting the error model for reweight.method = 'tc'. Add 'manual' to possible arguments for 'weight' - Test that FOCUS_2006_C can be evaluated with DFOP and reweight.method = 'tc' diff --git a/build.log b/build.log index f1ef44b2..c7663906 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_0.9.47.3.tar.gz’ +* building ‘mkin_0.9.47.4.tar.gz’ diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 195570b1..3ed8004e 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -29,7 +29,7 @@ mkin - 0.9.47.3 + 0.9.47.4 diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index f7bbf961..cc069d1a 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -29,7 +29,7 @@ mkin - 0.9.47.3 + 0.9.47.4 @@ -110,15 +110,15 @@ summary(m.L1.SFO) 
## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 06:39:28 2018 
-## Date of summary: Fri Sep 14 06:39:28 2018 
+## Date of fit:     Fri Sep 14 11:36:13 2018 
+## Date of summary: Fri Sep 14 11:36:13 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 0.091 s
+## Fitted with method Port using 37 model solutions performed in 0.085 s
 ## 
 ## Weighting: none
 ## 
@@ -201,15 +201,15 @@
 
 
## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 06:39:30 2018 
-## Date of summary: Fri Sep 14 06:39:30 2018 
+## Date of fit:     Fri Sep 14 11:36:14 2018 
+## Date of summary: Fri Sep 14 11:36:14 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 1.333 s
+## Fitted with method Port using 611 model solutions performed in 1.405 s
 ## 
 ## Weighting: none
 ## 
@@ -296,15 +296,15 @@
 
 
## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 06:39:30 2018 
-## Date of summary: Fri Sep 14 06:39:30 2018 
+## Date of fit:     Fri Sep 14 11:36:15 2018 
+## Date of summary: Fri Sep 14 11:36:15 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 0.172 s
+## Fitted with method Port using 81 model solutions performed in 0.188 s
 ## 
 ## Weighting: none
 ## 
@@ -367,8 +367,8 @@
 
 
## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 06:39:31 2018 
-## Date of summary: Fri Sep 14 06:39:31 2018 
+## Date of fit:     Fri Sep 14 11:36:16 2018 
+## Date of summary: Fri Sep 14 11:36:16 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 0.742 s
+## Fitted with method Port using 336 model solutions performed in 0.833 s
 ## 
 ## Weighting: none
 ## 
@@ -459,8 +459,8 @@
 
 
## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 06:39:32 2018 
-## Date of summary: Fri Sep 14 06:39:32 2018 
+## Date of fit:     Fri Sep 14 11:36:17 2018 
+## Date of summary: Fri Sep 14 11:36:17 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 0.312 s
+## Fitted with method Port using 137 model solutions performed in 0.335 s
 ## 
 ## Weighting: none
 ## 
@@ -560,15 +560,15 @@
 
 
## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 06:39:33 2018 
-## Date of summary: Fri Sep 14 06:39:33 2018 
+## Date of fit:     Fri Sep 14 11:36:18 2018 
+## Date of summary: Fri Sep 14 11:36:18 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 0.097 s
+## Fitted with method Port using 46 model solutions performed in 0.099 s
 ## 
 ## Weighting: none
 ## 
@@ -620,15 +620,15 @@
 
 
## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 06:39:33 2018 
-## Date of summary: Fri Sep 14 06:39:33 2018 
+## Date of fit:     Fri Sep 14 11:36:18 2018 
+## Date of summary: Fri Sep 14 11:36:18 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 0.143 s
+## Fitted with method Port using 66 model solutions performed in 0.152 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html
index 9753abd6..ff0bd537 100644
--- a/docs/articles/FOCUS_Z.html
+++ b/docs/articles/FOCUS_Z.html
@@ -29,7 +29,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index d93fe9e1..a6598fd4 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -29,7 +29,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
@@ -125,9 +125,9 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.110    1.000     2.108        0
-## 1 deSolve, not compiled            3  16.442    7.792    16.433        0
-## 2      Eigenvalue based            3   2.593    1.229     2.592        0
+## 3     deSolve, compiled            3   2.205    1.000     2.203        0
+## 1 deSolve, not compiled            3  17.206    7.803    17.196        0
+## 2      Eigenvalue based            3   2.829    1.283     2.828        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   3.781    1.000     3.778        0
-## 1 deSolve, not compiled            3  34.742    9.189    34.725        0
+## 2     deSolve, compiled            3   3.874    1.000     3.866    0.004
+## 1 deSolve, not compiled            3  35.712    9.218    35.692    0.000
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/articles/index.html b/docs/articles/index.html
index dcaf33b8..e20ad2d4 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -58,7 +58,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 4d62b50d..bc76c2cf 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -29,7 +29,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 2952e887..a2f7f72a 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -29,7 +29,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/authors.html b/docs/authors.html
index 20849b4a..61cf4fbc 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -58,7 +58,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/index.html b/docs/index.html
index ba838a39..5a3864bf 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -36,7 +36,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/news/index.html b/docs/news/index.html
index b76ca884..6cc7351d 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -58,7 +58,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
@@ -117,12 +117,20 @@
       
     
 
-    

+    

 

-mkin 0.9.47.3 (2018-09-13) Unreleased 
+mkin 0.9.47.4 (2018-09-14) Unreleased 
 

 
    
-
  • ‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’
    • 
+
  • Exclude more example code from testing on CRAN to avoid NOTES from long execution times
    • 
+

+

+    

+

+mkin 0.9.47.3 (not released to CRAN) Unreleased 
+

+
    
+
  • ‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’. Add ‘manual’ to possible arguments for ‘weight’
    • 
 
  • Test that FOCUS_2006_C can be evaluated with DFOP and reweight.method = ‘tc’
    • 
 

 

@@ -648,7 +656,8 @@
     

       
Contents

       
    
-        
  • 0.9.47.3
    • 
+        
  • 0.9.47.4
    • 
+        
  • 0.9.47.3
    • 
         
  • 0.9.47.2
    • 
         
  • 0.9.47.1
    • 
         
  • 0.9.46.3
    • 
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index 22709123..2f714f2c 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     

 
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 94c4d336..922479a1 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     

 
@@ -278,7 +278,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.165       0.000       0.165 
+#>       0.164       0.000       0.164 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -467,8 +467,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555bd36378>
-#> <environment: 0x55555bd42bc8>
+#> <bytecode: 0x55555bd535f0>
+#> <environment: 0x55555bd1c770>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -490,8 +490,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555c995188>
-#> <environment: 0x55555bd42bc8>
+#> <bytecode: 0x55555c9c70f8>
+#> <environment: 0x55555bd1c770>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -558,10 +558,10 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Fri Sep 14 06:38:57 2018"
+#> [1] "Fri Sep 14 11:34:38 2018"
 #> 
 #> $version
-#> [1] "0.9.47.3"
+#> [1] "0.9.47.4"
 #> 
 #> $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 2b6886ff..bea35e09 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
-        0.9.47.3
+        0.9.47.4
       
     
 
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 73b2450b..9122a546 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
-        0.9.47.3
+        0.9.47.4
       
     
 
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 e5621863..3d5677e8 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
-        0.9.47.3
+        0.9.47.4
       
     
 
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 872d68a9..524fbd79 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
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 232be6f3..a0bcc65d 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index c4f3158d..10f33260 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
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 8f1ff8de..cb9eb353 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index ae09fcf7..23f82d13 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/reference/SFO.solution-1.png b/docs/reference/SFO.solution-1.png
new file mode 100644
index 00000000..9e6bd786
Binary files /dev/null and b/docs/reference/SFO.solution-1.png differ
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index f4e8eb42..087ff46f 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
@@ -160,9 +160,7 @@
     
 
     
Examples

-    
  
# NOT RUN {
-plot(function(x) SFO.solution(x, 100, 3), 0, 2)
-# }

+    
  
plot(function(x) SFO.solution(x, 100, 3), 0, 2)

   
   
 
@@ -177,9 +177,7 @@
     
 
     
Examples

-    
  
# NOT RUN {
-plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)
-# }

+    
  
plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)

   
   
 
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index e39d1c15..fdf465a5 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
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index a5c63aeb..bddbab1a 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index ec49468a..e780d26b 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index af7642e6..185991d6 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -58,7 +58,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 8d31b0d2..ef7209bf 100644
--- a/docs/reference/max_twa_parent.html
+++ b/docs/reference/max_twa_parent.html
@@ -65,7 +65,7 @@ guidance." />
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index cea92155..ac2adf1e 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
@@ -155,19 +155,11 @@
     
Examples

     
  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.
  
