Example evaluation of FOCUS Example Dataset D • mkin

Date: Thu, 7 May 2020 08:59:29 +0200 Subject: Static documentation rebuilt by pkgdown --- docs/404.html | 37 ++-- docs/articles/FOCUS_D.html | 89 ++++----- docs/articles/FOCUS_D_files/figure-html/plot-1.png | Bin 97426 -> 101585 bytes docs/articles/index.html | 59 +++--- docs/authors.html | 33 ++-- docs/bootstrap-toc.css | 60 ++++++ docs/bootstrap-toc.js | 159 ++++++++++++++++ docs/index.html | 55 +++--- docs/news/index.html | 171 ++++++++--------- docs/pkgdown.css | 121 +++++++++++- docs/pkgdown.js | 5 - docs/pkgdown.yml | 3 +- docs/reference/DFOP.solution.html | 69 ++++--- docs/reference/FOMC.solution.html | 66 ++++--- docs/reference/HS.solution.html | 86 ++++----- docs/reference/IORE.solution.html | 80 ++++---- docs/reference/SFO.solution.html | 71 ++++--- docs/reference/SFORB.solution.html | 75 ++++---- docs/reference/index.html | 101 +++++++--- docs/reference/logistic.solution-1.png | Bin 63262 -> 80598 bytes docs/reference/logistic.solution-2.png | Bin 29336 -> 80598 bytes docs/reference/logistic.solution.html | 125 ++++++++----- docs/reference/mkinds.html | 57 +++--- docs/reference/mkinfit.html | 171 +++++------------ docs/reference/mkinmod.html | 57 +++--- docs/reference/mkinpredict.html | 205 +++++++++------------ 26 files changed, 1157 insertions(+), 798 deletions(-) create mode 100644 docs/bootstrap-toc.css create mode 100644 docs/bootstrap-toc.js (limited to 'docs') diff --git a/docs/404.html b/docs/404.html index b3193a23..12d9b275 100644 --- a/docs/404.html +++ b/docs/404.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -53,7 +57,7 @@ - +

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Site built with pkgdown 1.4.1.

Site built with pkgdown 1.5.1.

diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 42361b92..e9c6b005 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -6,19 +6,19 @@ Example evaluation of FOCUS Example Dataset D • mkin - - - - + + + + + - - + - +

@@ -87,12 +94,12 @@

@@ -100,8 +107,8 @@

This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using mkin. After loading the library we look at the data. We have observed concentrations in the column named value at the times specified in column time for the two observed variables named parent and m1.

library(mkin, quietly = TRUE)
-print(FOCUS_2006_D)

library(mkin, quietly = TRUE)
+print(FOCUS_2006_D)

##      name time  value
 ## 1  parent    0  99.46
 ## 2  parent    0 102.04
@@ -149,29 +156,29 @@
 ## 44     m1  120  33.31

Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.

The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector $diffs of the mkinmod object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.

SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))

SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))

## Successfully compiled differential equation model from auto-generated C code.

print(SFO_SFO$diffs)

print(SFO_SFO$diffs)

##                                                       parent 
 ## "d_parent = - k_parent_sink * parent - k_parent_m1 * parent" 
 ##                                                           m1 
 ##             "d_m1 = + k_parent_m1 * parent - k_m1_sink * m1"

We do the fitting without progress report (quiet = TRUE).

fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)

## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
-## value of zero were removed from the data

fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)

## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value
+## of zero were removed from the data

A plot of the fit including a residual plot for both observed variables is obtained using the plot_sep method for mkinfit objects, which shows separate graphs for all compounds and their residuals.

plot_sep(fit, lpos = c("topright", "bottomright"))

plot_sep(fit, lpos = c("topright", "bottomright"))

Confidence intervals for the parameter estimates are obtained using the mkinparplot function.

mkinparplot(fit)

mkinparplot(fit)

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)

## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.1 
-## Date of fit:     Fri Nov  1 10:10:44 2019 
-## Date of summary: Fri Nov  1 10:10:44 2019 
+summary(fit)
+## mkin version used for fitting:    0.9.49.11 
+## R version used for fitting:       4.0.0 
+## Date of fit:     Thu May  7 08:59:27 2020 
+## Date of summary: Thu May  7 08:59:27 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -179,7 +186,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 389 model solutions performed in 1.015 s
+## Fitted using 389 model solutions performed in 1.031 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -212,18 +219,18 @@
 ## sigma                3.126    0.35850  2.396   3.855
 ## 
 ## Parameter correlation:
-##                     parent_0 log_k_parent_sink log_k_parent_m1
-## parent_0           1.000e+00         6.067e-01      -6.372e-02
-## log_k_parent_sink  6.067e-01         1.000e+00      -8.550e-02
-## log_k_parent_m1   -6.372e-02        -8.550e-02       1.000e+00
-## log_k_m1_sink     -1.688e-01        -6.252e-01       4.731e-01
-## sigma              1.164e-09        -8.908e-10       1.652e-08
-##                   log_k_m1_sink      sigma
-## parent_0             -1.688e-01  1.164e-09
-## log_k_parent_sink    -6.252e-01 -8.908e-10
-## log_k_parent_m1       4.731e-01  1.652e-08
-## log_k_m1_sink         1.000e+00 -1.340e-10
-## sigma                -1.340e-10  1.000e+00
+##                     parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+## parent_0           1.000e+00         6.067e-01      -6.372e-02    -1.688e-01
+## log_k_parent_sink  6.067e-01         1.000e+00      -8.550e-02    -6.252e-01
+## log_k_parent_m1   -6.372e-02        -8.550e-02       1.000e+00     4.731e-01
+## log_k_m1_sink     -1.688e-01        -6.252e-01       4.731e-01     1.000e+00
+## sigma              5.287e-10         3.306e-09       4.421e-08    -3.319e-10
+##                        sigma
+## parent_0           5.287e-10
+## log_k_parent_sink  3.306e-09
+## log_k_parent_m1    4.421e-08
+## log_k_m1_sink     -3.319e-10
+## sigma              1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -295,7 +302,7 @@
 ##   120       m1    33.31  28.78984  4.520e+00


 
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diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png
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       All vignettes
       
 
-      
-        Example evaluation of FOCUS Example Dataset D
-        Example evaluation of FOCUS Laboratory Data L1 to L3
-        Introduction to mkin
-        Calculation of time weighted average concentrations with mkin
-        Example evaluation of FOCUS dataset Z
-        Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance
-        Benchmark timings for mkin on various systems
-        Performance benefit by using compiled model definitions in mkin
-      
+      
+        Example evaluation of FOCUS Example Dataset D
+        
+        
Example evaluation of FOCUS Laboratory Data L1 to L3
+        
+        
Introduction to mkin
+        
+        
Calculation of time weighted average concentrations with mkin
+        
+        
Example evaluation of FOCUS dataset Z
+        
+        
Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance
+        
+        
Benchmark timings for mkin on various systems
+        
+        
Performance benefit by using compiled model definitions in mkin
+        
+


 
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-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
 
       
diff --git a/docs/authors.html b/docs/authors.html
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-        Johannes Ranke. Author, maintainer, copyright holder. 
+        
Johannes Ranke. Author, maintainer, copyright holder. 
         
       
       
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-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
 
       
diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css
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+/*!
+ * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
+ * Copyright 2015 Aidan Feldman
+ * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
+
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+}
+
+/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */
+nav[data-toggle='toc'] .nav > .active > ul {
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+}
diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js
new file mode 100644
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+++ b/docs/bootstrap-toc.js
@@ -0,0 +1,159 @@
+/*!
+ * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
+ * Copyright 2015 Aidan Feldman
+ * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
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diff --git a/docs/index.html b/docs/index.html
index 5baaa718..546f9143 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -6,10 +6,11 @@
 
 
 Kinetic Evaluation of Chemical Degradation Data • mkin
-
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+
 
 
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@@ -80,7 +80,14 @@
   News
 
       
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+  
+    
+     
+  
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+      
 
 
   
@@ -101,7 +108,7 @@
 
 Installation
 You can install the latest released version from CRAN from within R:
-install.packages("mkin")
+install.packages("mkin")
 
 
 
@@ -141,7 +148,7 @@
 
 
 GUI
-There is a graphical user interface that I consider useful for real work. Please refer to its documentation page for installation instructions and a manual.
+There is a graphical user interface that may be useful. Please refer to its documentation page for installation instructions and a manual.
 
 
 
@@ -164,18 +171,16 @@
 

 References
 
-
-
+
+
+
+
+
+Ranke J, Meinecke S (2019)
-  Error Models for the Kinetic Evaluation of Chemical Degradation Data
-  Environments
-  6 (12) 124
-  doi:10.3390/environments6120124
-  
Ranke J, Wöltjen J, Meinecke S (2018)
-  Comparison of software tools for kinetic evaluation of chemical degradation data
-  Environmental Sciences Europe
-  30 17
-  doi:10.1186/s12302-018-0145-1
-  

+Ranke J, Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data Environments 6 (12) 124 doi:10.3390/environments6120124
+

+Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic evaluation of chemical degradation data Environmental Sciences Europe 30 17 doi:10.1186/s12302-018-0145-1
+
 
 
 
@@ -186,12 +191,14 @@
 
   
 
-  
+  
     
 Links
 
 Download from CRAN at 
https://cloud.r-project.org/package=mkin
 
+Browse source code at 
http://github.com/jranke/mkin/
+
 Report a bug at 
http://github.com/jranke/mkin/issues
 
 
@@ -205,7 +212,7 @@
 
 Developers
 
-Johannes Ranke 
 Author, maintainer, copyright holder   
+Johannes Ranke 
 Author, maintainer, copyright holder   
 All authors...
 
