From 6653ff2507f45eae909f491a9af3f1eb5358a600 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 1 Mar 2018 14:32:46 +0100 Subject: Static documentation rebuilt using current pkgdown::build_site() --- docs/reference/DFOP.solution-1.png | Bin 0 -> 17865 bytes docs/reference/DFOP.solution-2.png | Bin 6748 -> 0 bytes docs/reference/DFOP.solution.html | 24 +- docs/reference/Extract.mmkin.html | 57 +- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 25 +- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 25 +- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 25 +- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 25 +- docs/reference/FOCUS_2006_datasets.html | 21 +- docs/reference/FOMC.solution-1.png | Bin 0 -> 17331 bytes docs/reference/FOMC.solution-2.png | Bin 6774 -> 0 bytes docs/reference/FOMC.solution.html | 29 +- docs/reference/HS.solution-1.png | Bin 0 -> 17211 bytes docs/reference/HS.solution-2.png | Bin 6548 -> 0 bytes docs/reference/HS.solution.html | 24 +- 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delete mode 100644 docs/reference/FOMC.solution-2.png create mode 100644 docs/reference/HS.solution-1.png delete mode 100644 docs/reference/HS.solution-2.png create mode 100644 docs/reference/IORE.solution-1.png delete mode 100644 docs/reference/IORE.solution-2.png delete mode 100644 docs/reference/SFO.solution-2.png delete mode 100644 docs/reference/SFORB.solution-2.png create mode 100644 docs/reference/add_err-1.png create mode 100644 docs/reference/add_err-2.png create mode 100644 docs/reference/add_err-3.png delete mode 100644 docs/reference/add_err-4.png delete mode 100644 docs/reference/add_err-6.png delete mode 100644 docs/reference/add_err-8.png create mode 100644 docs/reference/mkinparplot-1.png delete mode 100644 docs/reference/mkinparplot-4.png create mode 100644 docs/reference/mkinresplot-1.png delete mode 100644 docs/reference/mkinresplot-4.png delete mode 100644 docs/reference/mmkin-12.png delete mode 100644 docs/reference/mmkin-14.png delete mode 100644 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docs/reference/synthetic_data_for_UBA_2014-10.png delete mode 100644 docs/reference/test_data_from_UBA_2014-12.png delete mode 100644 docs/reference/test_data_from_UBA_2014-16.png delete mode 100644 docs/reference/test_data_from_UBA_2014-4.png delete mode 100644 docs/reference/test_data_from_UBA_2014-6.png delete mode 100644 docs/reference/twa.html (limited to 'docs/reference') diff --git a/docs/reference/DFOP.solution-1.png b/docs/reference/DFOP.solution-1.png new file mode 100644 index 00000000..1549a73b Binary files /dev/null and b/docs/reference/DFOP.solution-1.png differ diff --git a/docs/reference/DFOP.solution-2.png b/docs/reference/DFOP.solution-2.png deleted file mode 100644 index 0902b9df..00000000 Binary files a/docs/reference/DFOP.solution-2.png and /dev/null differ diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 30b9d057..ff1ad823 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -18,12 +18,20 @@ + + + + + + + @@ -69,6 +77,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +94,7 @@ @@ -146,11 +152,11 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    - 
      plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim=c(0,100))
    + 
      plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim=c(0,100))
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 5d4eca29..11738484 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -18,12 +18,19 @@ + + + + + + + @@ -69,6 +76,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +93,7 @@ @@ -147,16 +152,16 @@ cores = 1, quiet = TRUE) fits["FOMC", ]
    #> dataset #> model B C -#> FOMC List,42 List,42 +#> FOMC List,45 List,45 #> attr(,"class") #> [1] "mmkin"
    fits[, "B"]
    #> dataset #> model B -#> SFO List,42 -#> FOMC List,42 +#> SFO List,45 +#> FOMC List,45 #> attr(,"class") #> [1] "mmkin"
    fits["SFO", "B"]
    #> dataset #> model B -#> SFO List,42 +#> SFO List,45 #> attr(,"class") #> [1] "mmkin"
    head( @@ -164,7 +169,7 @@ fits[["FOMC", "B"]] )
    #> $par #> parent_0 log_alpha log_beta -#> 99.666192 2.549849 5.050586 +#> 99.666193 2.549849 5.050586 #> #> $ssr #> [1] 28.58291 @@ -180,7 +185,7 @@ #> 25 78 #> #> $counts -#> [1] "both X-convergence and relative convergence (5)" +#> [1] "relative convergence (4)" #>
    head( # The same can be achieved by @@ -258,7 +263,7 @@ #> #> $time #> user system elapsed -#> 0.064 0.000 0.063 +#> 0.058 0.000 0.057 #> #> $mkinmod #> <mkinmod> model generated with @@ -398,7 +403,7 @@ #> { #> assign("calls", calls + 1, inherits = TRUE) #> if (trace_parms) -#> cat(P, "\\n") +#> cat(P, "\n") #> if (length(state.ini.optim) > 0) { #> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) #> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) @@ -420,7 +425,7 @@ #> if (mC$model < cost.old) { #> if (!quiet) #> cat("Model cost at call ", calls, ": ", mC$model, -#> "\\n") +#> "\n") #> if (plot) { #> outtimes_plot = seq(min(observed$time), max(observed$time), #> length.out = 100) @@ -447,8 +452,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x560110508c60> -#> <environment: 0x56010f8d8c30> +#> <bytecode: 0x55555ad80908> +#> <environment: 0x55555b1b4b90> #> #> $cost_notrans #> function (P) @@ -470,8 +475,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x56010fede550> -#> <environment: 0x56010f8d8c30> +#> <bytecode: 0x55555b174428> +#> <environment: 0x55555b1b4b90> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -512,6 +517,10 @@ #> $weight.ini #> [1] "none" #> +#> $tc.ini +#> sigma_low rsd_high +#> 0.50 0.07 +#> #> $reweight.tol #> [1] 1e-08 #> @@ -534,7 +543,13 @@ #> 99.17407 #> #> $date -#> [1] "Sat Jul 29 15:14:04 2017" +#> [1] "Thu Mar 1 14:26:09 2018" +#> +#> $version +#> [1] "0.9.47.1" +#> +#> $Rversion +#> [1] "3.4.3" #> #> attr(,"class") #> [1] "mkinfit" "modFit" @@ -563,7 +578,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    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 d79aaff6..5fb3ccfe 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -18,12 +18,23 @@ + + + + + + + @@ -69,6 +80,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +97,7 @@ @@ -132,7 +141,7 @@ in this fit.

    Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    @@ -158,7 +167,7 @@ in this fit.

    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    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 e0da5a8d..c1665dee 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -18,12 +18,23 @@ + + + + + + + @@ -69,6 +80,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +97,7 @@ @@ -131,7 +140,7 @@ in this fit.

    Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    @@ -157,7 +166,7 @@ in this fit.

    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    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 720073f2..db3d228d 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -18,12 +18,23 @@ + + + + + + + @@ -69,6 +80,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +97,7 @@ @@ -132,7 +141,7 @@ in this fit.

    Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    @@ -158,7 +167,7 @@ in this fit.

    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    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 b12abf8c..cc4fcb1d 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -18,12 +18,23 @@ + + + + + + + @@ -69,6 +80,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +97,7 @@ @@ -130,7 +139,7 @@ in this fit.

    Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    @@ -156,7 +165,7 @@ in this fit.

    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 65bc572a..4548c983 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -18,12 +18,19 @@ + + + + + + + @@ -69,6 +76,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +93,7 @@ @@ -123,7 +128,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    @@ -158,7 +163,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/FOMC.solution-1.png b/docs/reference/FOMC.solution-1.png new file mode 100644 index 00000000..58178df5 Binary files /dev/null and b/docs/reference/FOMC.solution-1.png differ diff --git a/docs/reference/FOMC.solution-2.png b/docs/reference/FOMC.solution-2.png deleted file mode 100644 index a673bc0e..00000000 Binary files a/docs/reference/FOMC.solution-2.png and /dev/null differ diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 9af30b7a..810b0eba 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -18,12 +18,23 @@ + + - + + + + + + @@ -69,6 +80,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +97,7 @@ @@ -152,14 +161,14 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A new model based on spatial variability. Environmental Science and Technology 24, 1032-1038

    Examples

    - 
      plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))
    + 
      plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/HS.solution-1.png b/docs/reference/HS.solution-1.png new file mode 100644 index 00000000..e259134e Binary files /dev/null and b/docs/reference/HS.solution-1.png differ diff --git a/docs/reference/HS.solution-2.png b/docs/reference/HS.solution-2.png deleted file mode 100644 index 2e516447..00000000 Binary files a/docs/reference/HS.solution-2.png and /dev/null differ diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 8f6bbbe2..79358efb 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -18,12 +18,20 @@ + + + + + + + @@ -69,6 +77,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +94,7 @@ @@ -147,11 +153,11 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    - 
      plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))
    + 
      plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/IORE.solution-1.png b/docs/reference/IORE.solution-1.png new file mode 100644 index 00000000..674c25d3 Binary files /dev/null and b/docs/reference/IORE.solution-1.png differ diff --git a/docs/reference/IORE.solution-2.png b/docs/reference/IORE.solution-2.png deleted file mode 100644 index a83d49c7..00000000 Binary files a/docs/reference/IORE.solution-2.png and /dev/null differ diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 45e090c0..f705ab2f 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -18,12 +18,20 @@ + + + + + + + @@ -86,12 +94,7 @@ @@ -154,7 +157,7 @@

    Examples

      plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2,
-                                       ylim = c(0, 100))
      fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
+                                       ylim = c(0, 100))
      fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
   fit.iore <- mkinfit("IORE", FOCUS_2006_C, quiet = TRUE)
   fit.iore.deS <- mkinfit("IORE", FOCUS_2006_C, solution_type = "deSolve", quiet = TRUE)
 
@@ -191,7 +194,7 @@
 
    
 
 
    
-  
    Site built with pkgdown.
    
+  
    Site built with pkgdown.
    
 
    
 
       
diff --git a/docs/reference/SFO.solution-2.png b/docs/reference/SFO.solution-2.png
deleted file mode 100644
index 9626091f..00000000
Binary files a/docs/reference/SFO.solution-2.png and /dev/null differ
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index ef9b8eb7..a7934a35 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -18,12 +18,19 @@
 
 
 
+
+
 
 
 
 
 
+  
+  
+
 
+
+
 
 
 
@@ -69,6 +76,9 @@
     
  • 
       Example evaluation of FOCUS Laboratory Data L1 to L3
     
    • 
+    
  • 
+      Example evaluation of FOCUS Example Dataset Z
+    
    • 
     
  • 
       Performance benefit by using compiled model definitions in mkin
     
    • 
@@ -83,12 +93,7 @@
       
       
       
     
   
@@ -136,11 +141,13 @@
   Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
   Registration” Report of the FOCUS Work Group on Degradation Kinetics,
   EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics
    
+  http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics
    
     
 
     
    Examples
    
-    
      plot(function(x) SFO.solution(x, 100, 3), 0, 2)
    
+    
      
    # NOT RUN {
+plot(function(x) SFO.solution(x, 100, 3), 0, 2)
+# }
    
   
   
 
 
    
-  
    Site built with pkgdown.
    
+  
    Site built with pkgdown.
    
 
    
 
       
diff --git a/docs/reference/SFORB.solution-2.png b/docs/reference/SFORB.solution-2.png
deleted file mode 100644
index 63a50bf9..00000000
Binary files a/docs/reference/SFORB.solution-2.png and /dev/null differ
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index ebe67733..aaae7cdd 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -18,12 +18,23 @@
 
 
 
+
+
 
 
 
 
 
+  
+  
+
 
+
+
 
 
 
@@ -69,6 +80,9 @@
     
  • 
       Example evaluation of FOCUS Laboratory Data L1 to L3
     
    • 
+    
  • 
+      Example evaluation of FOCUS Example Dataset Z
+    
    • 
     
  • 
       Performance benefit by using compiled model definitions in mkin
     
    • 
@@ -83,12 +97,7 @@
       
       
       
     
   
@@ -149,11 +158,13 @@
   Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
   Registration” Report of the FOCUS Work Group on Degradation Kinetics,
   EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics
    
+  http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics
    
     
 
     
    Examples
    
-    
      plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)
    
+    
      
    # NOT RUN {
+plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)
+# }
    
   
   
 
 
    
-  
    Site built with pkgdown.
    