# NOT RUN {
-    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
-    summary(fit.1, data = FALSE)
-
-# }
  # No convergence, no covariance matrix ...
-  # k_phenol_sink is really small, therefore fix it to zero
-  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:    0.9.47.3 
+                         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:    0.9.47.4 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 06:39:07 2018 
-#> Date of summary: Fri Sep 14 06:39:07 2018 
+#> Date of fit:     Fri Sep 14 11:34:50 2018 
+#> Date of summary: Fri Sep 14 11:34:50 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -177,7 +169,96 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.423 s
+#> Fitted with method Port using 574 model solutions performed in 3.33 s
+#> 
+#> Weighting: none
+#> 
+#> Starting values for parameters to be optimised:
+#>                     value   type
+#> T245_0           100.9000  state
+#> k_T245_sink        0.1000 deparm
+#> k_T245_phenol      0.1001 deparm
+#> k_phenol_sink      0.1002 deparm
+#> k_phenol_anisole   0.1003 deparm
+#> k_anisole_sink     0.1004 deparm
+#> 
+#> Starting values for the transformed parameters actually optimised:
+#>                           value lower upper
+#> T245_0               100.900000  -Inf   Inf
+#> log_k_T245_sink       -2.302585  -Inf   Inf
+#> log_k_T245_phenol     -2.301586  -Inf   Inf
+#> log_k_phenol_sink     -2.300587  -Inf   Inf
+#> log_k_phenol_anisole  -2.299590  -Inf   Inf
+#> log_k_anisole_sink    -2.298593  -Inf   Inf
+#> 
+#> Fixed parameter values:
+#>           value  type
+#> phenol_0      0 state
+#> anisole_0     0 state
+#> 
+#> Optimised, transformed parameters with symmetric confidence intervals:
+#>                      Estimate Std. Error Lower Upper
+#> T245_0               103.9000         NA    NA    NA
+#> log_k_T245_sink       -4.1130         NA    NA    NA
+#> log_k_T245_phenol     -3.6120         NA    NA    NA
+#> log_k_phenol_sink    -25.0800         NA    NA    NA
+#> log_k_phenol_anisole  -0.9037         NA    NA    NA
+#> log_k_anisole_sink    -5.0090         NA    NA    NA
+#> 
+#> Parameter correlation:
#> Warning: Could not estimate covariance matrix; singular system:
#> Could not estimate covariance matrix; singular system:
+#> 
+#> Residual standard error: 2.78 on 18 degrees of freedom
+#> 
+#> Backtransformed parameters:
+#> Confidence intervals for internally transformed parameters are asymmetric.
+#> t-test (unrealistically) based on the assumption of normal distribution
+#> for estimators of untransformed parameters.
+#>                   Estimate   t value    Pr(>t) Lower Upper
+#> T245_0           1.039e+02 4.282e+01 7.236e-20    NA    NA
+#> k_T245_sink      1.636e-02 8.901e-01 1.926e-01    NA    NA
+#> k_T245_phenol    2.701e-02 1.504e+00 7.498e-02    NA    NA
+#> k_phenol_sink    1.286e-11 4.575e-11 5.000e-01    NA    NA
+#> k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02    NA    NA
+#> k_anisole_sink   6.679e-03 8.146e+00 9.469e-08    NA    NA
+#> 
+#> Chi2 error levels in percent:
+#>          err.min n.optim df
+#> All data  10.070       6 16
+#> T245       7.908       3  5
+#> phenol   106.445       2  5
+#> anisole    5.379       1  6
+#> 
+#> Resulting formation fractions:
+#>                       ff
+#> T245_sink      3.772e-01
+#> T245_phenol    6.228e-01
+#> phenol_sink    3.175e-11
+#> phenol_anisole 1.000e+00
+#> anisole_sink   1.000e+00
+#> 
+#> Estimated disappearance times:
+#>            DT50    DT90
+#> T245     15.982  53.091
+#> phenol    1.711   5.685
+#> anisole 103.784 344.763
    # No convergence, no covariance matrix ...
+    # k_phenol_sink is really small, therefore fix it to zero
+    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:    0.9.47.4 
+#> R version used for fitting:       3.5.1 
+#> Date of fit:     Fri Sep 14 11:34:51 2018 
+#> Date of summary: Fri Sep 14 11:34:51 2018 
+#> 
+#> Equations:
+#> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
+#> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol -
+#>            k_phenol_anisole * phenol
+#> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole
+#> 
+#> Model predictions using solution type deSolve 
+#> 
+#> Fitted with method Port using 246 model solutions performed in 1.417 s
 #> 
 #> Weighting: none
 #> 
@@ -257,7 +338,7 @@
 #>            DT50    DT90
 #> T245     15.982  53.091
 #> phenol    1.711   5.685
-#> anisole 103.784 344.763

+#> anisole 103.784 344.763
  

   
   
 
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index e7342cee..e2b4ef61 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -62,7 +62,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index 16086f3e..c77945b9 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index c8fd8272..a18b226e 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
-        0.9.47.3
+        0.9.47.4
       
     
 
@@ -178,8 +178,8 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.

 round(mkinerrmin(fit_FOCUS_D), 4)
#>          err.min n.optim df
 #> All data  0.0640       4 15
 #> parent    0.0646       2  7
-#> m1        0.0469       2  8
fit_FOCUS_E = mkinfit(SFO_SFO, FOCUS_2006_E, quiet = TRUE)
-round(mkinerrmin(fit_FOCUS_E), 4)
#>          err.min n.optim df
+#> m1        0.0469       2  8
  fit_FOCUS_E = mkinfit(SFO_SFO, FOCUS_2006_E, quiet = TRUE)
+  round(mkinerrmin(fit_FOCUS_E), 4)
#>          err.min n.optim df
 #> All data  0.1544       4 13
 #> parent    0.1659       2  7
 #> m1        0.1095       2  6

diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index b1c42168..13029e91 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -71,7 +71,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
@@ -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:    0.9.47.3 
+summary(fit)
#> mkin version used for fitting:    0.9.47.4 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 06:39:09 2018 
-#> Date of summary: Fri Sep 14 06:39:09 2018 
+#> Date of fit:     Fri Sep 14 11:34:54 2018 
+#> Date of summary: Fri Sep 14 11:34:54 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 0.157 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 
-#>       0.892       0.000       0.892 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.906       0.000       0.907 
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 
@@ -523,19 +523,86 @@
 #>              DT50      DT90
 #> parent   7.022929  23.32967
 #> m1     131.760712 437.69961
-#> 
# NOT RUN {
-# deSolve is slower when no C compiler (gcc) was available during model generation
+#> 
# deSolve is slower when no C compiler (gcc) was available during model generation
 print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D,
-                           solution_type = "deSolve")))
-coef(fit.deSolve)
-endpoints(fit.deSolve)
-# }

+                           solution_type = "deSolve")))
#> Model cost at call  1 :  18915.53 
+#> Model cost at call  2 :  18915.53 
+#> Model cost at call  6 :  11424.02 
+#> Model cost at call  10 :  11424 
+#> Model cost at call  12 :  4094.396 
+#> Model cost at call  16 :  4094.396 
+#> Model cost at call  19 :  1340.595 
+#> Model cost at call  20 :  1340.593 
+#> Model cost at call  25 :  1072.239 
+#> Model cost at call  28 :  1072.236 
+#> Model cost at call  30 :  874.2615 
+#> Model cost at call  33 :  874.2611 
+#> Model cost at call  35 :  616.2377 
+#> Model cost at call  37 :  616.2372 
+#> Model cost at call  40 :  467.4386 
+#> Model cost at call  42 :  467.4381 
+#> Model cost at call  46 :  398.2914 
+#> Model cost at call  48 :  398.2914 
+#> Model cost at call  49 :  398.2913 
+#> Model cost at call  51 :  395.0712 
+#> Model cost at call  54 :  395.0711 
+#> Model cost at call  56 :  378.3298 
+#> Model cost at call  59 :  378.3298 
+#> Model cost at call  62 :  376.9812 
+#> Model cost at call  64 :  376.9811 
+#> Model cost at call  67 :  375.2085 
+#> Model cost at call  69 :  375.2085 
+#> Model cost at call  70 :  375.2085 
+#> Model cost at call  71 :  375.2085 
+#> Model cost at call  72 :  374.5723 
+#> Model cost at call  74 :  374.5723 
+#> Model cost at call  77 :  374.0075 
+#> Model cost at call  79 :  374.0075 
+#> Model cost at call  80 :  374.0075 
+#> Model cost at call  82 :  373.1711 
+#> Model cost at call  84 :  373.1711 
+#> Model cost at call  87 :  372.6445 
+#> Model cost at call  88 :  372.1614 
+#> Model cost at call  90 :  372.1614 
+#> Model cost at call  91 :  372.1614 
+#> Model cost at call  94 :  371.6464 
+#> Model cost at call  99 :  371.4299 
+#> Model cost at call  101 :  371.4299 
+#> Model cost at call  104 :  371.4071 
+#> Model cost at call  106 :  371.4071 
+#> Model cost at call  107 :  371.4071 
+#> Model cost at call  109 :  371.2524 
+#> Model cost at call  113 :  371.2524 
+#> Model cost at call  114 :  371.2136 
+#> Model cost at call  115 :  371.2136 
+#> Model cost at call  116 :  371.2136 
+#> Model cost at call  119 :  371.2134 
+#> Model cost at call  120 :  371.2134 
+#> Model cost at call  122 :  371.2134 
+#> Model cost at call  123 :  371.2134 
+#> Model cost at call  125 :  371.2134 
+#> Model cost at call  126 :  371.2134 
+#> Model cost at call  135 :  371.2134 
+#> Model cost at call  146 :  371.2134 
+#> Optimisation by method Port successfully terminated.
+#>        User      System verstrichen 
+#>       0.714       0.000       0.715 
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 
+#> 
+#> $SFORB
+#> logical(0)
+#> 
+#> $distimes
+#>              DT50      DT90
+#> parent   7.022929  23.32967
+#> m1     131.760711 437.69961
+#> 