 
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-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
 
       
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-      Changelog 
-      
+      Changelog 
+      Source: NEWS.md
     
 
-    
-
-mkin 0.9.49.11 (unreleased) Unreleased 
+    
+
+mkin 0.9.50.1 (unreleased) Unreleased 
+
+
+Support SFORB with formation fractions
+
+
+    
+
+mkin 0.9.49.11 (2020-04-20) 2020-04-20 
 
 
 Increase a test tolerance to make it pass on all CRAN check machines
 
 
     
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+

 mkin 0.9.49.10 (2020-04-18) 2020-04-18 
 
 
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 mkin 0.9.49.9 (2020-03-31) 2020-03-31 
 
 
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 mkin 0.9.49.8 (2020-01-09) 2020-01-09 
 
 
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 mkin 0.9.49.7 (2019-11-01) 2019-11-02 
 
 
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 mkin 0.9.49.6 (2019-10-31) 2019-10-31 
 
 
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 mkin 0.9.49.5 (2019-07-04) 2019-07-04 
 
 
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 mkin 0.9.48.1 (2019-03-04) 2019-03-04 
 
 
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 mkin 0.9.47.5 (2018-09-14) 2018-09-14 
 
 
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 mkin 0.9.47.3 Unreleased 
 
 
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 mkin 0.9.47.2 (2018-07-19) 2018-07-19 
 
 
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 mkin 0.9.47.1 (2018-02-06) 2018-02-06 
 
 
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 mkin 0.9.46.3 (2017-11-16) 2017-11-16 
 
 
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 mkin 0.9.46.2 (2017-10-10) 2017-10-10 
 
 
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 mkin 0.9.46.1 (2017-09-14) 2017-09-14 
 
 
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 mkin 0.9.46 (2017-07-24) 2017-07-29 
 
 
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+

 mkin 0.9.45.2 (2017-07-24) 2017-07-22 
 
 
@@ -325,7 +342,7 @@
 
 
     
-
+

 mkin 0.9.45.1 (2016-12-20) Unreleased 
 
 
@@ -337,7 +354,7 @@
 
 
     
-
+

 mkin 0.9.45 (2016-12-08) 2016-12-08 
 
 
@@ -351,7 +368,7 @@
 
 
     
-
+

 mkin 0.9.44 (2016-06-29) 2016-06-29 
 
 
@@ -363,7 +380,7 @@
 
 
     
-
+

 mkin 0.9.43 (2016-06-28) 2016-06-28 
 
 
@@ -402,7 +419,7 @@
 
 
     
-
+

 mkin 0.9.42 (2016-03-25) 2016-03-25 
 
 
@@ -423,7 +440,7 @@
 
 
     
-
+

 mkin 0.9-41 (2015-11-09) 2015-11-09 
 
 
@@ -446,7 +463,7 @@
 
 
     
-
+

 mkin 0.9-40 (2015-07-21) 2015-07-21 
 
 
@@ -467,7 +484,7 @@
 
 
     
-
+

 mkin 0.9-39 (2015-06-26) 2015-06-26 
 
 
@@ -488,7 +505,7 @@
 
 
     
-
+

 mkin 0.9-38 (2015-06-24) 2015-06-23 
 
 
@@ -509,7 +526,7 @@
 
 
     
-
+

 mkin 0.9-36 (2015-06-21) 2015-06-21 
 
 
@@ -531,7 +548,7 @@
 
 
     
-
+

 mkin 0.9-35 (2015-05-15) 2015-05-15 
 
 
@@ -563,7 +580,7 @@
 
 
     
-
+

 mkin 0.9-34 (2014-11-22) 2014-11-22 
 
 
@@ -585,7 +602,7 @@
 
 
     
-
+

 mkin 0.9-33 (2014-10-22) 2014-10-12 
 
 
@@ -618,7 +635,7 @@
 
 
     
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+

 mkin 0.9-32 (2014-07-24) 2014-07-24 
 
 
@@ -655,7 +672,7 @@
 
 
     
-
+

 mkin 0.9-31 (2014-07-14) 2014-07-14 
 
 
@@ -667,7 +684,7 @@
 
 
     
-
+

 mkin 0.9-30 (2014-07-11) 2014-07-11 
 
 
@@ -699,7 +716,7 @@
 
 
     
-
+

 mkin 0.9-29 (2014-06-27) 2014-06-27 
 
 
@@ -709,7 +726,7 @@
 
 
     
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+

 mkin 0.9-28 (2014-05-20) 2014-05-20 
 
 
@@ -719,7 +736,7 @@
 
 
     
-
+

 mkin 0.9-27 (2014-05-10) 2014-05-10 
 
 
@@ -743,7 +760,7 @@
 
 
     
-
+

 mkin 0.9-24 (2013-11-06) 2013-11-06 
 
 
@@ -753,7 +770,7 @@
 
 
     
-
+

 mkin 0.9-22 (2013-10-26) 2013-10-26 
 
 
@@ -773,50 +790,10 @@
 
   
 
-  
-    
-      Contents
-      
-        0.9.49.11
-        0.9.49.10
-        0.9.49.9
-        0.9.49.8
-        0.9.49.7
-        0.9.49.6
-        0.9.49.5
-        0.9.48.1
-        0.9.47.5
-        0.9.47.3
-        0.9.47.2
-        0.9.47.1
-        0.9.46.3
-        0.9.46.2
-        0.9.46.1
-        0.9.46
-        0.9.45.2
-        0.9.45.1
-        0.9.45
-        0.9.44
-        0.9.43
-        0.9.42
-        0.9-41
-        0.9-40
-        0.9-39
-        0.9-38
-        0.9-36
-        0.9-35
-        0.9-34
-        0.9-33
-        0.9-32
-        0.9-31
-        0.9-30
-        0.9-29
-        0.9-28
-        0.9-27
-        0.9-24
-        0.9-22
-      
-    
+  
+    
+      Contents
+    
   
 
 
@@ -828,7 +805,7 @@
 
 
 
-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
 
       
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index 91459581..c01e5923 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -17,6 +17,10 @@ html, body {
   height: 100%;
 }
 
+body {
+  position: relative;
+}
+
 body > .container {
   display: flex;
   height: 100%;
@@ -67,6 +71,10 @@ summary {
   margin-top: calc(-60px + 1em);
 }
 
+dd {
+  margin-left: 3em;
+}
+
 /* Section anchors ---------------------------------*/
 
 a.anchor {
@@ -100,29 +108,132 @@ a.anchor {
   margin-top: -40px;
 }
 
+/* Navbar submenu --------------------------*/
+
+.dropdown-submenu {
+  position: relative;
+}
+
+.dropdown-submenu>.dropdown-menu {
+  top: 0;
+  left: 100%;
+  margin-top: -6px;
+  margin-left: -1px;
+  border-radius: 0 6px 6px 6px;
+}
+
+.dropdown-submenu:hover>.dropdown-menu {
+  display: block;
+}
+
+.dropdown-submenu>a:after {
+  display: block;
+  content: " ";
+  float: right;
+  width: 0;
+  height: 0;
+  border-color: transparent;
+  border-style: solid;
+  border-width: 5px 0 5px 5px;
+  border-left-color: #cccccc;
+  margin-top: 5px;
+  margin-right: -10px;
+}
+
+.dropdown-submenu:hover>a:after {
+  border-left-color: #ffffff;
+}
+
+.dropdown-submenu.pull-left {
+  float: none;
+}
+
+.dropdown-submenu.pull-left>.dropdown-menu {
+  left: -100%;
+  margin-left: 10px;
+  border-radius: 6px 0 6px 6px;
+}
+
 /* Sidebar --------------------------*/
 
-#sidebar {
+#pkgdown-sidebar {
   margin-top: 30px;
   position: -webkit-sticky;
   position: sticky;
   top: 70px;
 }
-#sidebar h2 {
+
+#pkgdown-sidebar h2 {
   font-size: 1.5em;
   margin-top: 1em;
 }
 
-#sidebar h2:first-child {
+#pkgdown-sidebar h2:first-child {
   margin-top: 0;
 }
 
-#sidebar .list-unstyled li {
+#pkgdown-sidebar .list-unstyled li {
   margin-bottom: 0.5em;
 }
 
+/* bootstrap-toc tweaks ------------------------------------------------------*/
+
+/* All levels of nav */
+
+nav[data-toggle='toc'] .nav > li > a {
+  padding: 4px 20px 4px 6px;
+  font-size: 1.5rem;
+  font-weight: 400;
+  color: inherit;
+}
+
+nav[data-toggle='toc'] .nav > li > a:hover,
+nav[data-toggle='toc'] .nav > li > a:focus {
+  padding-left: 5px;
+  color: inherit;
+  border-left: 1px solid #878787;
+}
+
+nav[data-toggle='toc'] .nav > .active > a,
+nav[data-toggle='toc'] .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav > .active:focus > a {
+  padding-left: 5px;
+  font-size: 1.5rem;
+  font-weight: 400;
+  color: inherit;
+  border-left: 2px solid #878787;
+}
+
+/* Nav: second level (shown on .active) */
+
+nav[data-toggle='toc'] .nav .nav {
+  display: none; /* Hide by default, but at >768px, show it */
+  padding-bottom: 10px;
+}
+
+nav[data-toggle='toc'] .nav .nav > li > a {
+  padding-left: 16px;
+  font-size: 1.35rem;
+}
+
+nav[data-toggle='toc'] .nav .nav > li > a:hover,
+nav[data-toggle='toc'] .nav .nav > li > a:focus {
+  padding-left: 15px;
+}
+
+nav[data-toggle='toc'] .nav .nav > .active > a,
+nav[data-toggle='toc'] .nav .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav .nav > .active:focus > a {
+  padding-left: 15px;
+  font-weight: 500;
+  font-size: 1.35rem;
+}
+
+/* orcid ------------------------------------------------------------------- */
+
 .orcid {
-  height: 16px;
+  font-size: 16px;
+  color: #A6CE39;
   /* margins are required by official ORCID trademark and display guidelines */
   margin-left:4px;
   margin-right:4px;
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index 087a7622..7e7048fa 100644
--- a/docs/pkgdown.js
+++ b/docs/pkgdown.js
@@ -9,11 +9,6 @@
       $('body').css('padding-top', $('.navbar').height() + 10);
     });
 
-    $('body').scrollspy({
-      target: '#sidebar',
-      offset: 60
-    });
-
     $('[data-toggle="tooltip"]').tooltip();
 
     var cur_path = paths(location.pathname);
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index a1377251..5aec64b7 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
 pandoc: 2.2.1
-pkgdown: 1.4.1
+pkgdown: 1.5.1
 pkgdown_sha: ~
 articles:
   FOCUS_D: FOCUS_D.html
@@ -10,6 +10,7 @@ articles:
   NAFTA_examples: web_only/NAFTA_examples.html
   benchmarks: web_only/benchmarks.html
   compiled_models: web_only/compiled_models.html
+last_built: 2020-05-07T06:58Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index eef4f902..46e0cc91 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -38,7 +42,6 @@
 
 
-
 
 
 
@@ -56,7 +59,7 @@ two exponential decline functions." />
 
   
 
-  
+  
     
       
       
@@ -70,7 +73,7 @@ two exponential decline functions." />
       
       
         mkin
-        0.9.49.6
+        0.9.49.11
       
     
 
@@ -114,7 +117,12 @@ two exponential decline functions." />
 
       
       
-        
+        
+  
+    
+     
+  
+
       
       
     

@@ -129,7 +137,7 @@ two exponential decline functions." />
   
     
     Double First-Order in Parallel kinetics
-    
+    Source: R/parent_solutions.R
     DFOP.solution.Rd
     
 
@@ -138,7 +146,7 @@ two exponential decline functions." />
 two exponential decline functions.
     