+  
    Site built with pkgdown.
    
 
    
 
       
diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png
new file mode 100644
index 00000000..4f9b1534
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diff --git a/docs/reference/add_err-6.png b/docs/reference/add_err-6.png
deleted file mode 100644
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diff --git a/docs/reference/add_err-8.png b/docs/reference/add_err-8.png
deleted file mode 100644
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diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index d56a8728..42bec993 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -18,12 +18,21 @@
 
 
 
+
+
 
 
 
 
 
-
+  
+  
+
+
+
+
 
 
 
@@ -195,14 +204,14 @@
                    d_SFO_SFO_err, cores = 1,
                    quiet = TRUE, method.modFit = "Marq")
 
-plot(f_SFO_SFO)
    
+plot(f_SFO_SFO)
    
 # We would like to inspect the fit for dataset 3 more closely
 # Using double brackets makes the returned object an mkinfit object
 # instead of a list of mkinfit objects, so plot.mkinfit is used
-plot(f_SFO_SFO[[3]], show_residuals = TRUE)
    
+plot(f_SFO_SFO[[3]], show_residuals = TRUE)
    
 # If we use single brackets, we should give two indices (model and dataset),
 # and plot.mmkin is used
-plot(f_SFO_SFO[1, 3])
    
+plot(f_SFO_SFO[1, 3])
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index ed235a47..c45a0b7c 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -18,12 +18,22 @@ + + + + + + + @@ -86,12 +96,7 @@ @@ -171,7 +176,7 @@ with the advantage that the SFORB model can also be used for metabolites.

    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 4af50f48..2d46b4de 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -18,12 +18,19 @@ + + + + + + + @@ -86,12 +93,7 @@ @@ -152,7 +154,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 6c3979c5..2c51001f 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -18,12 +18,19 @@ + + + + + + + @@ -86,12 +93,7 @@ @@ -176,7 +178,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/index.html b/docs/reference/index.html index 4675748c..218194ad 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -18,12 +18,16 @@ + + - + + + @@ -442,7 +446,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 0e99e579..5d6baf6a 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -18,12 +18,23 @@ + + + + + + + @@ -86,12 +97,7 @@ @@ -139,7 +145,7 @@ guidance.

    Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    @@ -172,7 +178,7 @@ guidance.

    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 0111deb3..ec7f8ccd 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -18,12 +18,21 @@ + + + + + + + @@ -69,6 +78,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +95,7 @@ @@ -127,108 +134,25 @@

    Source

    McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 - http://dx.doi.org/10.1021/jf00103a026

    + http://dx.doi.org/10.1021/jf00103a026

    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.
    
+                         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)
    #> mkin version:    0.9.46 
-#> R version:       3.4.1 
-#> Date of fit:     Sat Jul 29 15:14:14 2017 
-#> Date of summary: Sat Jul 29 15:14:14 2017 
-#> 
-#> 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 612 model solutions performed in 3.558 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    -26.8400         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 7.499e-02    NA    NA
-#> k_phenol_sink    2.212e-12 7.870e-12 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    5.462e-12
-#> 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 ...
+    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:    0.9.46 
-#> R version:       3.4.1 
-#> Date of fit:     Sat Jul 29 15:14:15 2017 
-#> Date of summary: Sat Jul 29 15:14:15 2017 
+  summary(fit.2, data = FALSE)
    #> mkin version used for fitting:    0.9.47.1 
+#> R version used for fitting:       3.4.3 
+#> Date of fit:     Thu Mar  1 14:26:15 2018 
+#> Date of summary: Thu Mar  1 14:26:15 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -238,7 +162,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.431 s
+#> Fitted with method Port using 246 model solutions performed in 1.359 s
 #> 
 #> Weighting: none
 #> 
@@ -340,7 +264,7 @@
 
    
 
 
    
-  
    Site built with pkgdown.
    
+  
    Site built with pkgdown.
    
 
    
 
       
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index 042bdced..a5432dac 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -18,12 +18,21 @@
 
 
 
+
+
 
 
 
 
 
+  
+  
+
 
+
+
 
 
 
@@ -86,12 +95,7 @@
       
       
       
     
    
   
@@ -186,7 +190,7 @@
 
 
 
    
-  
    Site built with pkgdown.
    
+  
    Site built with pkgdown.
    
 
    
 
       
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index ddf28dd9..6798efa6 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -18,12 +18,20 @@
 
 
 
+
+
 
 
 
 
 
+  
+  
+
 
+
+
 
 
 
@@ -86,12 +94,7 @@
       
       
       
     
   
@@ -165,7 +168,7 @@
 
 
 
    
-  
    Site built with pkgdown.
    
+  
    Site built with pkgdown.
    
 
    
 
       
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index 2d8d64a5..ab06e903 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -18,12 +18,19 @@
 
 
 
+
+
 
 
 
 
 
+  
+  
+
 
+
+
 
 
 
@@ -86,12 +93,7 @@
       
       
       
     
   
@@ -154,7 +156,7 @@ in order to be compatible with mkinfit
    
 
 
 
    
-  
    Site built with pkgdown.
    
+  
    Site built with pkgdown.
    
 
    
 
       
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 67b7a35e..496cce15 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -18,12 +18,20 @@
 
 
 
+
+
 
 
 
 
 
+  
+  
+
 
+
+
 
 
 
@@ -69,6 +77,9 @@
     
  • 
       Example evaluation of FOCUS Laboratory Data L1 to L3
     
    • 
+    
  • 
+      Example evaluation of FOCUS Example Dataset Z
+    
    • 
     
  • 
       Performance benefit by using compiled model definitions in mkin
     
    • 
@@ -83,12 +94,7 @@
       
       
       
     
   
@@ -146,7 +152,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.
    
   Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
   Registration” Report of the FOCUS Work Group on Degradation Kinetics,
   EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics
    
+  http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics
    
     
 
     
    Examples
    
@@ -186,7 +192,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.
    
 
 
 
    
-  
    Site built with pkgdown.
    
+  
    Site built with pkgdown.
    
 
    
 
       
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 0102aecb..4fb5ef9a 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -18,12 +18,29 @@
 
 
 
+
+
 
 
 
 
 
+  
+  
+
 
+
+
 
 
 
@@ -395,17 +412,17 @@
     
    Examples
    
     
    # Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
    #> mkin version:    0.9.47.1 
-#> R version:       3.4.3 
-#> Date of fit:     Tue Jan 30 10:05:48 2018 
-#> Date of summary: Tue Jan 30 10:05:48 2018 
+summary(fit)
    #> mkin version used for fitting:    0.9.47.1 
+#> R version used for fitting:       3.4.3 
+#> Date of fit:     Thu Mar  1 14:26:18 2018 
+#> Date of summary: Thu Mar  1 14:26:18 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 0.31 s
+#> Fitted with method Port using 64 model solutions performed in 0.135 s
 #> 
 #> Weighting: none
 #> 
@@ -474,7 +491,7 @@
   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 elapsed 
-#>   1.196   0.000   1.195 
    coef(fit)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>    0.84    0.00    0.84 
    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 
@@ -486,92 +503,19 @@
 #>              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
 print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D,
-                           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 :  874.2614 
-#> Model cost at call  33 :  874.2611 
-#> Model cost at call  35 :  616.2379 
-#> Model cost at call  37 :  616.2374 
-#> Model cost at call  40 :  467.4387 
-#> Model cost at call  42 :  467.4382 
-#> Model cost at call  46 :  398.2913 
-#> Model cost at call  48 :  398.2912 
-#> Model cost at call  49 :  398.2911 
-#> Model cost at call  51 :  395.0711 
-#> Model cost at call  54 :  395.071 
-#> 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  147 :  371.2134 
-#> Model cost at call  151 :  371.2134 
-#> Model cost at call  152 :  371.2134 
-#> Model cost at call  153 :  371.2134 
-#> Optimisation by method Port successfully terminated.
-#>    user  system elapsed 
-#>   1.008   0.000   1.006 
    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     131.760712 437.69961
-#> 
    
-
-# Use stepwise fitting, using optimised parameters from parent only fit, FOMC
-
+                           solution_type = "deSolve")))
+coef(fit.deSolve)
+endpoints(fit.deSolve)
+# }
    
+# Use stepwise fitting, using optimised parameters from parent only fit, FOMC
+
    # NOT RUN {
 FOMC_SFO <- mkinmod(
   parent = mkinsub("FOMC", "m1"),
-  m1 = mkinsub("SFO"))
    #> Successfully compiled differential equation model from auto-generated C code.
    # Fit the model to the FOCUS example dataset D using defaults
+  m1 = mkinsub("SFO"))
+# 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)
@@ -581,739 +525,40 @@
 # 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"))
    #> Successfully compiled differential equation model from auto-generated C code.
    # Fit the model to the FOCUS example dataset D using defaults
+  m1 = list(type = "SFO"))
+# 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
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
-                      m1 = mkinsub("SFO"), use_of_ff = "max")
    #> Successfully compiled differential equation model from auto-generated C code.
    f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-summary(f.noweight)
    #> mkin version:    0.9.47.1 
-#> R version:       3.4.3 
-#> Date of fit:     Tue Jan 30 10:06:00 2018 
-#> Date of summary: Tue Jan 30 10:06:00 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 185 model solutions performed in 0.739 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 5.701e-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 4.374e-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:    0.9.47.1 
-#> R version:       3.4.3 
-#> Date of fit:     Tue Jan 30 10:06:02 2018 
-#> Date of summary: Tue Jan 30 10:06:02 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 523 model solutions performed in 2.151 s
-#> 
-#> Weighting: none
-#> 
-#> Iterative reweighting with method obs 
-#> Final mean squared residuals of observed variables:
-#>    parent        m1 
-#> 11.573408  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 8.184e-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  24.90287  2.367e+00 3.402
-#>    14   parent    26.64  24.90287  1.737e+00 3.402
-#>    21   parent    11.50  12.44764 -9.476e-01 3.402
-#>    21   parent    11.64  12.44764 -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  41.19338 -3.383e-03 2.722
-#>    50       m1    40.01  41.19338 -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  28.80897 -3.659e+00 2.722
-#>   120       m1    33.31  28.80897  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:    0.9.47.1 
-#> R version:       3.4.3 
-#> Date of fit:     Tue Jan 30 10:06:03 2018 
-#> Date of summary: Tue Jan 30 10:06:03 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 0.675 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 7.303e-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",
+                      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",
                      quiet = TRUE)
-summary(f.w.value)
    #> mkin version:    0.9.47.1 
-#> R version:       3.4.3 
-#> Date of fit:     Tue Jan 30 10:06:04 2018 
-#> Date of summary: Tue Jan 30 10:06:04 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 0.68 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       0.6844 -0.08687        -0.7564
-#> log_k_parent    0.68435       1.0000 -0.12694        -0.5812
-#> log_k_m1       -0.08687      -0.1269  1.00000         0.5195
-#> f_parent_ilr_1 -0.75644      -0.5812  0.51951         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  -0.195714  99.46
-#>     0   parent   102.04  99.65571   2.384286 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
    