 # Use stepwise fitting, using optimised parameters from parent only fit, FOMC
-
# NOT RUN {
-FOMC_SFO <- mkinmod(
+
FOMC_SFO <- mkinmod(
   parent = mkinsub("FOMC", "m1"),
-  m1 = mkinsub("SFO"))
-# Fit the model to the FOCUS example dataset D using defaults
+  m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE)
 # Use starting parameters from parent only FOMC fit
 fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE)
@@ -545,40 +612,733 @@
 # Use stepwise fitting, using optimised parameters from parent only fit, SFORB
 SFORB_SFO <- mkinmod(
   parent = list(type = "SFORB", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"))
-# Fit the model to the FOCUS example dataset D using defaults
+  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.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, quiet = TRUE)
 fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve",
                                  quiet = TRUE)
 # Use starting parameters from parent only SFORB fit (not really needed in this case)
 fit.SFORB = mkinfit("SFORB", FOCUS_2006_D, quiet = TRUE)
-fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE)
-# }

-
# NOT RUN {
-# Weighted fits, including IRLS
+fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE)

+
# Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
-                      m1 = mkinsub("SFO"), use_of_ff = "max")
-f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-summary(f.noweight)
-f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
-summary(f.irls)
-f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE)
-summary(f.w.mean)
-f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value",
+                      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:    0.9.47.4 
+#> R version used for fitting:       3.5.1 
+#> Date of fit:     Fri Sep 14 11:35:05 2018 
+#> Date of summary: Fri Sep 14 11:35:05 2018 
+#> 
+#> Equations:
+#> d_parent/dt = - k_parent * parent
+#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#> 
+#> Model predictions using solution type deSolve 
+#> 
+#> Fitted with method Port using 186 model solutions performed in 0.763 s
+#> 
+#> Weighting: none
+#> 
+#> Starting values for parameters to be optimised:
+#>                   value   type
+#> parent_0       100.7500  state
+#> k_parent         0.1000 deparm
+#> k_m1             0.1001 deparm
+#> f_parent_to_m1   0.5000 deparm
+#> 
+#> Starting values for the transformed parameters actually optimised:
+#>                     value lower upper
+#> parent_0       100.750000  -Inf   Inf
+#> log_k_parent    -2.302585  -Inf   Inf
+#> log_k_m1        -2.301586  -Inf   Inf
+#> f_parent_ilr_1   0.000000  -Inf   Inf
+#> 
+#> Fixed parameter values:
+#>      value  type
+#> m1_0     0 state
+#> 
+#> Optimised, transformed parameters with symmetric confidence intervals:
+#>                Estimate Std. Error   Lower    Upper
+#> parent_0       99.60000    1.61400 96.3300 102.9000
+#> log_k_parent   -2.31600    0.04187 -2.4010  -2.2310
+#> log_k_m1       -5.24800    0.13610 -5.5230  -4.9720
+#> f_parent_ilr_1  0.04096    0.06477 -0.0904   0.1723
+#> 
+#> Parameter correlation:
+#>                parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#> parent_0         1.0000       0.5178  -0.1701        -0.5489
+#> log_k_parent     0.5178       1.0000  -0.3285        -0.5451
+#> log_k_m1        -0.1701      -0.3285   1.0000         0.7466
+#> f_parent_ilr_1  -0.5489      -0.5451   0.7466         1.0000
+#> 
+#> Residual standard error: 3.211 on 36 degrees of freedom
+#> 
+#> Backtransformed parameters:
+#> Confidence intervals for internally transformed parameters are asymmetric.
+#> t-test (unrealistically) based on the assumption of normal distribution
+#> for estimators of untransformed parameters.
+#>                 Estimate t value    Pr(>t)     Lower     Upper
+#> parent_0       99.600000  61.720 2.024e-38 96.330000 1.029e+02
+#> k_parent        0.098700  23.880 5.700e-24  0.090660 1.074e-01
+#> k_m1            0.005261   7.349 5.758e-09  0.003992 6.933e-03
+#> f_parent_to_m1  0.514500  22.490 4.375e-23  0.468100 5.606e-01
+#> 
+#> Chi2 error levels in percent:
+#>          err.min n.optim df
+#> All data   6.398       4 15
+#> parent     6.459       2  7
+#> m1         4.690       2  8
+#> 
+#> Resulting formation fractions:
+#>                 ff
+#> parent_m1   0.5145
+#> parent_sink 0.4855
+#> 
+#> Estimated disappearance times:
+#>           DT50   DT90
+#> parent   7.023  23.33
+#> m1     131.761 437.70
+#> 
+#> Data:
+#>  time variable observed predicted   residual
+#>     0   parent    99.46  99.59848 -1.385e-01
+#>     0   parent   102.04  99.59848  2.442e+00
+#>     1   parent    93.50  90.23787  3.262e+00
+#>     1   parent    92.50  90.23787  2.262e+00
+#>     3   parent    63.23  74.07319 -1.084e+01
+#>     3   parent    68.99  74.07319 -5.083e+00
+#>     7   parent    52.32  49.91206  2.408e+00
+#>     7   parent    55.13  49.91206  5.218e+00
+#>    14   parent    27.27  25.01257  2.257e+00
+#>    14   parent    26.64  25.01257  1.627e+00
+#>    21   parent    11.50  12.53462 -1.035e+00
+#>    21   parent    11.64  12.53462 -8.946e-01
+#>    35   parent     2.85   3.14787 -2.979e-01
+#>    35   parent     2.91   3.14787 -2.379e-01
+#>    50   parent     0.69   0.71624 -2.624e-02
+#>    50   parent     0.63   0.71624 -8.624e-02
+#>    75   parent     0.05   0.06074 -1.074e-02
+#>    75   parent     0.06   0.06074 -7.381e-04
+#>     0       m1     0.00   0.00000  0.000e+00
+#>     0       m1     0.00   0.00000  0.000e+00
+#>     1       m1     4.84   4.80296  3.704e-02
+#>     1       m1     5.64   4.80296  8.370e-01
+#>     3       m1    12.91  13.02400 -1.140e-01
+#>     3       m1    12.96  13.02400 -6.400e-02
+#>     7       m1    22.97  25.04476 -2.075e+00
+#>     7       m1    24.47  25.04476 -5.748e-01
+#>    14       m1    41.69  36.69002  5.000e+00
+#>    14       m1    33.21  36.69002 -3.480e+00
+#>    21       m1    44.37  41.65310  2.717e+00
+#>    21       m1    46.44  41.65310  4.787e+00
+#>    35       m1    41.22  43.31312 -2.093e+00
+#>    35       m1    37.95  43.31312 -5.363e+00
+#>    50       m1    41.19  41.21831 -2.831e-02
+#>    50       m1    40.01  41.21831 -1.208e+00
+#>    75       m1    40.09  36.44703  3.643e+00
+#>    75       m1    33.85  36.44703 -2.597e+00
+#>   100       m1    31.04  31.98163 -9.416e-01
+#>   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:    0.9.47.4 
+#> R version used for fitting:       3.5.1 
+#> Date of fit:     Fri Sep 14 11:35:07 2018 
+#> Date of summary: Fri Sep 14 11:35:07 2018 
+#> 
+#> Equations:
+#> d_parent/dt = - k_parent * parent
+#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#> 
+#> Model predictions using solution type deSolve 
+#> 
+#> Fitted with method Port using 551 model solutions performed in 2.297 s
+#> 
+#> Weighting: none
+#> 
+#> Iterative reweighting with method obs 
+#> Final mean squared residuals of observed variables:
+#>    parent        m1 
+#> 11.573407  7.407845 
+#> 
+#> Starting values for parameters to be optimised:
+#>                   value   type
+#> parent_0       100.7500  state
+#> k_parent         0.1000 deparm
+#> k_m1             0.1001 deparm
+#> f_parent_to_m1   0.5000 deparm
+#> 
+#> Starting values for the transformed parameters actually optimised:
+#>                     value lower upper
+#> parent_0       100.750000  -Inf   Inf
+#> log_k_parent    -2.302585  -Inf   Inf
+#> log_k_m1        -2.301586  -Inf   Inf
+#> f_parent_ilr_1   0.000000  -Inf   Inf
+#> 
+#> Fixed parameter values:
+#>      value  type
+#> m1_0     0 state
+#> 
+#> Optimised, transformed parameters with symmetric confidence intervals:
+#>                Estimate Std. Error    Lower   Upper
+#> parent_0       99.67000    1.79200 96.04000 103.300
+#> log_k_parent   -2.31200    0.04560 -2.40400  -2.219
+#> log_k_m1       -5.25100    0.12510 -5.50500  -4.998
+#> f_parent_ilr_1  0.03785    0.06318 -0.09027   0.166
+#> 
+#> Parameter correlation:
+#>                parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#> parent_0         1.0000       0.5083  -0.1979        -0.6148