 
-    DFOP.solution(t, parent.0, k1, k2, g)
+    DFOP.solution(t, parent_0, k1, k2, g)
 
     Arguments
     
@@ -148,7 +156,7 @@ two exponential decline functions.
-      
+      
@@ -175,22 +183,31 @@ kinetic constant.
   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
+FOCUS (2014) “Generic guidance for Estimating Persistence
+  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+  EU Registration” Report of the FOCUS Work Group on Degradation Kinetics,
+  Version 1.1, 18 December 2014
   http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics
+    See also
+
+    Other parent solutions: 
+FOMC.solution(),
+HS.solution(),
+IORE.solution(),
+SFO.solution(),
+SFORB.solution(),
+logistic.solution()
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))

 
-  
-    Contents
-    
-      Arguments
-      Value
-      References
-      Examples
-    
-
+  
+    
+      Contents
+    
   
 
 
@@ -201,7 +218,7 @@ kinetic constant.

-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index f44ad713..8e2b154e 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
-
+
 
-
+
+
+
+
+
-
-
+
+
-
+
-
-
+
+
@@ -38,7 +42,6 @@
 
-
 
 
 
@@ -56,7 +59,7 @@ a decreasing rate constant." />
 
   
 
-  
+  
       
       
@@ -70,7 +73,7 @@ a decreasing rate constant." />
       
       
         mkin
-        0.9.49.6
+        0.9.49.11
       
     
 
@@ -114,7 +117,12 @@ a decreasing rate constant." />
 
       
       
-        
+        
+  
+    
+     
+  
+
       
       
     
@@ -129,7 +137,7 @@ a decreasing rate constant." />
   
     
     First-Order Multi-Compartment kinetics
-    
+    Source: R/parent_solutions.R
     FOMC.solution.Rd
     
 
@@ -138,7 +146,7 @@ a decreasing rate constant." />
 a decreasing rate constant.
     
 
-    FOMC.solution(t, parent.0, alpha, beta)
+    FOMC.solution(t, parent_0, alpha, beta)
Arguments

       Time.
     
     parent.0 parent_0
       Starting value for the response variable at time zero.
     
     
 
     
     
   
 
 
 
 
       
 
 
 
 
 
 
 
 
 
 
 
     
 
     
     
@@ -148,7 +156,7 @@ a decreasing rate constant.
-      
+      
@@ -185,23 +193,25 @@ in the original equation.
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
+    See also
+
+    Other parent solutions: 
+DFOP.solution(),
+HS.solution(),
+IORE.solution(),
+SFO.solution(),
+SFORB.solution(),
+logistic.solution()
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))

 
-  
-    Contents
-    
-      Arguments
-      Value
-      Details
-      Note
-      References
-      Examples
-    
-
+  
+    
+      Contents
+    
   
 
 
@@ -212,7 +222,7 @@ in the original equation.

-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 82b9324c..ad33d948 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
-
+
 
-
+
+
+
+
+
-
-
+
+
-
+
-
-
+
+
@@ -38,7 +42,6 @@
 
-
 
 
 
@@ -56,7 +59,7 @@ between them." />
 
   
 
-  
+  
       
       
@@ -70,7 +73,7 @@ between them." />
       
       
         mkin
-        0.9.49.6
+        0.9.49.11
       
     
 
@@ -114,7 +117,12 @@ between them." />
 
       
       
-        
+        
+  
+    
+     
+  
+
       
       
     
@@ -129,7 +137,7 @@ between them." />
   
     
     Hockey-Stick kinetics
-    
+    Source: R/parent_solutions.R
     HS.solution.Rd
     
 
@@ -138,27 +146,11 @@ between them." />
 between them.
     
 
-    HS.solution(t, parent.0, k1, k2, tb)
+    HS.solution(t, parent_0, k1, k2, tb)
Arguments

       Time.
     
     parent.0 parent_0
       Starting value for the response variable at time zero.
     
     
 
 
     
     
   
 
 
 
 
       
 
 
 
 
 
 
 
 
 
 
 
     
 
     
     
-    
-      
-      
-    
-    
-      
-      
-    
-    
-      
-      
-    
-    
-      
-      
-    
     t Time.
parent.0 Starting value for the response variable at time zero.
k1 First kinetic constant.
k2 Second kinetic constant.
     
       tb
       Break point. Before this time, exponential decline according to
@@ -167,31 +159,25 @@ according to k2.
     
     
 
-    Value
-
-    The value of the response variable at time t.
-    References
+    See also
 
-    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
+    Other parent solutions: 
+DFOP.solution(),
+FOMC.solution(),
+IORE.solution(),
+SFO.solution(),
+SFORB.solution(),
+logistic.solution()
 
     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))

 
   
-  
-    Contents
-    
-      Arguments
-      Value
-      References
-      Examples
-    
-
+  
+    
+      Contents
+    
   
 
 
@@ -202,7 +188,7 @@ according to k2.
 
 
 
-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
 
       
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 6af44ab8..677d4b43 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -38,7 +42,6 @@
 
 
-
 
 
 
@@ -56,7 +59,7 @@ a concentration dependent rate constant." />
 
   
 
-  
+  
     
       
       
@@ -70,7 +73,7 @@ a concentration dependent rate constant." />
       
       
         mkin
-        0.9.49.6
+        0.9.49.11
       
     
 
@@ -114,7 +117,12 @@ a concentration dependent rate constant." />
 
       
       
-        
+        
+  
+    
+     
+  
+
       
       
     

@@ -129,7 +137,7 @@ a concentration dependent rate constant." />
   
     
     Indeterminate order rate equation kinetics
-    
+    Source: R/parent_solutions.R
     IORE.solution.Rd
     
 
@@ -138,7 +146,7 @@ a concentration dependent rate constant." />
 a concentration dependent rate constant.
     
 
-    IORE.solution(t, parent.0, k__iore, N)
+    IORE.solution(t, parent_0, k__iore, N)
 
     Arguments
     
@@ -148,7 +156,7 @@ a concentration dependent rate constant.
-      
+      
@@ -175,37 +183,31 @@ units used.
NAFTA Technical Working Group on Pesticides (not dated) Guidance
   for Evaluating and Calculating Degradation Kinetics in Environmental Media
+    See also
+
+    Other parent solutions: 
+DFOP.solution(),
+FOMC.solution(),
+HS.solution(),
+SFO.solution(),
+SFORB.solution(),
+logistic.solution()
Examples

-  plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2, ylim = c(0, 100))
  # \dontrun{
-    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)
+  plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2, ylim = c(0, 100))
  # \dontrun{
+    fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
#> Error in (function (t, parent_0, alpha, beta) {    parent = parent_0/(t/beta + 1)^alpha})(t = c(0, 1, 1.2020202020202, 2.4040404040404, 3, 3.60606060606061, 4.80808080808081, 6.01010101010101, 7, 7.21212121212121, 8.41414141414141, 9.61616161616162, 10.8181818181818, 12.020202020202, 13.2222222222222, 14, 14.4242424242424, 15.6262626262626, 16.8282828282828, 18.030303030303, 19.2323232323232, 20.4343434343434, 21.6363636363636, 22.8383838383838, 24.040404040404, 25.2424242424242, 26.4444444444444, 27.6464646464646, 28, 28.8484848484848, 30.050505050505, 31.2525252525253, 32.4545454545455, 33.6565656565657, 34.8585858585859, 36.0606060606061, 37.2626262626263, 38.4646464646465, 39.6666666666667, 40.8686868686869, 42.0707070707071, 43.2727272727273, 44.4747474747475, 45.6767676767677, 46.8787878787879, 48.0808080808081, 49.2828282828283, 50.4848484848485, 51.6868686868687, 52.8888888888889, 54.0909090909091, 55.2929292929293, 56.4949494949495, 57.6969696969697, 58.8989898989899, 60.1010101010101, 61.3030303030303, 62.5050505050505, 63, 63.7070707070707, 64.9090909090909, 66.1111111111111, 67.3131313131313, 68.5151515151515, 69.7171717171717, 70.9191919191919, 72.1212121212121, 73.3232323232323, 74.5252525252525, 75.7272727272727, 76.9292929292929, 78.1313131313131, 79.3333333333333, 80.5353535353535, 81.7373737373737, 82.9393939393939, 84.1414141414141, 85.3434343434343, 86.5454545454545, 87.7474747474747, 88.9494949494949, 90.1515151515152, 91, 91.3535353535353, 92.5555555555556, 93.7575757575758, 94.959595959596, 96.1616161616162, 97.3636363636364, 98.5656565656566, 99.7676767676768, 100.969696969697, 102.171717171717, 103.373737373737, 104.575757575758, 105.777777777778, 106.979797979798, 108.181818181818, 109.383838383838, 110.585858585859, 111.787878787879, 112.989898989899, 114.191919191919, 115.393939393939, 116.59595959596, 117.79797979798, 119), parent.0 = c(parent = 85.1),     alpha = 1, beta = 10): unbenutztes Argument (parent.0 = 85.1)
#> Timing stopped at: 0.002 0 0.002
    fit.iore <- mkinfit("IORE", FOCUS_2006_C, quiet = TRUE)
#> Error in (function (t, parent_0, k__iore, N) {    parent = (parent_0^(1 - N) - (1 - N) * k__iore * t)^(1/(1 -         N))})(t = c(0, 1, 1.2020202020202, 2.4040404040404, 3, 3.60606060606061, 4.80808080808081, 6.01010101010101, 7, 7.21212121212121, 8.41414141414141, 9.61616161616162, 10.8181818181818, 12.020202020202, 13.2222222222222, 14, 14.4242424242424, 15.6262626262626, 16.8282828282828, 18.030303030303, 19.2323232323232, 20.4343434343434, 21.6363636363636, 22.8383838383838, 24.040404040404, 25.2424242424242, 26.4444444444444, 27.6464646464646, 28, 28.8484848484848, 30.050505050505, 31.2525252525253, 32.4545454545455, 33.6565656565657, 34.8585858585859, 36.0606060606061, 37.2626262626263, 38.4646464646465, 39.6666666666667, 40.8686868686869, 42.0707070707071, 43.2727272727273, 44.4747474747475, 45.6767676767677, 46.8787878787879, 48.0808080808081, 49.2828282828283, 50.4848484848485, 51.6868686868687, 52.8888888888889, 54.0909090909091, 55.2929292929293, 56.4949494949495, 57.6969696969697, 58.8989898989899, 60.1010101010101, 61.3030303030303, 62.5050505050505, 63, 63.7070707070707, 64.9090909090909, 66.1111111111111, 67.3131313131313, 68.5151515151515, 69.7171717171717, 70.9191919191919, 72.1212121212121, 73.3232323232323, 74.5252525252525, 75.7272727272727, 76.9292929292929, 78.1313131313131, 79.3333333333333, 80.5353535353535, 81.7373737373737, 82.9393939393939, 84.1414141414141, 85.3434343434343, 86.5454545454545, 87.7474747474747, 88.9494949494949, 90.1515151515152, 91, 91.3535353535353, 92.5555555555556, 93.7575757575758, 94.959595959596, 96.1616161616162, 97.3636363636364, 98.5656565656566, 99.7676767676768, 100.969696969697, 102.171717171717, 103.373737373737, 104.575757575758, 105.777777777778, 106.979797979798, 108.181818181818, 109.383838383838, 110.585858585859, 111.787878787879, 112.989898989899, 114.191919191919, 115.393939393939, 116.59595959596, 117.79797979798, 119), parent.0 = c(parent = 85.1),     k__iore = 0.1, N = 1.1): unbenutztes Argument (parent.0 = 85.1)
#> Timing stopped at: 0 0 0.001
    fit.iore.deS <- mkinfit("IORE", FOCUS_2006_C, solution_type = "deSolve", quiet = TRUE)
 