-
-
+summary(f.w.value)
+# }
    
+
    # NOT RUN {
 # 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)
    #> mkin version:    0.9.47.1 
-#> R version:       3.4.3 
-#> Date of fit:     Tue Jan 30 10:06:05 2018 
-#> Date of summary: Tue Jan 30 10:06:05 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 297 model solutions performed in 1.178 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  -0.025976   1
-#>     0   parent   102.04  99.48598   2.554024   1
-#>     1   parent    93.50  90.18612   3.313883   1
-#>     1   parent    92.50  90.18612   2.313883   1
-#>     3   parent    63.23  74.11316 -10.883162   1
-#>     3   parent    68.99  74.11316  -5.123162   1
-#>     7   parent    52.32  50.05029   2.269705   1
-#>     7   parent    55.13  50.05029   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  -2.026945   2
-#>     7       m1    24.47  24.99695  -0.526945   2
-#>    14       m1    41.69  36.66353   5.026473   2
-#>    14       m1    33.21  36.66353  -3.453527   2
-#>    21       m1    44.37  41.65681   2.713187   2
-#>    21       m1    46.44  41.65681   4.783187   2
-#>    35       m1    41.22  43.35031  -2.130312   2
-#>    35       m1    37.95  43.35031  -5.400312   2
-#>    50       m1    41.19  41.25637  -0.066365   2
-#>    50       m1    40.01  41.25637  -1.246365   2
-#>    75       m1    40.09  36.46057   3.629433   2
-#>    75       m1    33.85  36.46057  -2.610567   2
-#>   100       m1    31.04  31.96929  -0.929288   2
-#>   100       m1    33.13  31.96929   1.160712   2
-#>   120       m1    25.15  28.76062  -3.610616   2
-#>   120       m1    33.31  28.76062   4.549384   2
    f.w.man.irls <- 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,
                        reweight.method = "obs")
-summary(f.w.man.irls)
    #> mkin version:    0.9.47.1 
-#> R version:       3.4.3 
-#> Date of fit:     Tue Jan 30 10:06:08 2018 
-#> Date of summary: Tue Jan 30 10:06:08 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 692 model solutions performed in 2.733 s
-#> 
-#> Weighting: manual
-#> 
-#> 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  -2.220
-#> 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 8.184e-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.ini   err
-#>     0   parent    99.46  99.67218 -2.122e-01       1 3.402
-#>     0   parent   102.04  99.67218  2.368e+00       1 3.402
-#>     1   parent    93.50  90.27153  3.228e+00       1 3.402
-#>     1   parent    92.50  90.27153  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 -9.476e-01       1 3.402
-#>    21   parent    11.64  12.44765 -8.076e-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  8.662e-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  2.720e+00       2 2.722
-#>    21       m1    46.44  41.65050  4.790e+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 -3.386e-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
    
-
    
+summary(f.w.man.irls)
+# }
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 5703b188..c1287905 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -18,12 +18,24 @@ + + + + + + + @@ -69,6 +81,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +98,7 @@ @@ -182,7 +192,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    NAFTA Technical Working Group on Pesticides (not dated) Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media

    @@ -196,36 +206,17 @@ 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() SFO_SFO <- mkinmod( parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO"))
    #> Successfully compiled differential equation model from auto-generated C code.
    + m1 = list(type = "SFO")) + # Show details of creating the C function SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), - m1 = mkinsub("SFO"), verbose = TRUE)
    #> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file519167a14b3a.c 2> file519167a14b3a.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.
    + m1 = mkinsub("SFO"), verbose = TRUE) + # 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")), @@ -235,7 +226,8 @@ fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, synthetic_data_for_UBA_2014[[12]]$data, - quiet = TRUE)
    + quiet = TRUE) +# }
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png new file mode 100644 index 00000000..42811535 Binary files /dev/null and b/docs/reference/mkinparplot-1.png differ diff --git a/docs/reference/mkinparplot-4.png b/docs/reference/mkinparplot-4.png deleted file mode 100644 index c9f4aadb..00000000 Binary files a/docs/reference/mkinparplot-4.png and /dev/null differ diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 67ba6052..30954168 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -18,12 +18,20 @@ + + + + + + + @@ -86,12 +94,7 @@ @@ -132,7 +135,7 @@ T245 = mkinsub("SFO", to = c("phenol"), sink = FALSE), phenol = mkinsub("SFO", to = c("anisole")), anisole = mkinsub("SFO"), use_of_ff = "max")
    #> Successfully compiled differential equation model from auto-generated C code.
    fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE) -mkinparplot(fit)
    +mkinparplot(fit)
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 7c875ebe..5df3f872 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -18,12 +18,19 @@ + + + + + + + @@ -86,12 +93,7 @@ @@ -152,7 +154,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index b3453e6c..df6316e1 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -18,12 +18,21 @@ + + + + + + + @@ -69,6 +78,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +95,7 @@ @@ -299,17 +306,17 @@ 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 elapsed -#> 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 elapsed -#> 0.000 0.000 0.001
    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 elapsed -#> 0.032 0.000 0.032
    +#> 0.031 0.000 0.031
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png new file mode 100644 index 00000000..8636baf2 Binary files /dev/null and b/docs/reference/mkinresplot-1.png differ diff --git a/docs/reference/mkinresplot-4.png b/docs/reference/mkinresplot-4.png deleted file mode 100644 index 5f3a65e3..00000000 Binary files a/docs/reference/mkinresplot-4.png and /dev/null differ diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 5cb9fa96..036917f1 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -18,12 +18,22 @@ + + + + + + + @@ -86,12 +96,7 @@ @@ -175,7 +180,7 @@