+#> log_k_parent     0.5083       1.0000  -0.3894        -0.6062
+#> log_k_m1        -0.1979      -0.3894   1.0000         0.7417
+#> f_parent_ilr_1  -0.6148      -0.6062   0.7417         1.0000
+#> 
+#> Residual standard error: 1.054 on 36 degrees of freedom
+#> 
+#> Backtransformed parameters:
+#> Confidence intervals for internally transformed parameters are asymmetric.
+#> t-test (unrealistically) based on the assumption of normal distribution
+#> for estimators of untransformed parameters.
+#>                Estimate t value    Pr(>t)     Lower     Upper
+#> parent_0       99.67000  55.630 8.185e-37 96.040000 1.033e+02
+#> k_parent        0.09906  21.930 1.016e-22  0.090310 1.087e-01
+#> k_m1            0.00524   7.996 8.486e-10  0.004066 6.753e-03
+#> f_parent_to_m1  0.51340  23.000 2.038e-23  0.468100 5.584e-01
+#> 
+#> Chi2 error levels in percent:
+#>          err.min n.optim df
+#> All data   6.399       4 15
+#> parent     6.466       2  7
+#> m1         4.679       2  8
+#> 
+#> Resulting formation fractions:
+#>                 ff
+#> parent_m1   0.5134
+#> parent_sink 0.4866
+#> 
+#> Estimated disappearance times:
+#>           DT50   DT90
+#> parent   6.997  23.24
+#> m1     132.282 439.43
+#> 
+#> Data:
+#>  time variable observed predicted   residual   err
+#>     0   parent    99.46  99.67218 -2.122e-01 3.402
+#>     0   parent   102.04  99.67218  2.368e+00 3.402
+#>     1   parent    93.50  90.27153  3.228e+00 3.402
+#>     1   parent    92.50  90.27153  2.228e+00 3.402
+#>     3   parent    63.23  74.04648 -1.082e+01 3.402
+#>     3   parent    68.99  74.04648 -5.056e+00 3.402
+#>     7   parent    52.32  49.82092  2.499e+00 3.402
+#>     7   parent    55.13  49.82092  5.309e+00 3.402
+#>    14   parent    27.27  24.90288  2.367e+00 3.402
+#>    14   parent    26.64  24.90288  1.737e+00 3.402
+#>    21   parent    11.50  12.44765 -9.476e-01 3.402
+#>    21   parent    11.64  12.44765 -8.076e-01 3.402
+#>    35   parent     2.85   3.11002 -2.600e-01 3.402
+#>    35   parent     2.91   3.11002 -2.000e-01 3.402
+#>    50   parent     0.69   0.70374 -1.374e-02 3.402
+#>    50   parent     0.63   0.70374 -7.374e-02 3.402
+#>    75   parent     0.05   0.05913 -9.134e-03 3.402
+#>    75   parent     0.06   0.05913  8.662e-04 3.402
+#>     0       m1     0.00   0.00000  0.000e+00 2.722
+#>     0       m1     0.00   0.00000  0.000e+00 2.722
+#>     1       m1     4.84   4.81328  2.672e-02 2.722
+#>     1       m1     5.64   4.81328  8.267e-01 2.722
+#>     3       m1    12.91  13.04779 -1.378e-01 2.722
+#>     3       m1    12.96  13.04779 -8.779e-02 2.722
+#>     7       m1    22.97  25.07615 -2.106e+00 2.722
+#>     7       m1    24.47  25.07615 -6.062e-01 2.722
+#>    14       m1    41.69  36.70729  4.983e+00 2.722
+#>    14       m1    33.21  36.70729 -3.497e+00 2.722
+#>    21       m1    44.37  41.65050  2.720e+00 2.722
+#>    21       m1    46.44  41.65050  4.790e+00 2.722
+#>    35       m1    41.22  43.28866 -2.069e+00 2.722
+#>    35       m1    37.95  43.28866 -5.339e+00 2.722
+#>    50       m1    41.19  41.19339 -3.386e-03 2.722
+#>    50       m1    40.01  41.19339 -1.183e+00 2.722
+#>    75       m1    40.09  36.43820  3.652e+00 2.722
+#>    75       m1    33.85  36.43820 -2.588e+00 2.722
+#>   100       m1    31.04  31.98971 -9.497e-01 2.722
+#>   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:    0.9.47.4 
+#> R version used for fitting:       3.5.1 
+#> Date of fit:     Fri Sep 14 11:35:08 2018 
+#> Date of summary: Fri Sep 14 11:35:08 2018 
+#> 
+#> Equations:
+#> d_parent/dt = - k_parent * parent
+#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#> 
+#> Model predictions using solution type deSolve 
+#> 
+#> Fitted with method Port using 155 model solutions performed in 0.618 s
+#> 
+#> Weighting: mean
+#> 
+#> Starting values for parameters to be optimised:
+#>                   value   type
+#> parent_0       100.7500  state
+#> k_parent         0.1000 deparm
+#> k_m1             0.1001 deparm
+#> f_parent_to_m1   0.5000 deparm
+#> 
+#> Starting values for the transformed parameters actually optimised:
+#>                     value lower upper
+#> parent_0       100.750000  -Inf   Inf
+#> log_k_parent    -2.302585  -Inf   Inf
+#> log_k_m1        -2.301586  -Inf   Inf
+#> f_parent_ilr_1   0.000000  -Inf   Inf
+#> 
+#> Fixed parameter values:
+#>      value  type
+#> m1_0     0 state
+#> 
+#> Optimised, transformed parameters with symmetric confidence intervals:
+#>                Estimate Std. Error    Lower    Upper
+#> parent_0        99.7300    1.93200 95.81000 103.6000
+#> log_k_parent    -2.3090    0.04837 -2.40700  -2.2110
+#> log_k_m1        -5.2550    0.12070 -5.49900  -5.0100
+#> f_parent_ilr_1   0.0354    0.06344 -0.09327   0.1641
+#> 
+#> Parameter correlation:
+#>                parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#> parent_0         1.0000       0.5004  -0.2143        -0.6514
+#> log_k_parent     0.5004       1.0000  -0.4282        -0.6383
+#> log_k_m1        -0.2143      -0.4282   1.0000         0.7390
+#> f_parent_ilr_1  -0.6514      -0.6383   0.7390         1.0000
+#> 
+#> Residual standard error: 0.09829 on 36 degrees of freedom
+#> 
+#> Backtransformed parameters:
+#> Confidence intervals for internally transformed parameters are asymmetric.
+#> t-test (unrealistically) based on the assumption of normal distribution
+#> for estimators of untransformed parameters.
+#>                 Estimate t value    Pr(>t)    Lower     Upper
+#> parent_0       99.730000  51.630 1.166e-35 95.81000 1.036e+02
+#> k_parent        0.099360  20.670 7.304e-22  0.09007 1.096e-01
+#> k_m1            0.005224   8.287 3.649e-10  0.00409 6.672e-03
+#> f_parent_to_m1  0.512500  22.860 2.497e-23  0.46710 5.578e-01
+#> 
+#> Chi2 error levels in percent:
+#>          err.min n.optim df
+#> All data   6.401       4 15
+#> parent     6.473       2  7
+#> m1         4.671       2  8
+#> 
+#> Resulting formation fractions:
+#>                 ff
+#> parent_m1   0.5125
+#> parent_sink 0.4875
+#> 
+#> Estimated disappearance times:
+#>           DT50   DT90
+#> parent   6.976  23.18
+#> m1     132.696 440.81
+#> 
+#> Data:
+#>  time variable observed predicted   residual
+#>     0   parent    99.46  99.73057  -0.270570
+#>     0   parent   102.04  99.73057   2.309430
+#>     1   parent    93.50  90.29805   3.201945
+#>     1   parent    92.50  90.29805   2.201945
+#>     3   parent    63.23  74.02503 -10.795028
+#>     3   parent    68.99  74.02503  -5.035028
+#>     7   parent    52.32  49.74838   2.571618
+#>     7   parent    55.13  49.74838   5.381618
+#>    14   parent    27.27  24.81588   2.454124
+#>    14   parent    26.64  24.81588   1.824124
+#>    21   parent    11.50  12.37885  -0.878849
+#>    21   parent    11.64  12.37885  -0.738849
+#>    35   parent     2.85   3.08022  -0.230219
+#>    35   parent     2.91   3.08022  -0.170219
+#>    50   parent     0.69   0.69396  -0.003958
+#>    50   parent     0.63   0.69396  -0.063958
+#>    75   parent     0.05   0.05789  -0.007888
+#>    75   parent     0.06   0.05789   0.002112
+#>     0       m1     0.00   0.00000   0.000000
+#>     0       m1     0.00   0.00000   0.000000
+#>     1       m1     4.84   4.82149   0.018512
+#>     1       m1     5.64   4.82149   0.818512
+#>     3       m1    12.91  13.06669  -0.156692
+#>     3       m1    12.96  13.06669  -0.106692
+#>     7       m1    22.97  25.10106  -2.131058
+#>     7       m1    24.47  25.10106  -0.631058
+#>    14       m1    41.69  36.72092   4.969077
+#>    14       m1    33.21  36.72092  -3.510923
+#>    21       m1    44.37  41.64835   2.721647
+#>    21       m1    46.44  41.64835   4.791647
+#>    35       m1    41.22  43.26923  -2.049225
+#>    35       m1    37.95  43.26923  -5.319225
+#>    50       m1    41.19  41.17364   0.016361
+#>    50       m1    40.01  41.17364  -1.163639
+#>    75       m1    40.09  36.43122   3.658776
+#>    75       m1    33.85  36.43122  -2.581224
+#>   100       m1    31.04  31.99612  -0.956124
+#>   100       m1    33.13  31.99612   1.133876
+#>   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)
-# }