     print(data.frame(fit.fomc$par, fit.iore$par, fit.iore.deS$par,
-                     row.names = paste("model par", 1:4)))
#>             fit.fomc.par fit.iore.par fit.iore.deS.par
-#> model par 1  85.87489063    85.874890        85.874890
-#> model par 2   0.05192238    -4.826631        -4.826631
-#> model par 3   0.65096665     1.949403         1.949403
-#> model par 4   1.85744396     1.857444         1.857444
    print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes,
-                iore.deS = endpoints(fit.iore)$distimes))
#>              DT50    DT90 DT50back
-#> fomc     1.785233 15.1479 4.559973
-#> iore     1.785233 15.1479 4.559973
-#> iore.deS 1.785233 15.1479 4.559973
  # }
+                     row.names = paste("model par", 1:4)))
#> Error in data.frame(fit.fomc$par, fit.iore$par, fit.iore.deS$par, row.names = paste("model par",     1:4)): Objekt 'fit.fomc' nicht gefunden
    print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes,
+                iore.deS = endpoints(fit.iore)$distimes))
#> Error in endpoints(fit.fomc): Objekt 'fit.fomc' nicht gefunden
  # }
 
 
-  
-    Contents
-    
-      Arguments
-      Value
-      Note
-      References
-      Examples
-    
-
+  
+    
+      Contents
+    
   
 
 
@@ -216,7 +218,7 @@ units used.

-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 55fd61a4..93da04eb 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
-
+
 
-
+
+
+
+
+
-
-
+
+
-
+
-
-
+
+
@@ -37,7 +41,6 @@
 
 
-
 
 
 
@@ -55,7 +58,7 @@
 
   
 
-  
+  
       
       
@@ -69,7 +72,7 @@
       
       
         mkin
-        0.9.49.6
+        0.9.49.11
       
     
 
@@ -113,7 +116,12 @@
 
       
       
-        
+        
+  
+    
+     
+  
+
       
       
     
@@ -128,7 +136,7 @@
   
     
     Single First-Order kinetics
-    
+    Source: R/parent_solutions.R
     SFO.solution.Rd
     
 
@@ -136,7 +144,7 @@
     Function describing exponential decline from a defined starting value.
     
 
-    SFO.solution(t, parent.0, k)
+    SFO.solution(t, parent_0, k)
Arguments

       Time.
     
     parent.0 parent_0
       Starting value for the response variable at time zero.
     
     
 
     
 
     
     
   
 
 
 
 
       
 
 
 
 
 
 
 
 
 
 
 
     
 
     
     
@@ -146,12 +154,12 @@
       
-      
+      
-      
+      Time.
     
     parent.0 parent_0
       Starting value for the response variable at time zero.
     
     
       k Kinetic constant. Kinetic rate constant.
     
     
 
@@ -164,22 +172,31 @@
   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
+FOCUS (2014) “Generic guidance for Estimating Persistence
+  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+  EU Registration” Report of the FOCUS Work Group on Degradation Kinetics,
+  Version 1.1, 18 December 2014
   http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics
+    See also
+
+    Other parent solutions: 
+DFOP.solution(),
+FOMC.solution(),
+HS.solution(),
+IORE.solution(),
+SFORB.solution(),
+logistic.solution()
 
     Examples
     
-  plot(function(x) SFO.solution(x, 100, 3), 0, 2)

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

 
   
-  
-    Contents
-    
-      Arguments
-      Value
-      References
-      Examples
-    
-
+  
+    
+      Contents
+    
   
 
 
@@ -190,7 +207,7 @@
 
 
 
-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
 
       
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index fbf067af..c9f1b471 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -41,7 +45,6 @@ the kinetic model with first-order terms for a two-way transfer from a free
 to a bound fraction, and a first-order degradation term for the free
 fraction.  The initial condition is a defined amount in the free fraction
 and no substance in the bound fraction." />
-
 
 
 
@@ -59,7 +62,7 @@ and no substance in the bound fraction." />
 
   
 
-  
+  
     
       
       
@@ -73,7 +76,7 @@ and no substance in the bound fraction." />
       
       
         mkin
-        0.9.49.6
+        0.9.49.11
       
     
 
@@ -117,7 +120,12 @@ and no substance in the bound fraction." />
 
       
       
-        
+        
+  
+    
+     
+  
+
       
       
     

@@ -132,7 +140,7 @@ and no substance in the bound fraction." />
   
     
     Single First-Order Reversible Binding kinetics
-    
+    Source: R/parent_solutions.R
     SFORB.solution.Rd
     
 
@@ -144,19 +152,11 @@ fraction.  The initial condition is a defined amount in the free fraction
 and no substance in the bound fraction.
     
 
-    SFORB.solution(t, parent.0, k_12, k_21, k_1output)
+    SFORB.solution(t, parent_0, k_12, k_21, k_1output)
 
     
Arguments
     
-    
-      
-      
-    
-    
-      
-      
-    
@@ -176,28 +176,25 @@ fraction.
The value of the response variable, which is the sum of free and
   bound fractions at time t.
-    References
+    See also
 
-    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
+    Other parent solutions: 
+DFOP.solution(),
+FOMC.solution(),
+HS.solution(),
+IORE.solution(),
+SFO.solution(),
+logistic.solution()
Examples

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

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

 
-  
-    Contents
-    
-      Arguments
-      Value
-      References
-      Examples
-    
-
+  
+    
+      Contents
+    
   
 
 
@@ -208,7 +205,7 @@ fraction.

-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index e6a373d6..f77881fe 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
-
+
 
-
+
+
+
+
+
-
-
+
+
-
+
-
-
+
+
@@ -53,7 +57,7 @@
 
   
 
-  
+  
       
       
@@ -111,7 +115,12 @@
 
       
       
-        
+        
+  
+    
+     
+  
+
       
       
     

@@ -143,6 +152,11 @@
           
Essential functionality

         
       
+      
+      
+    
+      
+      
       
Functions working with mkinfit objects

+      
+      
+    
+      
+      
       
Functions working with aggregated results

+      
+      
+    
+      
+      
       
Create and work with nonlinear mixed models

+      
+      
+    
+      
+      
       
+      
+      
+    
+      
+      
       
+      
+      
+    
+      
+      
       
+      
+      
+    
+      
+      
       
Parent only model solutions

+      
+      
+    
+      
+      
       
@@ -571,6 +620,11 @@ kinetic models fitted with mkinfit

+      
+      
+    
+      
+      
       
Functions that have been superseded

+      
+      
+    
+      
+      
       
     t Time.
parent.0 Starting value for the response variable at time zero.
     
       k_12
       Kinetic constant describing transfer from free to bound.
 
     
 
     
     
   
 
 
 
 
       
 
 
 
 
 
 
 
 
 
 
     

         
         
@@ -176,6 +190,11 @@ more datasets
           
         
       

         
         
@@ -251,6 +270,11 @@ with mkinfit
           
         
       

         
         
@@ -278,6 +302,11 @@ of an mmkin object
           
         
       

         
         
@@ -310,6 +339,11 @@ of an mmkin object
           
         
       

         
         
@@ -402,6 +436,11 @@ of an mmkin object
           
         
       

         
         
@@ -422,6 +461,11 @@ of an mmkin object
           
         
       

         
         
@@ -521,6 +565,11 @@ kinetic models fitted with mkinfit
           
         
       

         
         
@@ -560,7 +609,7 @@ kinetic models fitted with mkinfit
       

         
         
-          logistic.solution() 
+          logistic.solution() logistic.solution() 
         
         Logistic kinetics
       
           
         
       

         
         
@@ -585,6 +639,11 @@ kinetic models fitted with mkinfit
           
         
       

         
         
@@ -596,20 +655,10 @@ kinetic models fitted with mkinfit
     
   
 
-  
-    Contents
-    
-      Main functions
-      Show results
-      Work with mmkin objects
-      Mixed models
-      Datasets and known results
-      NAFTA guidance
-      Helper functions mainly used internally
-      Analytical solutions
-      Generate synthetic datasets
-      Deprecated functions
-    
+  
+    
+      Contents
+    
   
 
 
@@ -620,7 +669,7 @@ kinetic models fitted with mkinfit
 
 
 
-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
 
       
diff --git a/docs/reference/logistic.solution-1.png b/docs/reference/logistic.solution-1.png
index b9fb891c..fd11d0c0 100644
Binary files a/docs/reference/logistic.solution-1.png and b/docs/reference/logistic.solution-1.png differ
diff --git a/docs/reference/logistic.solution-2.png b/docs/reference/logistic.solution-2.png
index 78a31f93..fd11d0c0 100644
Binary files a/docs/reference/logistic.solution-2.png and b/docs/reference/logistic.solution-2.png differ
diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index b2f24d45..3e87b90d 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -37,8 +41,9 @@
 
 
 
-
 
 
 
@@ -56,7 +61,7 @@ an increasing rate constant, supposedly caused by microbial growth" />
 
   
 
-  
+  
     
       
       
@@ -70,7 +75,7 @@ an increasing rate constant, supposedly caused by microbial growth" />
       
       
         mkin
-        0.9.49.6
+        0.9.49.11
       
     
 
@@ -114,7 +119,12 @@ an increasing rate constant, supposedly caused by microbial growth" />
 
       
       
-        
+        
+  
+    
+     
+  
+
       
       
     

@@ -129,16 +139,20 @@ an increasing rate constant, supposedly caused by microbial growth" />
   
     
     Logistic kinetics
-    
+    Source: R/logistic.solution.R, R/parent_solutions.R
     logistic.solution.Rd
     
 
     
     Function describing exponential decline from a defined starting value, with
+an increasing rate constant, supposedly caused by microbial growth
+Function describing exponential decline from a defined starting value, with
 an increasing rate constant, supposedly caused by microbial growth
     
 
-    logistic.solution(t, parent.0, kmax, k0, r)
+    logistic.solution(t, parent_0, kmax, k0, r)
+
+logistic.solution(t, parent_0, kmax, k0, r)
 
     Arguments
     
@@ -148,7 +162,7 @@ an increasing rate constant, supposedly caused by microbial growth
-      
+      
@@ -163,6 +177,10 @@ an increasing rate constant, supposedly caused by microbial growth
+    
+      
+      
+    
       Time.
     
     parent.0 parent_0
       Starting value for the response variable at time zero.
     
     
       r
       Growth rate of the increase in the rate constant.
     
parent.0 Starting value for the response variable at time zero.
     