    Examples

    model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
    #> Successfully compiled differential equation model from auto-generated C code.
    fit <- mkinfit(model, FOCUS_2006_D, quiet = TRUE)
-mkinresplot(fit, "m1")
    +mkinresplot(fit, "m1")
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 257d3f89..7724220f 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -18,12 +18,20 @@ + + + + + + + @@ -86,12 +94,7 @@ @@ -182,7 +185,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/mmkin-12.png b/docs/reference/mmkin-12.png deleted file mode 100644 index 9e40d451..00000000 Binary files a/docs/reference/mmkin-12.png and /dev/null differ diff --git a/docs/reference/mmkin-14.png b/docs/reference/mmkin-14.png deleted file mode 100644 index 72cfc5e7..00000000 Binary files a/docs/reference/mmkin-14.png and /dev/null differ diff --git a/docs/reference/mmkin-15.png b/docs/reference/mmkin-15.png deleted file mode 100644 index e8a23a55..00000000 Binary files a/docs/reference/mmkin-15.png and /dev/null differ diff --git a/docs/reference/mmkin-16.png b/docs/reference/mmkin-16.png deleted file mode 100644 index 0b315b1a..00000000 Binary files a/docs/reference/mmkin-16.png and /dev/null differ diff --git a/docs/reference/mmkin-17.png b/docs/reference/mmkin-17.png deleted file mode 100644 index 01bb3ae3..00000000 Binary files a/docs/reference/mmkin-17.png and /dev/null differ diff --git a/docs/reference/mmkin-18.png b/docs/reference/mmkin-18.png deleted file mode 100644 index b98940ff..00000000 Binary files a/docs/reference/mmkin-18.png and /dev/null differ diff --git a/docs/reference/mmkin-19.png b/docs/reference/mmkin-19.png deleted file mode 100644 index b5ac70f7..00000000 Binary files a/docs/reference/mmkin-19.png and /dev/null differ diff --git a/docs/reference/mmkin-20.png b/docs/reference/mmkin-20.png deleted file mode 100644 index c2e9e5ae..00000000 Binary files a/docs/reference/mmkin-20.png and /dev/null differ diff --git a/docs/reference/mmkin-21.png b/docs/reference/mmkin-21.png deleted file mode 100644 index 7e15e1b3..00000000 Binary files a/docs/reference/mmkin-21.png and /dev/null differ diff --git a/docs/reference/mmkin-23.png b/docs/reference/mmkin-23.png deleted file mode 100644 index 45e8efc1..00000000 Binary files a/docs/reference/mmkin-23.png and /dev/null differ diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index d649563f..e97e3f81 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -18,12 +18,20 @@ + + + + + + + @@ -69,6 +77,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +94,7 @@ @@ -152,45 +158,39 @@

    Examples

    - 
    
+    
    # NOT RUN {
 m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
                            M1 = mkinsub("SFO", "M2"),
-                           M2 = mkinsub("SFO"), use_of_ff = "max")
    #> Successfully compiled differential equation model from auto-generated C code.
    
+                           M2 = mkinsub("SFO"), use_of_ff = "max")
+
 m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"),
                             M1 = mkinsub("SFO", "M2"),
-                            M2 = mkinsub("SFO"), use_of_ff = "max")
    #> Successfully compiled differential equation model from auto-generated C code.
    
+                            M2 = mkinsub("SFO"), use_of_ff = "max")
+
 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)
 
 time_default <- system.time(fits.0 <- mmkin(models, datasets, quiet = TRUE))
-time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
    #> Warning: Optimisation by method Port did not converge.
-#> Convergence code is 1
    #> Warning: Optimisation by method Port did not converge.
-#> Convergence code is 1
    
-time_default
    #>    user  system elapsed 
-#>  15.992   0.188  11.440 
    time_1
    #>    user  system elapsed 
-#>  24.576   0.000  24.578 
    
-endpoints(fits.0[["SFO_lin", 2]])
    #> $ff
-#>   parent_M1 parent_sink       M1_M2     M1_sink 
-#>   0.7340479   0.2659521   0.7505687   0.2494313 
-#> 
-#> $SFORB
-#> logical(0)
-#> 
-#> $distimes
-#>              DT50       DT90
-#> parent  0.8777689   2.915885
-#> M1      2.3257456   7.725960
-#> M2     33.7200862 112.015702
-#> 
    