-
# NOT RUN {
-# Manual weighting
+summary(f.w.value)
#> mkin version used for fitting:    0.9.47.4 
+#> R version used for fitting:       3.5.1 
+#> Date of fit:     Fri Sep 14 11:35:09 2018 
+#> Date of summary: Fri Sep 14 11:35:09 2018 
+#> 
+#> Equations:
+#> d_parent/dt = - k_parent * parent
+#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#> 
+#> Model predictions using solution type deSolve 
+#> 
+#> Fitted with method Port using 174 model solutions performed in 0.704 s
+#> 
+#> Weighting: manual
+#> 
+#> Starting values for parameters to be optimised:
+#>                   value   type
+#> parent_0       100.7500  state
+#> k_parent         0.1000 deparm
+#> k_m1             0.1001 deparm
+#> f_parent_to_m1   0.5000 deparm
+#> 
+#> Starting values for the transformed parameters actually optimised:
+#>                     value lower upper
+#> parent_0       100.750000  -Inf   Inf
+#> log_k_parent    -2.302585  -Inf   Inf
+#> log_k_m1        -2.301586  -Inf   Inf
+#> f_parent_ilr_1   0.000000  -Inf   Inf
+#> 
+#> Fixed parameter values:
+#>      value  type
+#> m1_0     0 state
+#> 
+#> Optimised, transformed parameters with symmetric confidence intervals:
+#>                Estimate Std. Error    Lower    Upper
+#> parent_0        99.6600   2.712000 94.14000 105.2000
+#> log_k_parent    -2.2980   0.008118 -2.31500  -2.2820
+#> log_k_m1        -5.2410   0.096690 -5.43800  -5.0450
+#> f_parent_ilr_1   0.0231   0.057990 -0.09474   0.1409
+#> 
+#> Parameter correlation:
+#>                parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#> parent_0        1.00000       0.6843 -0.08687        -0.7564
+#> log_k_parent    0.68435       1.0000 -0.12695        -0.5812
+#> log_k_m1       -0.08687      -0.1269  1.00000         0.5195
+#> f_parent_ilr_1 -0.75644      -0.5812  0.51952         1.0000
+#> 
+#> Residual standard error: 0.08396 on 34 degrees of freedom
+#> 
+#> Backtransformed parameters:
+#> Confidence intervals for internally transformed parameters are asymmetric.
+#> t-test (unrealistically) based on the assumption of normal distribution
+#> for estimators of untransformed parameters.
+#>                 Estimate t value    Pr(>t)    Lower     Upper
+#> parent_0       99.660000   36.75 2.957e-29 94.14000 1.052e+02
+#> k_parent        0.100400  123.20 5.927e-47  0.09878 1.021e-01
+#> k_m1            0.005295   10.34 2.447e-12  0.00435 6.444e-03
+#> f_parent_to_m1  0.508200   24.79 1.184e-23  0.46660 5.497e-01
+#> 
+#> Chi2 error levels in percent:
+#>          err.min n.optim df
+#> All data   6.461       4 15
+#> parent     6.520       2  7
+#> m1         4.744       2  8
+#> 
+#> Resulting formation fractions:
+#>                 ff
+#> parent_m1   0.5082
+#> parent_sink 0.4918
+#> 
+#> Estimated disappearance times:
+#>           DT50   DT90
+#> parent   6.902  22.93
+#> m1     130.916 434.89
+#> 
+#> Data:
+#>  time variable observed predicted   residual    err
+#>     0   parent    99.46  99.65571  -0.195715  99.46
+#>     0   parent   102.04  99.65571   2.384285 102.04
+#>     1   parent    93.50  90.13383   3.366170  93.50
+#>     1   parent    92.50  90.13383   2.366170  92.50
+#>     3   parent    63.23  73.73252 -10.502518  63.23
+#>     3   parent    68.99  73.73252  -4.742518  68.99
+#>     7   parent    52.32  49.34027   2.979728  52.32
+#>     7   parent    55.13  49.34027   5.789728  55.13
+#>    14   parent    27.27  24.42873   2.841271  27.27
+#>    14   parent    26.64  24.42873   2.211271  26.64
+#>    21   parent    11.50  12.09484  -0.594842  11.50
+#>    21   parent    11.64  12.09484  -0.454842  11.64
+#>    35   parent     2.85   2.96482  -0.114824   2.85
+#>    35   parent     2.91   2.96482  -0.054824   2.91
+#>    50   parent     0.69   0.65733   0.032670   0.69
+#>    50   parent     0.63   0.65733  -0.027330   0.63
+#>    75   parent     0.05   0.05339  -0.003386   0.05
+#>    75   parent     0.06   0.05339   0.006614   0.06
+#>     1       m1     4.84   4.82570   0.014301   4.84
+#>     1       m1     5.64   4.82570   0.814301   5.64
+#>     3       m1    12.91  13.06402  -0.154020  12.91
+#>     3       m1    12.96  13.06402  -0.104020  12.96
+#>     7       m1    22.97  25.04656  -2.076564  22.97
+#>     7       m1    24.47  25.04656  -0.576564  24.47
+#>    14       m1    41.69  36.53601   5.153988  41.69
+#>    14       m1    33.21  36.53601  -3.326012  33.21
+#>    21       m1    44.37  41.34639   3.023609  44.37
+#>    21       m1    46.44  41.34639   5.093609  46.44
+#>    35       m1    41.22  42.82669  -1.606690  41.22
+#>    35       m1    37.95  42.82669  -4.876690  37.95
+#>    50       m1    41.19  40.67342   0.516578  41.19
+#>    50       m1    40.01  40.67342  -0.663422  40.01
+#>    75       m1    40.09  35.91105   4.178947  40.09
+#>    75       m1    33.85  35.91105  -2.061053  33.85
+#>   100       m1    31.04  31.48161  -0.441612  31.04
+#>   100       m1    33.13  31.48161   1.648388  33.13
+#>   120       m1    25.15  28.32018  -3.170181  25.15
+#>   120       m1    33.31  28.32018   4.989819  33.31

+
# Manual weighting
 dw <- FOCUS_2006_D
 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)
-f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE,
+summary(f.w.man)
#> mkin version used for fitting:    0.9.47.4 
+#> R version used for fitting:       3.5.1 
+#> Date of fit:     Fri Sep 14 11:35:10 2018 
+#> Date of summary: Fri Sep 14 11:35:10 2018 
+#> 
+#> Equations:
+#> d_parent/dt = - k_parent * parent
+#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#> 
+#> Model predictions using solution type deSolve 
+#> 
+#> Fitted with method Port using 270 model solutions performed in 1.109 s
+#> 
+#> Weighting: manual
+#> 
+#> Starting values for parameters to be optimised:
+#>                   value   type
+#> parent_0       100.7500  state
+#> k_parent         0.1000 deparm
+#> k_m1             0.1001 deparm
+#> f_parent_to_m1   0.5000 deparm
+#> 
+#> Starting values for the transformed parameters actually optimised:
+#>                     value lower upper
+#> parent_0       100.750000  -Inf   Inf
+#> log_k_parent    -2.302585  -Inf   Inf
+#> log_k_m1        -2.301586  -Inf   Inf
+#> f_parent_ilr_1   0.000000  -Inf   Inf
+#> 
+#> Fixed parameter values:
+#>      value  type
+#> m1_0     0 state
+#> 
+#> Optimised, transformed parameters with symmetric confidence intervals:
+#>                Estimate Std. Error   Lower    Upper
+#> parent_0       99.49000    1.33200 96.7800 102.2000
+#> log_k_parent   -2.32100    0.03550 -2.3930  -2.2490
+#> log_k_m1       -5.24100    0.21280 -5.6730  -4.8100
+#> f_parent_ilr_1  0.04571    0.08966 -0.1361   0.2275
+#> 
+#> Parameter correlation:
+#>                parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#> parent_0        1.00000       0.5312 -0.09456        -0.3351
+#> log_k_parent    0.53123       1.0000 -0.17800        -0.3360
+#> log_k_m1       -0.09456      -0.1780  1.00000         0.7616
+#> f_parent_ilr_1 -0.33514      -0.3360  0.76156         1.0000
+#> 
+#> Residual standard error: 2.628 on 36 degrees of freedom
+#> 
+#> Backtransformed parameters:
+#> Confidence intervals for internally transformed parameters are asymmetric.
+#> t-test (unrealistically) based on the assumption of normal distribution
+#> for estimators of untransformed parameters.
+#>                 Estimate t value    Pr(>t)     Lower     Upper
+#> parent_0       99.490000   74.69 2.221e-41 96.780000 1.022e+02
+#> k_parent        0.098140   28.17 2.012e-26  0.091320 1.055e-01
+#> k_m1            0.005292    4.70 1.873e-05  0.003437 8.148e-03
+#> f_parent_to_m1  0.516200   16.30 1.686e-18  0.452000 5.798e-01
+#> 
+#> Chi2 error levels in percent:
+#>          err.min n.optim df
+#> All data   6.400       4 15
+#> parent     6.454       2  7
+#> m1         4.708       2  8
+#> 
+#> Resulting formation fractions:
+#>                 ff
+#> parent_m1   0.5162
+#> parent_sink 0.4838
+#> 
+#> Estimated disappearance times:
+#>           DT50   DT90
+#> parent   7.063  23.46
+#> m1     130.971 435.08
+#> 
+#> Data:
+#>  time variable observed predicted   residual err
+#>     0   parent    99.46  99.48598  -0.025979   1
+#>     0   parent   102.04  99.48598   2.554021   1
+#>     1   parent    93.50  90.18612   3.313880   1
+#>     1   parent    92.50  90.18612   2.313880   1
+#>     3   parent    63.23  74.11316 -10.883163   1
+#>     3   parent    68.99  74.11316  -5.123163   1
+#>     7   parent    52.32  50.05030   2.269705   1
+#>     7   parent    55.13  50.05030   5.079705   1
+#>    14   parent    27.27  25.17975   2.090250   1
+#>    14   parent    26.64  25.17975   1.460250   1
+#>    21   parent    11.50  12.66765  -1.167654   1
+#>    21   parent    11.64  12.66765  -1.027654   1
+#>    35   parent     2.85   3.20616  -0.356164   1
+#>    35   parent     2.91   3.20616  -0.296164   1
+#>    50   parent     0.69   0.73562  -0.045619   1
+#>    50   parent     0.63   0.73562  -0.105619   1
+#>    75   parent     0.05   0.06326  -0.013256   1
+#>    75   parent     0.06   0.06326  -0.003256   1
+#>     0       m1     0.00   0.00000   0.000000   2
+#>     0       m1     0.00   0.00000   0.000000   2
+#>     1       m1     4.84   4.78729   0.052713   2
+#>     1       m1     5.64   4.78729   0.852713   2
+#>     3       m1    12.91  12.98785  -0.077848   2
+#>     3       m1    12.96  12.98785  -0.027848   2
+#>     7       m1    22.97  24.99695  -2.026946   2
+#>     7       m1    24.47  24.99695  -0.526946   2
+#>    14       m1    41.69  36.66353   5.026472   2
+#>    14       m1    33.21  36.66353  -3.453528   2
+#>    21       m1    44.37  41.65681   2.713186   2
+#>    21       m1    46.44  41.65681   4.783186   2
+#>    35       m1    41.22  43.35031  -2.130314   2
+#>    35       m1    37.95  43.35031  -5.400314   2
+#>    50       m1    41.19  41.25637  -0.066368   2
+#>    50       m1    40.01  41.25637  -1.246368   2
+#>    75       m1    40.09  36.46057   3.629429   2
+#>    75       m1    33.85  36.46057  -2.610571   2
+#>   100       m1    31.04  31.96929  -0.929293   2
+#>   100       m1    33.13  31.96929   1.160707   2
+#>   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)
-# }