 
     Value
@@ -171,6 +189,8 @@ an increasing rate constant, supposedly caused by microbial growth
     Note
 
     The solution of the logistic model reduces to the
+  SFO.solution if k0 is equal to kmax.
+The solution of the logistic model reduces to the
   SFO.solution if k0 is equal to kmax.
     References
 
@@ -179,16 +199,25 @@ an increasing rate constant, supposedly caused by microbial growth
   EU Registration” Report of the FOCUS Work Group on Degradation Kinetics,
   Version 1.1, 18 December 2014
   http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics
+    See also
+
+    Other parent solutions: 
+DFOP.solution(),
+FOMC.solution(),
+HS.solution(),
+IORE.solution(),
+SFO.solution(),
+SFORB.solution()
 
     Examples
     
   # Reproduce the plot on page 57 of FOCUS (2014)
-  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.2),
+  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.2),
        from = 0, to = 100, ylim = c(0, 100),
-       xlab = "Time", ylab = "Residue")
  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.4),
-       from = 0, to = 100, add = TRUE, lty = 2, col = 2)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.8),
-       from = 0, to = 100, add = TRUE, lty = 3, col = 3)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.001, 0.2),
-       from = 0, to = 100, add = TRUE, lty = 4, col = 4)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.08, 0.2),
+       xlab = "Time", ylab = "Residue")
  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.4),
+       from = 0, to = 100, add = TRUE, lty = 2, col = 2)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.8),
+       from = 0, to = 100, add = TRUE, lty = 3, col = 3)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.001, 0.2),
+       from = 0, to = 100, add = TRUE, lty = 4, col = 4)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.08, 0.2),
        from = 0, to = 100, add = TRUE, lty = 5, col = 5)
  legend("topright", inset = 0.05,
          legend = paste0("k0 = ", c(0.0001, 0.0001, 0.0001, 0.001, 0.08),
                          ", r = ", c(0.2, 0.4, 0.8, 0.2, 0.2)),
@@ -205,32 +234,38 @@ an increasing rate constant, supposedly caused by microbial growth
     sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07),
     n = 1, reps = 2, digits = 5, LOD = 0.1, seed = 123456)[[1]]
 
-  m <- mkinfit("logistic", d_2_1, quiet = TRUE)
-  plot_sep(m)
  summary(m)$bpar
#>              Estimate   se_notrans   t value       Pr(>t)        Lower
-#> parent_0 1.057896e+02 1.9023449649 55.610120 3.768361e-16 1.016451e+02
-#> kmax     6.398190e-02 0.0143201029  4.467978 3.841828e-04 3.929235e-02
-#> k0       1.612775e-04 0.0005866813  0.274898 3.940351e-01 5.846685e-08
-#> r        2.263946e-01 0.1718110773  1.317695 1.061044e-01 4.335843e-02
-#> sigma    5.332935e+00 0.9145907310  5.830952 4.036926e-05 3.340213e+00
-#>                Upper
-#> parent_0 109.9341588
-#> kmax       0.1041853
-#> k0         0.4448750
-#> r          1.1821121
-#> sigma      7.3256566
  endpoints(m)$distimes
#>            DT50     DT90  DT50_k0 DT50_kmax
-#> parent 36.86533 62.41511 4297.854  10.83349

+  m <- mkinfit("logistic", d_2_1, quiet = TRUE)
#> Error in (function (t, parent_0, kmax, k0, r) {    parent = parent_0 * (kmax/(kmax - k0 + k0 * exp(r * t)))^(kmax/r)})(t = c(0, 1, 1.21212121212121, 2.42424242424242, 3, 3.63636363636364, 4.84848484848485, 6.06060606060606, 7, 7.27272727272727, 8.48484848484848, 9.6969696969697, 10.9090909090909, 12.1212121212121, 13.3333333333333, 14, 14.5454545454545, 15.7575757575758, 16.969696969697, 18.1818181818182, 19.3939393939394, 20.6060606060606, 21.8181818181818, 23.030303030303, 24.2424242424242, 25.4545454545455, 26.6666666666667, 27.8787878787879, 28, 29.0909090909091, 30.3030303030303, 31.5151515151515, 32.7272727272727, 33.9393939393939, 35.1515151515152, 36.3636363636364, 37.5757575757576, 38.7878787878788, 40, 41.2121212121212, 42.4242424242424, 43.6363636363636, 44.8484848484849, 46.0606060606061, 47.2727272727273, 48.4848484848485, 49.6969696969697, 50.9090909090909, 52.1212121212121, 53.3333333333333, 54.5454545454545, 55.7575757575758, 56.969696969697, 58.1818181818182, 59.3939393939394, 60, 60.6060606060606, 61.8181818181818, 63.030303030303, 64.2424242424242, 65.4545454545455, 66.6666666666667, 67.8787878787879, 69.0909090909091, 70.3030303030303, 71.5151515151515, 72.7272727272727, 73.9393939393939, 75.1515151515152, 76.3636363636364, 77.5757575757576, 78.7878787878788, 80, 81.2121212121212, 82.4242424242424, 83.6363636363636, 84.8484848484848, 86.0606060606061, 87.2727272727273, 88.4848484848485, 89.6969696969697, 90, 90.9090909090909, 92.1212121212121, 93.3333333333333, 94.5454545454545, 95.7575757575758, 96.969696969697, 98.1818181818182, 99.3939393939394, 100.606060606061, 101.818181818182, 103.030303030303, 104.242424242424, 105.454545454545, 106.666666666667, 107.878787878788, 109.090909090909, 110.30303030303, 111.515151515152, 112.727272727273, 113.939393939394, 115.151515151515, 116.363636363636, 117.575757575758, 118.787878787879, 120), parent.0 = c(parent = 101.95687), kmax = 0.1,     k0 = 1e-04, r = 0.2): unbenutztes Argument (parent.0 = 101.95687)
#> Timing stopped at: 0.001 0 0.001
  plot_sep(m)
#> Error in identical(fit$err_mod, "const"): Objekt 'm' nicht gefunden
  summary(m)$bpar
#> Error in summary(m): Objekt 'm' nicht gefunden
  endpoints(m)$distimes
#> Error in endpoints(m): Objekt 'm' nicht gefunden

+
+  # Reproduce the plot on page 57 of FOCUS (2014)
+  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.2),
+       from = 0, to = 100, ylim = c(0, 100),
+       xlab = "Time", ylab = "Residue")
  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.4),
+       from = 0, to = 100, add = TRUE, lty = 2, col = 2)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.8),
+       from = 0, to = 100, add = TRUE, lty = 3, col = 3)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.001, 0.2),
+       from = 0, to = 100, add = TRUE, lty = 4, col = 4)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.08, 0.2),
+       from = 0, to = 100, add = TRUE, lty = 5, col = 5)
  legend("topright", inset = 0.05,
+         legend = paste0("k0 = ", c(0.0001, 0.0001, 0.0001, 0.001, 0.08),
+                         ", r = ", c(0.2, 0.4, 0.8, 0.2, 0.2)),
+         lty = 1:5, col = 1:5)

+  # Fit with synthetic data
+  logistic <- mkinmod(parent = mkinsub("logistic"))
+
+  sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+  parms_logistic <- c(kmax = 0.08, k0 = 0.0001, r = 0.2)
+  d_logistic <- mkinpredict(logistic,
+    parms_logistic, c(parent = 100),
+    sampling_times)
+  d_2_1 <- add_err(d_logistic,
+    sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07),
+    n = 1, reps = 2, digits = 5, LOD = 0.1, seed = 123456)[[1]]
+
+  m <- mkinfit("logistic", d_2_1, quiet = TRUE)
#> Error in (function (t, parent_0, kmax, k0, r) {    parent = parent_0 * (kmax/(kmax - k0 + k0 * exp(r * t)))^(kmax/r)})(t = c(0, 1, 1.21212121212121, 2.42424242424242, 3, 3.63636363636364, 4.84848484848485, 6.06060606060606, 7, 7.27272727272727, 8.48484848484848, 9.6969696969697, 10.9090909090909, 12.1212121212121, 13.3333333333333, 14, 14.5454545454545, 15.7575757575758, 16.969696969697, 18.1818181818182, 19.3939393939394, 20.6060606060606, 21.8181818181818, 23.030303030303, 24.2424242424242, 25.4545454545455, 26.6666666666667, 27.8787878787879, 28, 29.0909090909091, 30.3030303030303, 31.5151515151515, 32.7272727272727, 33.9393939393939, 35.1515151515152, 36.3636363636364, 37.5757575757576, 38.7878787878788, 40, 41.2121212121212, 42.4242424242424, 43.6363636363636, 44.8484848484849, 46.0606060606061, 47.2727272727273, 48.4848484848485, 49.6969696969697, 50.9090909090909, 52.1212121212121, 53.3333333333333, 54.5454545454545, 55.7575757575758, 56.969696969697, 58.1818181818182, 59.3939393939394, 60, 60.6060606060606, 61.8181818181818, 63.030303030303, 64.2424242424242, 65.4545454545455, 66.6666666666667, 67.8787878787879, 69.0909090909091, 70.3030303030303, 71.5151515151515, 72.7272727272727, 73.9393939393939, 75.1515151515152, 76.3636363636364, 77.5757575757576, 78.7878787878788, 80, 81.2121212121212, 82.4242424242424, 83.6363636363636, 84.8484848484848, 86.0606060606061, 87.2727272727273, 88.4848484848485, 89.6969696969697, 90, 90.9090909090909, 92.1212121212121, 93.3333333333333, 94.5454545454545, 95.7575757575758, 96.969696969697, 98.1818181818182, 99.3939393939394, 100.606060606061, 101.818181818182, 103.030303030303, 104.242424242424, 105.454545454545, 106.666666666667, 107.878787878788, 109.090909090909, 110.30303030303, 111.515151515152, 112.727272727273, 113.939393939394, 115.151515151515, 116.363636363636, 117.575757575758, 118.787878787879, 120), parent.0 = c(parent = 101.95687), kmax = 0.1,     k0 = 1e-04, r = 0.2): unbenutztes Argument (parent.0 = 101.95687)
#> Timing stopped at: 0 0 0
  plot_sep(m)
#> Error in identical(fit$err_mod, "const"): Objekt 'm' nicht gefunden
  summary(m)$bpar
#> Error in summary(m): Objekt 'm' nicht gefunden
  endpoints(m)$distimes
#> Error in endpoints(m): Objekt 'm' nicht gefunden