+time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
+
+time_default
+time_1
+
+endpoints(fits.0[["SFO_lin", 2]])
+
 # 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]) +# }
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png new file mode 100644 index 00000000..2bb8f5dd Binary files /dev/null and b/docs/reference/plot.mkinfit-1.png differ diff --git a/docs/reference/plot.mkinfit-10.png b/docs/reference/plot.mkinfit-10.png deleted file mode 100644 index 48ab5271..00000000 Binary files a/docs/reference/plot.mkinfit-10.png and /dev/null differ diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png new file mode 100644 index 00000000..22a3f8b0 Binary files /dev/null and b/docs/reference/plot.mkinfit-2.png differ diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png new file mode 100644 index 00000000..93e859c7 Binary files /dev/null and b/docs/reference/plot.mkinfit-3.png differ diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png index cb52d4ac..27edd6f3 100644 Binary files a/docs/reference/plot.mkinfit-4.png and b/docs/reference/plot.mkinfit-4.png differ diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png deleted file mode 100644 index 8e0faa21..00000000 Binary files a/docs/reference/plot.mkinfit-6.png and /dev/null differ diff --git a/docs/reference/plot.mkinfit-8.png b/docs/reference/plot.mkinfit-8.png deleted file mode 100644 index 129f1445..00000000 Binary files a/docs/reference/plot.mkinfit-8.png and /dev/null differ diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 0af2bbf6..4bdad93f 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -18,12 +18,24 @@ + + + + + + + @@ -86,12 +98,7 @@ @@ -237,12 +244,12 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … # parent to sink included, use Levenberg-Marquardt for speed SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"), m1 = mkinsub("SFO", full = "Metabolite M1" ))
    #> Successfully compiled differential equation model from auto-generated C code.
    fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = "Marq") -plot(fit)
    plot(fit, show_residuals = TRUE)
    +plot(fit)
    plot(fit, show_residuals = TRUE)
    # Show the observed variables separately -plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))
    +plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))
    # Show the observed variables separately, with residuals plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"), - show_errmin = TRUE)
    + show_errmin = TRUE)
    # The same can be obtained with less typing, using the convenience function plot_sep plot_sep(fit, lpos = c("topright", "bottomright"))
    @@ -269,7 +276,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png new file mode 100644 index 00000000..2554b68b Binary files /dev/null and b/docs/reference/plot.mmkin-1.png differ diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png index 21af1e7b..9a66294f 100644 Binary files a/docs/reference/plot.mmkin-2.png and b/docs/reference/plot.mmkin-2.png differ diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png new file mode 100644 index 00000000..b0f7fa21 Binary files /dev/null and b/docs/reference/plot.mmkin-3.png differ diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png deleted file mode 100644 index 3004f48f..00000000 Binary files a/docs/reference/plot.mmkin-4.png and /dev/null differ diff --git a/docs/reference/plot.mmkin-6.png b/docs/reference/plot.mmkin-6.png deleted file mode 100644 index 02ed2ab1..00000000 Binary files a/docs/reference/plot.mmkin-6.png and /dev/null differ diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index aa3df77a..11da6685 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -18,12 +18,23 @@ + + + + + + + @@ -86,12 +97,7 @@ @@ -165,11 +171,11 @@ fits <- mmkin(c("FOMC", "HS"), list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C), # named list for titles cores = 1, quiet = TRUE, method.modFit = "Marq") - plot(fits[, "FOCUS C"])
    plot(fits["FOMC", ])
    + plot(fits[, "FOCUS C"])
    plot(fits["FOMC", ])
    # We can also plot a single fit, if we like the way plot.mmkin works, but then the plot # height should be smaller than the plot width (this is not possible for the html pages # generated by pkgdown, as far as I know). - plot(fits["FOMC", "FOCUS C"]) # same as plot(fits[1, 2])
    + plot(fits["FOMC", "FOCUS C"]) # same as plot(fits[1, 2])
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 14342f21..8e0d18b2 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -18,12 +18,19 @@ + + + + + + + @@ -86,12 +93,7 @@ @@ -143,7 +145,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 33782b7d..db15cc60 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -18,12 +18,19 @@ + + + + + + + @@ -86,12 +93,7 @@ @@ -164,7 +166,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/schaefer07_complex_case-4.png b/docs/reference/schaefer07_complex_case-4.png deleted file mode 100644 index b90185a1..00000000 Binary files a/docs/reference/schaefer07_complex_case-4.png and /dev/null differ diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 605f572e..6c53f805 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -18,12 +18,21 @@ + + + + + + + @@ -86,12 +95,7 @@ @@ -140,24 +144,12 @@ 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.
    + 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)
    #> $ff -#> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink -#> 0.3809618 0.1954667 0.4235715 0.0000000 0.4479596 0.5520404 -#> -#> $SFORB -#> logical(0) -#> -#> $distimes -#> DT50 DT90 -#> parent 13.95078 46.34349 -#> A1 49.75345 165.27739 -#> B1 37.26908 123.80521 -#> C1 11.23130 37.30957 -#> A2 28.50652 94.69662 -#>
    - # Compare with the results obtained in the original publication + plot(fit) + endpoints(fit) + +# }
    # 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 @@ -194,7 +186,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/sigma_rl.html b/docs/reference/sigma_rl.html index b7c93961..868c0d4f 100644 --- a/docs/reference/sigma_rl.html +++ b/docs/reference/sigma_rl.html @@ -18,12 +18,21 @@ + + - + + + + + + @@ -157,7 +166,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index f20e3948..977ff8d8 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -18,12 +18,22 @@ + + + + + + + @@ -69,6 +79,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +96,7 @@ @@ -177,21 +185,21 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    - 
      summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
    #> mkin version:    0.9.46 
-#> R version:       3.4.1 
-#> Date of fit:     Sat Jul 29 15:15:30 2017 
-#> Date of summary: Sat Jul 29 15:15:30 2017 
+    
      summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
    #> mkin version used for fitting:    0.9.47.1 
+#> R version used for fitting:       3.4.3 
+#> Date of fit:     Thu Mar  1 14:26:27 2018 
+#> Date of summary: Thu Mar  1 14:26:27 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 0.084 s
+#> Fitted with method Port using 35 model solutions performed in 0.076 s
 #> 
 #> Weighting: none
 #> 
@@ -277,7 +285,7 @@
 
    
 
 
    
-  
    Site built with pkgdown.
    
+  
    Site built with pkgdown.
    
 
    
 
       
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index f9603f34..192e8dc2 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -18,12 +18,31 @@
 
 
 
+
+
 
 
 
 
 
+  
+  
+
 
+
+
 
 
 
@@ -136,7 +155,7 @@
     
 
     
    Examples
    
-    
    
+    
    # NOT RUN {
 # 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"),
@@ -235,11 +254,8 @@ fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data,
                quiet = TRUE)
 plot_sep(fit)
 summary(fit)
-
-
    #> Error: <text>:68:43: Unerwartete(s) SPECIAL
-#> 67: 
-#> 68:   d_rep[d_rep$time == 0 & d_rep$name <!-- %in%
-#>                                               ^
    
+# }
+
    
   
    
   
 
 
    
-  
    Site built with pkgdown.
    
+  
    Site built with pkgdown.
    
 
    
 
       
diff --git a/docs/reference/synthetic_data_for_UBA_2014-10.png b/docs/reference/synthetic_data_for_UBA_2014-10.png
deleted file mode 100644
index 7e15e1b3..00000000
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diff --git a/docs/reference/test_data_from_UBA_2014-12.png b/docs/reference/test_data_from_UBA_2014-12.png
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diff --git a/docs/reference/test_data_from_UBA_2014-16.png b/docs/reference/test_data_from_UBA_2014-16.png
deleted file mode 100644
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deleted file mode 100644
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diff --git a/docs/reference/test_data_from_UBA_2014-6.png b/docs/reference/test_data_from_UBA_2014-6.png
deleted file mode 100644
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diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index ed2ccd9c..c4292d9c 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -18,12 +18,20 @@
 
 
 
+
+
 
 
 
 
 
+  
+  
+
 
+
+
 
 
 
@@ -123,7 +131,7 @@
     
 
     
    Examples
    
-    
    
+    
      
    # NOT RUN {
   # 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
@@ -131,57 +139,27 @@
   # 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"))
    #> 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 2.33959810 4.102657e+01 9.568973e-19    NA
-#> k_parent_w_sink     3.603743e-01 0.03497716 1.030313e+01 4.988281e-09    NA
-#> k_parent_w_parent_s 6.031370e-02 0.01746026 3.454342e+00 1.514738e-03    NA
-#> k_parent_s_sink     5.099834e-11 0.10381939 4.912217e-10 5.000000e-01    NA
-#> k_parent_s_parent_w 7.419672e-02 0.11338174 6.543974e-01 2.608057e-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
    
+                  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)
+
   # 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")
    #> Successfully compiled differential equation model from auto-generated C code.
    