+summary(f.w.man.irls)
#> mkin version used for fitting:    0.9.47.4 
+#> R version used for fitting:       3.5.1 
+#> Date of fit:     Fri Sep 14 11:35:13 2018 
+#> Date of summary: Fri Sep 14 11:35:13 2018 
+#> 
+#> Equations:
+#> d_parent/dt = - k_parent * parent
+#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#> 
+#> Model predictions using solution type deSolve 
+#> 
+#> Fitted with method Port using 692 model solutions performed in 2.903 s
+#> 
+#> Weighting: manual
+#> 
+#> Iterative reweighting with method obs 
+#> Final mean squared residuals of observed variables:
+#>    parent        m1 
+#> 11.573406  7.407846 
+#> 
+#> Starting values for parameters to be optimised:
+#>                   value   type
+#> parent_0       100.7500  state
+#> k_parent         0.1000 deparm
+#> k_m1             0.1001 deparm
+#> f_parent_to_m1   0.5000 deparm
+#> 
+#> Starting values for the transformed parameters actually optimised:
+#>                     value lower upper
+#> parent_0       100.750000  -Inf   Inf
+#> log_k_parent    -2.302585  -Inf   Inf
+#> log_k_m1        -2.301586  -Inf   Inf
+#> f_parent_ilr_1   0.000000  -Inf   Inf
+#> 
+#> Fixed parameter values:
+#>      value  type
+#> m1_0     0 state
+#> 
+#> Optimised, transformed parameters with symmetric confidence intervals:
+#>                Estimate Std. Error    Lower   Upper
+#> parent_0       99.67000    1.79200 96.04000 103.300
+#> log_k_parent   -2.31200    0.04560 -2.40400  -2.220
+#> log_k_m1       -5.25100    0.12510 -5.50500  -4.998
+#> f_parent_ilr_1  0.03785    0.06318 -0.09027   0.166
+#> 
+#> Parameter correlation:
+#>                parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#> parent_0         1.0000       0.5083  -0.1979        -0.6148
+#> log_k_parent     0.5083       1.0000  -0.3894        -0.6062
+#> log_k_m1        -0.1979      -0.3894   1.0000         0.7417
+#> f_parent_ilr_1  -0.6148      -0.6062   0.7417         1.0000
+#> 
+#> Residual standard error: 1.054 on 36 degrees of freedom
+#> 
+#> Backtransformed parameters:
+#> Confidence intervals for internally transformed parameters are asymmetric.
+#> t-test (unrealistically) based on the assumption of normal distribution
+#> for estimators of untransformed parameters.
+#>                Estimate t value    Pr(>t)     Lower     Upper
+#> parent_0       99.67000  55.630 8.185e-37 96.040000 1.033e+02
+#> k_parent        0.09906  21.930 1.016e-22  0.090310 1.087e-01
+#> k_m1            0.00524   7.996 8.486e-10  0.004066 6.753e-03
+#> f_parent_to_m1  0.51340  23.000 2.039e-23  0.468100 5.584e-01
+#> 
+#> Chi2 error levels in percent:
+#>          err.min n.optim df
+#> All data   6.399       4 15
+#> parent     6.466       2  7
+#> m1         4.679       2  8
+#> 
+#> Resulting formation fractions:
+#>                 ff
+#> parent_m1   0.5134
+#> parent_sink 0.4866
+#> 
+#> Estimated disappearance times:
+#>           DT50   DT90
+#> parent   6.997  23.24
+#> m1     132.282 439.43
+#> 
+#> Data:
+#>  time variable observed predicted   residual err.ini   err
+#>     0   parent    99.46  99.67217 -2.122e-01       1 3.402
+#>     0   parent   102.04  99.67217  2.368e+00       1 3.402
+#>     1   parent    93.50  90.27152  3.228e+00       1 3.402
+#>     1   parent    92.50  90.27152  2.228e+00       1 3.402
+#>     3   parent    63.23  74.04648 -1.082e+01       1 3.402
+#>     3   parent    68.99  74.04648 -5.056e+00       1 3.402
+#>     7   parent    52.32  49.82092  2.499e+00       1 3.402
+#>     7   parent    55.13  49.82092  5.309e+00       1 3.402
+#>    14   parent    27.27  24.90288  2.367e+00       1 3.402
+#>    14   parent    26.64  24.90288  1.737e+00       1 3.402
+#>    21   parent    11.50  12.44765 -9.477e-01       1 3.402
+#>    21   parent    11.64  12.44765 -8.077e-01       1 3.402
+#>    35   parent     2.85   3.11002 -2.600e-01       1 3.402
+#>    35   parent     2.91   3.11002 -2.000e-01       1 3.402
+#>    50   parent     0.69   0.70375 -1.375e-02       1 3.402
+#>    50   parent     0.63   0.70375 -7.375e-02       1 3.402
+#>    75   parent     0.05   0.05913 -9.134e-03       1 3.402
+#>    75   parent     0.06   0.05913  8.661e-04       1 3.402
+#>     0       m1     0.00   0.00000  0.000e+00       2 2.722
+#>     0       m1     0.00   0.00000  0.000e+00       2 2.722
+#>     1       m1     4.84   4.81328  2.672e-02       2 2.722
+#>     1       m1     5.64   4.81328  8.267e-01       2 2.722
+#>     3       m1    12.91  13.04779 -1.378e-01       2 2.722
+#>     3       m1    12.96  13.04779 -8.779e-02       2 2.722
+#>     7       m1    22.97  25.07615 -2.106e+00       2 2.722
+#>     7       m1    24.47  25.07615 -6.062e-01       2 2.722
+#>    14       m1    41.69  36.70729  4.983e+00       2 2.722
+#>    14       m1    33.21  36.70729 -3.497e+00       2 2.722
+#>    21       m1    44.37  41.65050  2.719e+00       2 2.722
+#>    21       m1    46.44  41.65050  4.789e+00       2 2.722
+#>    35       m1    41.22  43.28866 -2.069e+00       2 2.722
+#>    35       m1    37.95  43.28866 -5.339e+00       2 2.722
+#>    50       m1    41.19  41.19339 -3.387e-03       2 2.722
+#>    50       m1    40.01  41.19339 -1.183e+00       2 2.722
+#>    75       m1    40.09  36.43820  3.652e+00       2 2.722
+#>    75       m1    33.85  36.43820 -2.588e+00       2 2.722
+#>   100       m1    31.04  31.98971 -9.497e-01       2 2.722
+#>   100       m1    33.13  31.98971  1.140e+00       2 2.722
+#>   120       m1    25.15  28.80897 -3.659e+00       2 2.722
+#>   120       m1    33.31  28.80897  4.501e+00       2 2.722

   
   
 
@@ -221,17 +221,35 @@ For the definition of model types and their parameters, the equations given
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.