 
   
-  
-    Contents
-    
-      Arguments
-      Value
-      Note
-      References
-      Examples
-    
-
+  
+    
+      Contents
+    
   
 
 
@@ -241,7 +276,7 @@ an increasing rate constant, supposedly caused by microbial growth
 
 
 
-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
 
       
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index 4f5d9f67..778c5132 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -40,7 +44,6 @@
 mkinfit does not take mkinds datasets as argument, but works with dataframes
 such as the on contained in the data field of mkinds objects. Some datasets
 provided by this package come as mkinds objects nevertheless." />
-
 
 
 
@@ -58,7 +61,7 @@ provided by this package come as mkinds objects nevertheless." />
 
   
 
-  
+  
     
       
       
@@ -116,7 +119,12 @@ provided by this package come as mkinds objects nevertheless." />
 
       
       
-        
+        
+  
+    
+     
+  
+
       
       
     

@@ -131,7 +139,7 @@ provided by this package come as mkinds objects nevertheless." />
   
     
     A dataset class for mkin
-    
+    Source: R/mkinds.R
     mkinds.Rd
     
 
@@ -149,7 +157,7 @@ provided by this package come as mkinds objects nevertheless.
     The S3 printing method print.mkinds
     Public fields
 
-    

+    

 title
A full title for the dataset
 
 sampling_times
The sampling times
@@ -178,10 +186,10 @@ and value in order to be compatible with mkinfit
 

 
Method new()
 Create a new mkinds object
Usage
-
mkinds$new(title = "", data, time_unit = NA, unit = NA)

+
mkinds$new(title = "", data, time_unit = NA, unit = NA)

 
 Arguments
-

+

 title
The dataset title
 
 data
The data
@@ -194,10 +202,10 @@ and value in order to be compatible with mkinfit
 

 
Method clone()
 The objects of this class are cloneable with this method.
Usage
-
mkinds$clone(deep = FALSE)

+
mkinds$clone(deep = FALSE)

 
 Arguments
-

+

 deep
Whether to make a deep clone.
 
 

@@ -213,15 +221,10 @@ and value in order to be compatible with mkinfit
 #> With a maximum of  1  replicates

 
   
-  
-    Contents
-    
-      See also
-      Public fields
-      Methods
-      Examples
-    
-
+  
+    
+      Contents
+    
   
 
 
@@ -232,7 +235,7 @@ and value in order to be compatible with mkinfit
 
 
 
-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
 
       
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 09837505..62823c58 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -43,7 +47,6 @@ kinetic model is solved using the function mkinpredict. The
 parameters of the selected error model are fitted simultaneously with the
 degradation model parameters, as both of them are arguments of the
 likelihood function." />
-
 
 
 
@@ -61,7 +64,7 @@ likelihood function." />
 
   
 
-  
+  
     
       
       
@@ -119,7 +122,12 @@ likelihood function." />
 
       
       
-        
+        
+  
+    
+     
+  
+
       
       
     

@@ -134,7 +142,7 @@ likelihood function." />
   
     
     Fit a kinetic model to data with one or more state variables
-    
+    Source: R/mkinfit.R
     mkinfit.Rd
     
 
@@ -168,8 +176,8 @@ likelihood function.
   rtol = 1e-10,
   n.outtimes = 100,
   error_model = c("const", "obs", "tc"),
-  error_model_algorithm = c("auto", "d_3", "direct", "twostep", "threestep", "fourstep",
-    "IRLS", "OLS"),
+  error_model_algorithm = c("auto", "d_3", "direct", "twostep", "threestep",
+    "fourstep", "IRLS", "OLS"),
   reweight.tol = 1e-08,
   reweight.max.iter = 10,
   trace_parms = FALSE,
@@ -414,82 +422,7 @@ estimators.
     Examples
     
 # Use shorthand notation for parent only degradation
-fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.49.11 
-#> R version used for fitting:       3.6.3 
-#> Date of fit:     Mon Apr 20 18:52:22 2020 
-#> Date of summary: Mon Apr 20 18:52:22 2020 
-#> 
-#> Equations:
-#> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
-#> 
-#> Model predictions using solution type analytical 
-#> 
-#> Fitted using 222 model solutions performed in 0.473 s
-#> 
-#> Error model: Constant variance 
-#> 
-#> Error model algorithm: OLS 
-#> 
-#> Starting values for parameters to be optimised:
-#>          value   type
-#> parent_0  85.1  state
-#> alpha      1.0 deparm
-#> beta      10.0 deparm
-#> 
-#> Starting values for the transformed parameters actually optimised:
-#>               value lower upper
-#> parent_0  85.100000  -Inf   Inf
-#> log_alpha  0.000000  -Inf   Inf
-#> log_beta   2.302585  -Inf   Inf
-#> 
-#> Fixed parameter values:
-#> None
-#> 
-#> Optimised, transformed parameters with symmetric confidence intervals:
-#>           Estimate Std. Error    Lower   Upper
-#> parent_0  85.87000     1.8070 81.23000 90.5200
-#> log_alpha  0.05192     0.1353 -0.29580  0.3996
-#> log_beta   0.65100     0.2287  0.06315  1.2390
-#> sigma      1.85700     0.4378  0.73200  2.9830
-#> 
-#> Parameter correlation:
-#>             parent_0  log_alpha   log_beta     sigma
-#> parent_0   1.000e+00 -1.565e-01 -3.142e-01 4.758e-08
-#> log_alpha -1.565e-01  1.000e+00  9.564e-01 1.007e-07
-#> log_beta  -3.142e-01  9.564e-01  1.000e+00 8.568e-08
-#> sigma      4.758e-08  1.007e-07  8.568e-08 1.000e+00
-#> 
-#> 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   85.870  47.530 3.893e-08 81.2300 90.520
-#> alpha       1.053   7.393 3.562e-04  0.7439  1.491
-#> beta        1.917   4.373 3.601e-03  1.0650  3.451
-#> sigma       1.857   4.243 4.074e-03  0.7320  2.983
-#> 
-#> FOCUS Chi2 error levels in percent:
-#>          err.min n.optim df
-#> All data   6.657       3  6
-#> parent     6.657       3  6
-#> 
-#> Estimated disappearance times:
-#>         DT50  DT90 DT50back
-#> parent 1.785 15.15     4.56
-#> 
-#> Data:
-#>  time variable observed predicted residual
-#>     0   parent     85.1    85.875  -0.7749
-#>     1   parent     57.9    55.191   2.7091
-#>     3   parent     29.9    31.845  -1.9452
-#>     7   parent     14.6    17.012  -2.4124
-#>    14   parent      9.7     9.241   0.4590
-#>    28   parent      6.6     4.754   1.8460
-#>    63   parent      4.0     2.102   1.8977
-#>    91   parent      3.9     1.441   2.4590
-#>   119   parent      0.6     1.092  -0.4919

+fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
#> Error in (function (t, parent_0, alpha, beta) {    parent = parent_0/(t/beta + 1)^alpha})(t = c(0, 1, 1.2020202020202, 2.4040404040404, 3, 3.60606060606061, 4.80808080808081, 6.01010101010101, 7, 7.21212121212121, 8.41414141414141, 9.61616161616162, 10.8181818181818, 12.020202020202, 13.2222222222222, 14, 14.4242424242424, 15.6262626262626, 16.8282828282828, 18.030303030303, 19.2323232323232, 20.4343434343434, 21.6363636363636, 22.8383838383838, 24.040404040404, 25.2424242424242, 26.4444444444444, 27.6464646464646, 28, 28.8484848484848, 30.050505050505, 31.2525252525253, 32.4545454545455, 33.6565656565657, 34.8585858585859, 36.0606060606061, 37.2626262626263, 38.4646464646465, 39.6666666666667, 40.8686868686869, 42.0707070707071, 43.2727272727273, 44.4747474747475, 45.6767676767677, 46.8787878787879, 48.0808080808081, 49.2828282828283, 50.4848484848485, 51.6868686868687, 52.8888888888889, 54.0909090909091, 55.2929292929293, 56.4949494949495, 57.6969696969697, 58.8989898989899, 60.1010101010101, 61.3030303030303, 62.5050505050505, 63, 63.7070707070707, 64.9090909090909, 66.1111111111111, 67.3131313131313, 68.5151515151515, 69.7171717171717, 70.9191919191919, 72.1212121212121, 73.3232323232323, 74.5252525252525, 75.7272727272727, 76.9292929292929, 78.1313131313131, 79.3333333333333, 80.5353535353535, 81.7373737373737, 82.9393939393939, 84.1414141414141, 85.3434343434343, 86.5454545454545, 87.7474747474747, 88.9494949494949, 90.1515151515152, 91, 91.3535353535353, 92.5555555555556, 93.7575757575758, 94.959595959596, 96.1616161616162, 97.3636363636364, 98.5656565656566, 99.7676767676768, 100.969696969697, 102.171717171717, 103.373737373737, 104.575757575758, 105.777777777778, 106.979797979798, 108.181818181818, 109.383838383838, 110.585858585859, 111.787878787879, 112.989898989899, 114.191919191919, 115.393939393939, 116.59595959596, 117.79797979798, 119), parent.0 = c(parent = 85.1),     alpha = 1, beta = 10): unbenutztes Argument (parent.0 = 85.1)
#> Timing stopped at: 0 0 0.001
summary(fit)
#> Error in summary(fit): Objekt 'fit' nicht gefunden