+                    use_of_ff = "max")
+
   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
    #>                   Estimate  se_notrans    t value       Pr(>t)        Lower
-#> parent_0       76.55425583 0.943443834 81.1434164 4.422340e-30 74.602593306
-#> k_parent        0.12081956 0.004815515 25.0896457 1.639665e-18  0.111257526
-#> k_M1            0.84258650 0.930121206  0.9058889 1.871937e-01  0.085876305
-#> k_M2            0.04210878 0.013729902  3.0669396 2.729137e-03  0.021450631
-#> k_M3            0.01122919 0.008044866  1.3958205 8.804914e-02  0.002550985
-#> f_parent_to_M1  0.32240199 0.278620411  1.1571370 1.295466e-01           NA
-#> f_parent_to_M2  0.16099854 0.030548889  5.2701930 1.196191e-05           NA
-#> f_M1_to_M3      0.27921500 0.314732717  0.8871496 1.920907e-01  0.015016888
-#> f_M2_to_M3      0.55641332 0.650247079  0.8556952 2.004966e-01  0.005360551
-#>                      Upper
-#> parent_0       78.50591836
-#> k_parent        0.13120340
-#> k_M1            8.26714671
-#> k_M2            0.08266187
-#> k_M3            0.04942980
-#> f_parent_to_M1          NA
-#> f_parent_to_M2          NA
-#> f_M1_to_M3      0.90777217
-#> f_M2_to_M3      0.99658634
      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
      
-
    
+  plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright"))
+  summary(f_soil)$bpar
+  mkinerrmin(f_soil)
+
+# }
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index bbf15a41..630a5103 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -18,12 +18,27 @@ + + + + + + + @@ -69,6 +84,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +101,7 @@ @@ -170,10 +183,10 @@ 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: 0.9.46 -#> R version: 3.4.1 -#> Date of fit: Sat Jul 29 15:15:35 2017 -#> Date of summary: Sat Jul 29 15:15:35 2017 +summary(fit, data=FALSE) # See transformed and backtransformed parameters
    #> mkin version used for fitting: 0.9.47.1 +#> R version used for fitting: 3.4.3 +#> Date of fit: Thu Mar 1 14:26:28 2018 +#> Date of summary: Thu Mar 1 14:26:28 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -181,7 +194,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.608 s +#> Fitted with method Port using 153 model solutions performed in 0.571 s #> #> Weighting: none #> @@ -245,84 +258,10 @@ #> 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)
    #> mkin version: 0.9.46 -#> R version: 3.4.1 -#> Date of fit: Sat Jul 29 15:15:36 2017 -#> Date of summary: Sat Jul 29 15:15:36 2017 -#> -#> 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 352 model solutions performed in 1.401 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
    - +summary(fit.2, data=FALSE) +# }
    initials <- fit$start$value names(initials) <- rownames(fit$start) transformed <- fit$start_transformed$value @@ -330,162 +269,29 @@ 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 SFO_SFO.ff <- mkinmod( parent = list(type = "SFO", to = "m1", sink = TRUE), m1 = list(type = "SFO"), - use_of_ff = "max")
    #> Successfully compiled differential equation model from auto-generated C code.
    + use_of_ff = "max") + fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) -summary(fit.ff, data = FALSE)
    #> mkin version: 0.9.46 -#> R version: 3.4.1 -#> Date of fit: Sat Jul 29 15:15:37 2017 -#> Date of summary: Sat Jul 29 15:15:37 2017 -#> -#> 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 185 model solutions performed in 0.772 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 5.701e-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 4.374e-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) +summary(fit.ff, data = FALSE) +initials <- c("f_parent_to_m1" = 0.5) transformed <- transform_odeparms(initials, SFO_SFO.ff) -backtransform_odeparms(transformed, SFO_SFO.ff)
    #> f_parent_to_m1 -#> 0.5
    +backtransform_odeparms(transformed, SFO_SFO.ff) + # And without sink SFO_SFO.ff.2 <- mkinmod( parent = list(type = "SFO", to = "m1", sink = FALSE), m1 = list(type = "SFO"), - use_of_ff = "max")
    #> Successfully compiled differential equation model from auto-generated C code.
    + use_of_ff = "max") + fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE) -summary(fit.ff.2, data = FALSE)
    #> mkin version: 0.9.46 -#> R version: 3.4.1 -#> Date of fit: Sat Jul 29 15:15:38 2017 -#> Date of summary: Sat Jul 29 15:15:38 2017 -#> -#> 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 0.416 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 0.11059 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 3.938e-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
    -
    +summary(fit.ff.2, data = FALSE) +# }
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/twa.html b/docs/reference/twa.html deleted file mode 100644 index be76b439..00000000 --- a/docs/reference/twa.html +++ /dev/null @@ -1,179 +0,0 @@ - - - - - - - - -Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit — twa • mkin - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -
    - - - -
    - -
    -
    -
    -

    Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit

    -
    - - -

    This function calculates maximum moving window time weighted average concentrations -(TWAs) for kinetic models fitted with mkinfit. Currently, only -calculations for the parent are implemented for the SFO, FOMC and DFOP models, -using the analytical formulas given in the PEC soil section of the FOCUS -guidance.

    - - - 
    twa(fit, windows)
    - -

    Arguments

    - - - - - - - - - - -
    fit

    An object of class mkinfit.

    windows

    The width of the time windows for which the TWAs should be calculated.

    - -

    Value

    - -

    A numeric vector, named using the windows argument.

    - -

    References

    - -

    FOCUS (2006) “Guidance Document on Estimating Persistence and - Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    - - -

    Examples

    - 
      fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-  twa(fit, c(7, 21))
    #>        7       21 
-#> 34.71343 18.22124
    -
    - -
    - - -
    - - - -- cgit v1.2.1