-
# NOT RUN {
-# The above model used to be specified like this, before the advent of mkinsub()
+
# The above model used to be specified like this, before the advent of mkinsub()
 SFO_SFO <- mkinmod(
   parent = list(type = "SFO", to = "m1"),
-  m1 = list(type = "SFO"))
-
+  m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.

 # Show details of creating the C function
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"), verbose = TRUE)
-
+  m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
+#>  /usr/lib/R/bin/R CMD SHLIB file3c104e6e45e4.c 2> file3c104e6e45e4.c.err.txt 
+#> Program source:
+#>   1: #include <R.h>
+#>   2: 
+#>   3: 
+#>   4: static double parms [3];
+#>   5: #define k_parent_sink parms[0]
+#>   6: #define k_parent_m1 parms[1]
+#>   7: #define k_m1_sink parms[2]
+#>   8: 
+#>   9: void initpar(void (* odeparms)(int *, double *)) {
+#>  10:     int N = 3;
+#>  11:     odeparms(&N, parms);
+#>  12: }
+#>  13: 
+#>  14: 
+#>  15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
+#>  16: 
+#>  17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0];
+#>  18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1];
+#>  19: }
#> Successfully compiled differential equation model from auto-generated C code.

 # If we have several parallel metabolites 
 # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
 m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
@@ -241,8 +259,7 @@ For the definition of model types and their parameters, the equations given
 
 fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par,
                           synthetic_data_for_UBA_2014[[12]]$data,
-                          quiet = TRUE)
-# }

+                          quiet = TRUE)

   
   
 
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 6aa67e5b..2d878175 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -61,7 +61,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 6c2ba992..ffd6e89f 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.3
+        0.9.47.4
       
     
 
@@ -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 
-#>       0.035       0.000       0.036
+#> 0.035 0.000 0.035 diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 65de0664..a34f1dae 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -62,7 +62,7 @@ mkin - 0.9.47.3 + 0.9.47.4 diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png new file mode 100644 index 00000000..6f24b369 Binary files /dev/null and b/docs/reference/mmkin-1.png differ diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png new file mode 100644 index 00000000..1ed2b216 Binary files /dev/null and b/docs/reference/mmkin-2.png differ diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png new file mode 100644 index 00000000..952e6af3 Binary files /dev/null and b/docs/reference/mmkin-3.png differ diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png new file mode 100644 index 00000000..cad6ee11 Binary files /dev/null and b/docs/reference/mmkin-4.png differ diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png new file mode 100644 index 00000000..7ab171d1 Binary files /dev/null and b/docs/reference/mmkin-5.png differ diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 557da0d7..621571c1 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -62,7 +62,7 @@ mkin - 0.9.47.3 + 0.9.47.4 @@ -175,15 +175,12 @@

Examples

- 
# NOT RUN {
-m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
+    
m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
                            M1 = mkinsub("SFO", "M2"),
-                           M2 = mkinsub("SFO"), use_of_ff = "max")
-
+                           M2 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"),
                             M1 = mkinsub("SFO", "M2"),
-                            M2 = mkinsub("SFO"), use_of_ff = "max")
-
+                            M2 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)
 datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)
 names(datasets) <- paste("Dataset", 1:3)
@@ -191,23 +188,29 @@
 time_default <- system.time(fits.0 <- mmkin(models, datasets, quiet = TRUE))
 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
-time_default
-time_1
-
-endpoints(fits.0[["SFO_lin", 2]])
-
+time_default
#>        User      System verstrichen 
+#>       0.046       0.033       6.654 
time_1
#>        User      System verstrichen 
+#>      20.150       0.000      20.163 

+endpoints(fits.0[["SFO_lin", 2]])
#> $ff
+#>   parent_M1 parent_sink       M1_M2     M1_sink 
+#>   0.7340480   0.2659520   0.7505686   0.2494314 
+#> 
+#> $SFORB
+#> logical(0)
+#> 
+#> $distimes
+#>              DT50       DT90
+#> parent  0.8777689   2.915885
+#> M1      2.3257453   7.725959
+#> M2     33.7200874 112.015706
+#> 

 # plot.mkinfit handles rows or columns of mmkin result objects
-plot(fits.0[1, ])
-plot(fits.0[1, ], obs_var = c("M1", "M2"))
-plot(fits.0[, 1])
-# Use double brackets to extract a single mkinfit object, which will be plotted
+plot(fits.0[1, ])
plot(fits.0[1, ], obs_var = c("M1", "M2"))
plot(fits.0[, 1])
# Use double brackets to extract a single mkinfit object, which will be plotted
 # by plot.mkinfit and can be plotted using plot_sep
-plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)
-plot_sep(fits.0[[1, 1]])
+plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)
plot_sep(fits.0[[1, 1]])
 # Plotting with mmkin (single brackets, extracting an mmkin object) does not
 # allow to plot the observed variables separately
-plot(fits.0[1, 1])
-# }

+plot(fits.0[1, 1])
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 0599907d..478a5682 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 - 0.9.47.3 + 0.9.47.4 diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 86bb58e5..f59325f9 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -61,7 +61,7 @@ mkin - 0.9.47.3 + 0.9.47.4 diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index bc4c644a..299fdfbb 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -61,7 +61,7 @@ mkin - 0.9.47.3 + 0.9.47.4 diff --git a/docs/reference/schaefer07_complex_case-1.png b/docs/reference/schaefer07_complex_case-1.png new file mode 100644 index 00000000..6a621369 Binary files /dev/null and b/docs/reference/schaefer07_complex_case-1.png differ diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index b212aa53..9fd60805 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -63,7 +63,7 @@ mkin - 0.9.47.3 + 0.9.47.4 @@ -159,12 +159,22 @@ A1 = list(type = "SFO", to = "A2"), B1 = list(type = "SFO"), C1 = list(type = "SFO"), - A2 = list(type = "SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
# NOT RUN { - fit <- mkinfit(model, data, quiet = TRUE) - plot(fit) - endpoints(fit) - -# }
# Compare with the results obtained in the original publication + A2 = list(type = "SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
fit <- mkinfit(model, data, quiet = TRUE) + plot(fit)
endpoints(fit)
#> $ff +#> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink +#> 0.3809621 0.1954665 0.4235714 0.0000000 0.4479674 0.5520326 +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 +#> parent 13.95078 46.34350 +#> A1 49.75342 165.27728 +#> B1 37.26913 123.80536 +#> C1 11.23133 37.30968 +#> A2 28.50591 94.69457 +#>
# Compare with the results obtained in the original publication print(schaefer07_complex_results)
#> compound parameter KinGUI ModelMaker deviation #> 1 parent degradation rate 0.0496 0.0506 2.0 #> 2 parent DT50 13.9900 13.6900 2.2 diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index c8000ae5..6db7d74c 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 - 0.9.47.3 + 0.9.47.4
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 28447e64..1d0a7c52 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -64,7 +64,7 @@ mkin - 0.9.47.3 + 0.9.47.4 @@ -204,17 +204,17 @@

Examples

- 
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.3 
+    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.4 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 06:39:24 2018 
-#> Date of summary: Fri Sep 14 06:39:24 2018 
+#> Date of fit:     Fri Sep 14 11:35:59 2018 
+#> Date of summary: Fri Sep 14 11:35:59 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 0.076 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index dd44a450..25cfc012 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
-        0.9.47.3
+        0.9.47.4
       
     

 
@@ -176,8 +176,7 @@ Compare also the code in the example section to see the degradation models." />
     
 
     
Examples

-    
# NOT RUN {
-# The data have been generated using the following kinetic models
+    
# The data have been generated using the following kinetic models
 m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
                            M1 = list(type = "SFO", to = "M2"),
                            M2 = list(type = "SFO"), use_of_ff = "max")
@@ -275,8 +274,10 @@ fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data,
                quiet = TRUE)
 plot_sep(fit)
 summary(fit)
-# }
-

+
#> Error: <text>:67:43: Unerwartete(s) SPECIAL
+#> 66: 
+#> 67:   d_rep[d_rep$time == 0 & d_rep$name <!-- %in%
+#>                                               ^
@@ -146,35 +146,63 @@

Examples

- 
  
# NOT RUN {
-  # This is a level P-II evaluation of the dataset according to the FOCUS kinetics
+    
  
  # This is a level P-II evaluation of the dataset according to the FOCUS kinetics
   # guidance. Due to the strong correlation of the parameter estimates, the
   # covariance matrix is not returned. Note that level P-II evaluations are
   # generally considered deprecated due to the frequent occurrence of such
   # large parameter correlations, among other reasons (e.g. the adequacy of the
   # model).
   m_ws <- mkinmod(parent_w = mkinsub("SFO", "parent_s"),
-                  parent_s = mkinsub("SFO", "parent_w"))
-  f_river <- mkinfit(m_ws, test_data_from_UBA_2014[[1]]$data, quiet = TRUE)
-  plot_sep(f_river)
-
-  summary(f_river)$bpar
-  mkinerrmin(f_river)
-
+                  parent_s = mkinsub("SFO", "parent_w"))
#> Successfully compiled differential equation model from auto-generated C code.
  f_river <- mkinfit(m_ws, test_data_from_UBA_2014[[1]]$data, quiet = TRUE)
+  plot_sep(f_river)