 # One parent compound, one metabolite, both single first order.
 # Use mkinsub for convenience in model formulation. Pathway to sink included per default.
 SFO_SFO <- mkinmod(
@@ -497,7 +430,8 @@ estimators.
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#> Warning: Observations with value of zero were removed from the data
#>        User      System verstrichen 
-#>       1.465       0.003       1.474 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.526       0.000       1.526 
parms(fit)
#>      parent_0 k_parent_sink   k_parent_m1     k_m1_sink         sigma 
+#>  99.598483069   0.047920122   0.050777612   0.005260651   3.125503875 
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -567,7 +501,8 @@ estimators.
 #> Sum of squared residuals at call 126: 371.2134
 #> Sum of squared residuals at call 135: 371.2134
 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>       1.052       0.000       1.068 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.084       0.000       1.085 
parms(fit.deSolve)
#>      parent_0 k_parent_sink   k_parent_m1     k_m1_sink         sigma 
+#>  99.598483072   0.047920122   0.050777612   0.005260651   3.125503874 
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -583,25 +518,23 @@ estimators.
   parent = mkinsub("FOMC", "m1"),
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
# Use starting parameters from parent only FOMC fit
-fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE)
-fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE,
-  parms.ini = fit.FOMC$bparms.ode)
#> Warning: Observations with value of zero were removed from the data

+fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE)
#> Error in (function (t, parent_0, alpha, beta) {    parent = parent_0/(t/beta + 1)^alpha})(t = c(0, 0.757575757575758, 1, 1.51515151515152, 2.27272727272727, 3, 3.03030303030303, 3.78787878787879, 4.54545454545454, 5.3030303030303, 6.06060606060606, 6.81818181818182, 7, 7.57575757575758, 8.33333333333333, 9.09090909090909, 9.84848484848485, 10.6060606060606, 11.3636363636364, 12.1212121212121, 12.8787878787879, 13.6363636363636, 14, 14.3939393939394, 15.1515151515152, 15.9090909090909, 16.6666666666667, 17.4242424242424, 18.1818181818182, 18.9393939393939, 19.6969696969697, 20.4545454545455, 21, 21.2121212121212, 21.969696969697, 22.7272727272727, 23.4848484848485, 24.2424242424242, 25, 25.7575757575758, 26.5151515151515, 27.2727272727273, 28.030303030303, 28.7878787878788, 29.5454545454545, 30.3030303030303, 31.0606060606061, 31.8181818181818, 32.5757575757576, 33.3333333333333, 34.0909090909091, 34.8484848484849, 35, 35.6060606060606, 36.3636363636364, 37.1212121212121, 37.8787878787879, 38.6363636363636, 39.3939393939394, 40.1515151515151, 40.9090909090909, 41.6666666666667, 42.4242424242424, 43.1818181818182, 43.9393939393939, 44.6969696969697, 45.4545454545455, 46.2121212121212, 46.969696969697, 47.7272727272727, 48.4848484848485, 49.2424242424242, 50, 50.7575757575758, 51.5151515151515, 52.2727272727273, 53.030303030303, 53.7878787878788, 54.5454545454545, 55.3030303030303, 56.0606060606061, 56.8181818181818, 57.5757575757576, 58.3333333333333, 59.0909090909091, 59.8484848484849, 60.6060606060606, 61.3636363636364, 62.1212121212121, 62.8787878787879, 63.6363636363636, 64.3939393939394, 65.1515151515152, 65.9090909090909, 66.6666666666667, 67.4242424242424, 68.1818181818182, 68.9393939393939, 69.6969696969697, 70.4545454545455, 71.2121212121212, 71.969696969697, 72.7272727272727, 73.4848484848485, 74.2424242424242, 75), parent.0 = c(parent = 100.75), alpha = 1,     beta = 10): unbenutztes Argument (parent.0 = 100.75)
#> Timing stopped at: 0 0 0.001
fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE,
+  parms.ini = fit.FOMC$bparms.ode)
#> Warning: Observations with value of zero were removed from the data
#> Error in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE, parms.ini = fit.FOMC$bparms.ode): Objekt 'fit.FOMC' nicht gefunden

 # 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
 fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve",
                                  quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
# 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)
#> Warning: Observations with value of zero were removed from the data
# }
+fit.SFORB = mkinfit("SFORB", FOCUS_2006_D, quiet = TRUE)
#> Error in (function (t, parent_0, k_12, k_21, k_1output) {    sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 + k_12 *         k_21 - (k_12 + k_1output) * k_21)    b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp    b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp    parent = parent_0 * (((k_12 + k_21 - b1)/(b2 - b1)) * exp(-b1 *         t) + ((k_12 + k_21 - b2)/(b1 - b2)) * exp(-b2 * t))})(t = c(0, 0.757575757575758, 1, 1.51515151515152, 2.27272727272727, 3, 3.03030303030303, 3.78787878787879, 4.54545454545454, 5.3030303030303, 6.06060606060606, 6.81818181818182, 7, 7.57575757575758, 8.33333333333333, 9.09090909090909, 9.84848484848485, 10.6060606060606, 11.3636363636364, 12.1212121212121, 12.8787878787879, 13.6363636363636, 14, 14.3939393939394, 15.1515151515152, 15.9090909090909, 16.6666666666667, 17.4242424242424, 18.1818181818182, 18.9393939393939, 19.6969696969697, 20.4545454545455, 21, 21.2121212121212, 21.969696969697, 22.7272727272727, 23.4848484848485, 24.2424242424242, 25, 25.7575757575758, 26.5151515151515, 27.2727272727273, 28.030303030303, 28.7878787878788, 29.5454545454545, 30.3030303030303, 31.0606060606061, 31.8181818181818, 32.5757575757576, 33.3333333333333, 34.0909090909091, 34.8484848484849, 35, 35.6060606060606, 36.3636363636364, 37.1212121212121, 37.8787878787879, 38.6363636363636, 39.3939393939394, 40.1515151515151, 40.9090909090909, 41.6666666666667, 42.4242424242424, 43.1818181818182, 43.9393939393939, 44.6969696969697, 45.4545454545455, 46.2121212121212, 46.969696969697, 47.7272727272727, 48.4848484848485, 49.2424242424242, 50, 50.7575757575758, 51.5151515151515, 52.2727272727273, 53.030303030303, 53.7878787878788, 54.5454545454545, 55.3030303030303, 56.0606060606061, 56.8181818181818, 57.5757575757576, 58.3333333333333, 59.0909090909091, 59.8484848484849, 60.6060606060606, 61.3636363636364, 62.1212121212121, 62.8787878787879, 63.6363636363636, 64.3939393939394, 65.1515151515152, 65.9090909090909, 66.6666666666667, 67.4242424242424, 68.1818181818182, 68.9393939393939, 69.6969696969697, 70.4545454545455, 71.2121212121212, 71.969696969697, 72.7272727272727, 73.4848484848485, 74.2424242424242, 75), parent.0 = c(parent_free = 100.75), k_1output = 0.1,     k_12 = 0.1, k_21 = 0.02): unbenutztes Argument (parent.0 = 100.75)
#> Timing stopped at: 0.001 0 0.001
fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
#> Error in mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode,     quiet = TRUE): Objekt 'fit.SFORB' nicht gefunden
# }
 
 # \dontrun{
 # 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)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.11 
-#> R version used for fitting:       3.6.3 
-#> Date of fit:     Mon Apr 20 18:52:37 2020 
-#> Date of summary: Mon Apr 20 18:52:37 2020 
+#> R version used for fitting:       4.0.0 
+#> Date of fit:     Thu May  7 08:59:03 2020 
+#> Date of summary: Thu May  7 08:59:03 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -609,7 +542,7 @@ estimators.
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 422 model solutions performed in 1.087 s
+#> Fitted using 422 model solutions performed in 1.106 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -716,9 +649,9 @@ estimators.
 #>   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.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.11 
-#> R version used for fitting:       3.6.3 
-#> Date of fit:     Mon Apr 20 18:52:40 2020 
-#> Date of summary: Mon Apr 20 18:52:40 2020 
+#> R version used for fitting:       4.0.0 
+#> Date of fit:     Thu May  7 08:59:06 2020 
+#> Date of summary: Thu May  7 08:59:06 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -726,7 +659,7 @@ estimators.
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 979 model solutions performed in 2.518 s
+#> Fitted using 979 model solutions performed in 2.604 s
 #> 
 #> Error model: Variance unique to each observed variable 
 #> 
@@ -848,9 +781,9 @@ estimators.
 #>   100       m1    33.13  31.98773  1.142e+00
 #>   120       m1    25.15  28.80429 -3.654e+00
 #>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.11 
-#> R version used for fitting:       3.6.3 
-#> Date of fit:     Mon Apr 20 18:52:50 2020 
-#> Date of summary: Mon Apr 20 18:52:50 2020 
+#> R version used for fitting:       4.0.0 
+#> Date of fit:     Thu May  7 08:59:16 2020 
+#> Date of summary: Thu May  7 08:59:16 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -858,7 +791,7 @@ estimators.
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 2552 model solutions performed in 10.186 s
+#> Fitted using 2552 model solutions performed in 10.544 s
 #> 
 #> Error model: Two-component variance function 
 #> 
@@ -977,20 +910,10 @@ estimators.
 
 
   
-  
-    Contents
-    
-      Arguments
-      Source
-      Value
-      Details
-      Note
-      See also
-      Examples
-    
-
-    Author
-    Johannes Ranke
+  
+    
+      Contents
+    
   
 
 
@@ -1001,7 +924,7 @@ estimators.
 
 
 
-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
 
       
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index b25f2da3..d1204e2e 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -40,7 +44,6 @@
 name to a list, specifying the kinetic model type and reaction or transfer
 to other observed compartments. Instead of specifying several expressions, a
 list of lists can be given in the speclist argument." />
-
 
 
 
@@ -58,7 +61,7 @@ list of lists can be given in the speclist argument." />
 
   
 
-  
+  
     
       
       
@@ -72,7 +75,7 @@ list of lists can be given in the speclist argument." />
       
       
         mkin
-        0.9.49.9
+        0.9.49.11
       
     
 
@@ -116,7 +119,12 @@ list of lists can be given in the speclist argument." />
 
       
       
-        
+        
+  
+    
+     
+  
+
       
       
     

@@ -131,7 +139,7 @@ list of lists can be given in the speclist argument." />
   
     
     Function to set up a kinetic model with one or more state variables
-    
+    Source: R/mkinmod.R
     mkinmod.Rd
     
 
@@ -205,7 +213,7 @@ applicable to give detailed information about the C function being built.
use_of_ffThe content of use_of_ff is passed on in this list component.
   coefmat
The coefficient matrix, if the system of differential equations can be
     represented by one.
-  ll
The likelihood function, taking the parameter vector as the first argument.
+  cf
If generated, the compiled function as returned by cfunction.
 