+  summary(f_river)$bpar
#>                         Estimate se_notrans      t value       Pr(>t) Lower
+#> parent_w_0          9.598567e+01 2.33959800 4.102657e+01 9.568967e-19    NA
+#> k_parent_w_sink     3.603743e-01 0.03497750 1.030303e+01 4.989002e-09    NA
+#> k_parent_w_parent_s 6.031371e-02 0.01746024 3.454346e+00 1.514723e-03    NA
+#> k_parent_s_sink     5.108539e-11 0.10382001 4.920572e-10 5.000000e-01    NA
+#> k_parent_s_parent_w 7.419672e-02 0.11338240 6.543936e-01 2.608069e-01    NA
+#>                     Upper
+#> parent_w_0             NA
+#> k_parent_w_sink        NA
+#> k_parent_w_parent_s    NA
+#> k_parent_s_sink        NA
+#> k_parent_s_parent_w    NA
  mkinerrmin(f_river)
#>             err.min n.optim df
+#> All data 0.09246946       5  6
+#> parent_w 0.06377096       3  3
+#> parent_s 0.20882324       2  3

   # This is the evaluation used for the validation of software packages
   # in the expertise from 2014
   m_soil <- mkinmod(parent = mkinsub("SFO", c("M1", "M2")),
                     M1 = mkinsub("SFO", "M3"),
                     M2 = mkinsub("SFO", "M3"),
                     M3 = mkinsub("SFO"),
-                    use_of_ff = "max")
-
+                    use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

   f_soil <- mkinfit(m_soil, test_data_from_UBA_2014[[3]]$data, quiet = TRUE)
-  plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright"))
-  summary(f_soil)$bpar
-  mkinerrmin(f_soil)
-
-# }

+  plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright"))
  summary(f_soil)$bpar
#>                   Estimate  se_notrans    t value       Pr(>t)        Lower
+#> parent_0       76.55425584 0.943443794 81.1434198 4.422336e-30 74.602593773
+#> k_parent        0.12081956 0.004815515 25.0896457 1.639665e-18  0.111257517
+#> k_M1            0.84258651 0.930121548  0.9058886 1.871938e-01  0.085876516
+#> k_M2            0.04210878 0.013729902  3.0669396 2.729137e-03  0.021450630
+#> k_M3            0.01122919 0.008044865  1.3958206 8.804912e-02  0.002550984
+#> f_parent_to_M1  0.32240199 0.278620579  1.1571363 1.295467e-01           NA
+#> f_parent_to_M2  0.16099854 0.030548888  5.2701931 1.196190e-05           NA
+#> f_M1_to_M3      0.27921500 0.314732842  0.8871492 1.920908e-01  0.015016983
+#> f_M2_to_M3      0.55641333 0.650246995  0.8556954 2.004966e-01  0.005360555
+#>                      Upper
+#> parent_0       78.50591790
+#> k_parent        0.13120341
+#> k_M1            8.26712661
+#> k_M2            0.08266188
+#> k_M3            0.04942981
+#> f_parent_to_M1          NA
+#> f_parent_to_M2          NA
+#> f_M1_to_M3      0.90777163
+#> f_M2_to_M3      0.99658633
  mkinerrmin(f_soil)
#>             err.min n.optim df
+#> All data 0.09649963       9 20
+#> parent   0.04721283       2  6
+#> M1       0.26551209       2  5
+#> M2       0.20327575       2  5
+#> M3       0.05196549       3  4
@@ -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: 0.9.47.3 +summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting: 0.9.47.4 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 06:39:25 2018 -#> Date of summary: Fri Sep 14 06:39:25 2018 +#> Date of fit: Fri Sep 14 11:36:07 2018 +#> Date of summary: Fri Sep 14 11:36:07 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 0.642 s +#> Fitted with method Port using 153 model solutions performed in 0.627 s #> #> Weighting: none #> @@ -273,10 +273,82 @@ The transformation of sets of formation fractions is fragile, as it supposes #> DT50 DT90 #> parent 7.023 23.33 #> m1 131.761 437.70
-
# NOT RUN { -fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) -summary(fit.2, data=FALSE) -# }
+
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) +summary(fit.2, data=FALSE)
#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:36:08 2018 +#> Date of summary: Fri Sep 14 11:36:08 2018 +#> +#> Equations: +#> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent +#> d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 350 model solutions performed in 1.437 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent_sink 0.1000 deparm +#> k_parent_m1 0.1001 deparm +#> k_m1_sink 0.1002 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.7500 -Inf Inf +#> k_parent_sink 0.1000 0 Inf +#> k_parent_m1 0.1001 0 Inf +#> k_m1_sink 0.1002 0 Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.600000 1.6140000 96.330000 1.029e+02 +#> k_parent_sink 0.047920 0.0037500 0.040310 5.553e-02 +#> k_parent_m1 0.050780 0.0020940 0.046530 5.502e-02 +#> k_m1_sink 0.005261 0.0007159 0.003809 6.713e-03 +#> +#> Parameter correlation: +#> parent_0 k_parent_sink k_parent_m1 k_m1_sink +#> parent_0 1.00000 0.6075 -0.06625 -0.1701 +#> k_parent_sink 0.60752 1.0000 -0.08740 -0.6253 +#> k_parent_m1 -0.06625 -0.0874 1.00000 0.4716 +#> k_m1_sink -0.17006 -0.6253 0.47164 1.0000 +#> +#> Residual standard error: 3.211 on 36 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 +#> k_parent_sink 0.047920 12.780 3.050e-15 0.040310 5.553e-02 +#> k_parent_m1 0.050780 24.250 3.407e-24 0.046530 5.502e-02 +#> k_m1_sink 0.005261 7.349 5.758e-09 0.003809 6.713e-03 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.398 4 15 +#> parent 6.827 3 6 +#> m1 4.490 1 9 +#> +#> Resulting formation fractions: +#> ff +#> parent_sink 0.4855 +#> parent_m1 0.5145 +#> m1_sink 1.0000 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.023 23.33 +#> m1 131.761 437.70
initials <- fit$start$value names(initials) <- rownames(fit$start) transformed <- fit$start_transformed$value @@ -284,29 +356,160 @@ The transformation of sets of formation fractions is fragile, as it supposes transform_odeparms(initials, SFO_SFO)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 100.750000 -2.302585 -2.301586 -2.300587
backtransform_odeparms(transformed, SFO_SFO)
#> parent_0 k_parent_sink k_parent_m1 k_m1_sink #> 100.7500 0.1000 0.1001 0.1002
-
# NOT RUN { -# The case of formation fractions +
# The case of formation fractions SFO_SFO.ff <- mkinmod( parent = list(type = "SFO", to = "m1", sink = TRUE), m1 = list(type = "SFO"), - use_of_ff = "max") - + 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) -initials <- c("f_parent_to_m1" = 0.5) +summary(fit.ff, data = FALSE)
#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:36:09 2018 +#> Date of summary: Fri Sep 14 11:36:09 2018 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 186 model solutions performed in 0.773 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.60000 1.61400 96.3300 102.9000 +#> log_k_parent -2.31600 0.04187 -2.4010 -2.2310 +#> log_k_m1 -5.24800 0.13610 -5.5230 -4.9720 +#> f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5178 -0.1701 -0.5489 +#> log_k_parent 0.5178 1.0000 -0.3285 -0.5451 +#> log_k_m1 -0.1701 -0.3285 1.0000 0.7466 +#> f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000 +#> +#> Residual standard error: 3.211 on 36 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 +#> k_parent 0.098700 23.880 5.700e-24 0.090660 1.074e-01 +#> k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03 +#> f_parent_to_m1 0.514500 22.490 4.375e-23 0.468100 5.606e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.398 4 15 +#> parent 6.459 2 7 +#> m1 4.690 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5145 +#> parent_sink 0.4855 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.023 23.33 +#> m1 131.761 437.70
initials <- c("f_parent_to_m1" = 0.5) transformed <- transform_odeparms(initials, SFO_SFO.ff) -backtransform_odeparms(transformed, SFO_SFO.ff) - +backtransform_odeparms(transformed, SFO_SFO.ff)
#> f_parent_to_m1 +#> 0.5
# And without sink SFO_SFO.ff.2 <- mkinmod( parent = list(type = "SFO", to = "m1", sink = FALSE), m1 = list(type = "SFO"), - use_of_ff = "max") - + 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) -# } +summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:36:10 2018 +#> Date of summary: Fri Sep 14 11:36:10 2018 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 104 model solutions performed in 0.424 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 84.790 2.96500 78.78 90.800 +#> log_k_parent -2.756 0.08088 -2.92 -2.593 +#> log_k_m1 -4.214 0.11150 -4.44 -3.988 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 +#> parent_0 1.0000 0.11058 0.46156 +#> log_k_parent 0.1106 1.00000 0.06274 +#> log_k_m1 0.4616 0.06274 1.00000 +#> +#> Residual standard error: 8.333 on 37 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 84.79000 28.600 3.939e-27 78.78000 90.80000 +#> k_parent 0.06352 12.360 5.237e-15 0.05392 0.07483 +#> k_m1 0.01478 8.966 4.114e-11 0.01179 0.01853 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 19.66 3 16 +#> parent 17.56 2 7 +#> m1 18.71 1 9 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 10.91 36.25 +#> m1 46.89 155.75