     Details
 
@@ -244,7 +252,7 @@ in the FOCUS and NAFTA guidance documents are used.
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file414965c335f6.c 2> file414965c335f6.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file66a9718e919b.c 2> file66a9718e919b.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
@@ -277,19 +285,10 @@ in the FOCUS and NAFTA guidance documents are used.
                           quiet = TRUE)
 # }
   
-  
-    Contents
-    
-      Arguments
-      Value
-      Details
-      Note
-      References
-      Examples
-    
-
-    Author
-    Johannes Ranke
+  
+    
+      Contents
+    
   
 
 
@@ -300,7 +299,7 @@ in the FOCUS and NAFTA guidance documents are used.
 
 
 
-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
 
       
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index fe5bc975..689fb7c7 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -39,7 +43,6 @@
 
-
 
 
 
@@ -57,7 +60,7 @@ kinetic parameters and initial values for the state variables." />
 
   
 
-  
+  
     
       
       
@@ -71,7 +74,7 @@ kinetic parameters and initial values for the state variables." />
       
       
         mkin
-        0.9.49.9
+        0.9.49.11
       
     
 
@@ -115,7 +118,12 @@ kinetic parameters and initial values for the state variables." />
 
       
       
-        
+        
+  
+    
+     
+  
+
       
       
     

@@ -130,7 +138,7 @@ kinetic parameters and initial values for the state variables." />
   
     
     Produce predictions from a kinetic model using specific parameters
-    
+    Source: R/mkinpredict.R
     mkinpredict.Rd
     
 
@@ -258,32 +266,11 @@ solver is used.
 
     Examples
     
-  SFO <- mkinmod(degradinol = mkinsub("SFO"))
-  # Compare solution types
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-        solution_type = "analytical")
#>    time  degradinol
-#> 1     0 100.0000000
-#> 2     1  74.0818221
-#> 3     2  54.8811636
-#> 4     3  40.6569660
-#> 5     4  30.1194212
-#> 6     5  22.3130160
-#> 7     6  16.5298888
-#> 8     7  12.2456428
-#> 9     8   9.0717953
-#> 10    9   6.7205513
-#> 11   10   4.9787068
-#> 12   11   3.6883167
-#> 13   12   2.7323722
-#> 14   13   2.0241911
-#> 15   14   1.4995577
-#> 16   15   1.1108997
-#> 17   16   0.8229747
-#> 18   17   0.6096747
-#> 19   18   0.4516581
-#> 20   19   0.3345965
-#> 21   20   0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-        solution_type = "deSolve")
#>    time  degradinol
+SFO <- mkinmod(degradinol = mkinsub("SFO"))
+# Compare solution types
+mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+      solution_type = "analytical")
#> Error in (function (t, parent_0, k) {    parent = parent_0 * exp(-k * t)})(t = 0:20, parent.0 = c(degradinol = 100), k = 0.3): unbenutztes Argument (parent.0 = 100)
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+      solution_type = "deSolve")
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
 #> 3     2  54.8811636
@@ -304,8 +291,8 @@ solver is used.
 #> 18   17   0.6096747
 #> 19   18   0.4516581
 #> 20   19   0.3345965
-#> 21   20   0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-        solution_type = "deSolve", use_compiled = FALSE)
#>    time  degradinol
+#> 21   20   0.2478752
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+      solution_type = "deSolve", use_compiled = FALSE)
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
 #> 3     2  54.8811636
@@ -326,8 +313,8 @@ solver is used.
 #> 18   17   0.6096747
 #> 19   18   0.4516581
 #> 20   19   0.3345965
-#> 21   20   0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-        solution_type = "eigen")
#>    time  degradinol
+#> 21   20   0.2478752
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+      solution_type = "eigen")
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
 #> 3     2  54.8811636
@@ -349,92 +336,68 @@ solver is used.
 #> 19   18   0.4516581
 #> 20   19   0.3345965
 #> 21   20   0.2478752

-
-  # Compare integration methods to analytical solution
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-        solution_type = "analytical")[21,]
#>    time degradinol
-#> 21   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-        method = "lsoda")[21,]
#>    time degradinol
-#> 21   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-        method = "ode45")[21,]
#>    time degradinol
-#> 21   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-        method = "rk4")[21,]
#>    time degradinol
-#> 21   20  0.2480043
 # rk4 is not as precise here
-
-  # The number of output times used to make a lot of difference until the
-  # default for atol was adjusted
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
-        seq(0, 20, by = 0.1))[201,]
#>     time degradinol
-#> 201   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
-        seq(0, 20, by = 0.01))[2001,]
#>      time degradinol
+# Compare integration methods to analytical solution
+mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+      solution_type = "analytical")[21,]
#> Error in (function (t, parent_0, k) {    parent = parent_0 * exp(-k * t)})(t = 0:20, parent.0 = c(degradinol = 100), k = 0.3): unbenutztes Argument (parent.0 = 100)
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+      method = "lsoda")[21,]
#>    time degradinol
+#> 21   20  0.2478752
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+      method = "ode45")[21,]
#>    time degradinol
+#> 21   20  0.2478752
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+      method = "rk4")[21,]
#>    time degradinol
+#> 21   20  0.2480043
# rk4 is not as precise here
+
+# The number of output times used to make a lot of difference until the
+# default for atol was adjusted
+mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
+      seq(0, 20, by = 0.1))[201,]
#>     time degradinol
+#> 201   20  0.2478752
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
+      seq(0, 20, by = 0.01))[2001,]
#>      time degradinol
 #> 2001   20  0.2478752

-  # Check compiled model versions - they are faster than the eigenvalue based solutions!
-  SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
-                    m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  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 = "eigen")[201,]))
#>     time   parent       m1
-#> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.003       0.000       0.003 
  system.time(
-    print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
-                c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
-                solution_type = "deSolve")[201,]))
#>     time   parent       m1
-#> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.002       0.000       0.002 
  system.time(
-    print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
-                c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
-                solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
-#> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.021       0.000       0.021 

-  # \dontrun{
-    # Predict from a fitted model
-    f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Ordinary least squares optimisation
#> Sum of squared residuals at call 1: 552.5739
-#> Sum of squared residuals at call 3: 552.5739
-#> Sum of squared residuals at call 4: 552.5739
-#> Sum of squared residuals at call 6: 279.9345
-#> Sum of squared residuals at call 7: 279.9344
-#> Sum of squared residuals at call 8: 279.9294
-#> Sum of squared residuals at call 9: 279.9294
-#> Sum of squared residuals at call 12: 200.3629
-#> Sum of squared residuals at call 13: 200.3629
-#> Sum of squared residuals at call 18: 197.904
-#> Sum of squared residuals at call 22: 197.904
-#> Sum of squared residuals at call 25: 196.6753
-#> Sum of squared residuals at call 27: 196.6753
-#> Sum of squared residuals at call 32: 196.5742
-#> Sum of squared residuals at call 33: 196.5742
-#> Sum of squared residuals at call 34: 196.5742
-#> Sum of squared residuals at call 38: 196.5361
-#> Sum of squared residuals at call 40: 196.5361
-#> Sum of squared residuals at call 44: 196.5336
-#> Sum of squared residuals at call 45: 196.5336
-#> Sum of squared residuals at call 50: 196.5334
-#> Sum of squared residuals at call 51: 196.5334
-#> Sum of squared residuals at call 52: 196.5334
-#> Sum of squared residuals at call 56: 196.5334
-#> Sum of squared residuals at call 58: 196.5334
-#> Sum of squared residuals at call 59: 196.5334
-#> Sum of squared residuals at call 65: 196.5334
-#> Negative log-likelihood at call 75: 26.64668
#> Optimisation successfully terminated.
    head(mkinpredict(f))
#>   time   parent       m1
+# Check compiled model versions - they are faster than the eigenvalue based solutions!
+SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
+                  m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
if(require(rbenchmark)) {
+  benchmark(
+    eigen = 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 = "eigen")[201,],
+    deSolve_compiled = 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,],
+    deSolve = 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,],
+    replications = 10)
+}
#> Lade nötiges Paket: rbenchmark
#>               test replications elapsed relative user.self sys.self user.child
+#> 3          deSolve           10   0.229   28.625     0.229        0          0
+#> 2 deSolve_compiled           10   0.008    1.000     0.008        0          0
+#> 1            eigen           10   0.025    3.125     0.026        0          0
+#>   sys.child
+#> 3         0
+#> 2         0
+#> 1         0

+# Since mkin 0.9.49.11 we also have analytical solutions for some models, including SFO-SFO
+#    deSolve = 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 = "analytical", use_compiled = FALSE)[201,],
+
+# \dontrun{
+  # Predict from a fitted model
+  f <- mkinfit(SFO_SFO, FOCUS_2006_C, quiet = TRUE)
+  head(mkinpredict(f))
#>   time   parent       m1
 #> 1  0.0 82.49216 0.000000
 #> 2  0.1 80.00563 1.179963
 #> 3  0.2 77.59404 2.312596
 #> 4  0.3 75.25515 3.399443
 #> 5  0.4 72.98675 4.442000
-#> 6  0.5 70.78673 5.441717
  # }
+#> 6  0.5 70.78673 5.441717
# }
 
 
   
-  
-    Contents
-    
-      Arguments
-      Value
-      Examples
-    
-
-    Author
-    Johannes Ranke
+  
+    
+      Contents
+    
   
 
 
@@ -445,7 +408,7 @@ solver is used.
 
 
 
-  Site built with pkgdown 1.4.1.
+  Site built with pkgdown 1.5.1.
 
 
       
-- 
cgit v1.2.1

t	Time.
parent.0	Starting value for the response variable at time zero.
k_12	Kinetic constant describing transfer from free to bound.
@@ -176,6 +190,11 @@ more datasets
@@ -251,6 +270,11 @@ with mkinfit
@@ -278,6 +302,11 @@ of an mmkin object
@@ -310,6 +339,11 @@ of an mmkin object
@@ -402,6 +436,11 @@ of an mmkin object
@@ -422,6 +461,11 @@ of an mmkin object
@@ -521,6 +565,11 @@ kinetic models fitted with mkinfit
@@ -560,7 +609,7 @@ kinetic models fitted with mkinfit
- `logistic.solution()` + `logistic.solution()` `logistic.solution()`	Logistic kinetics
@@ -585,6 +639,11 @@ kinetic models fitted with mkinfit
@@ -596,20 +655,10 @@ kinetic models fitted with mkinfit

Time.
parent.0	parent_0	Starting value for the response variable at time zero.
r	Growth rate of the increase in the rate constant.
parent.0	Starting value for the response variable at time zero.