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authorJohannes Ranke <jranke@uni-bremen.de>2017-07-29 15:15:41 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2017-07-29 15:15:41 +0200
commit20d7834a633d32b663c6bcc1a7f7b0300aa65d5b (patch)
tree77338f14ecaf26a4059ada9933ffde1fb5c19072
parent5447af959b2a9b0dc52695bf6a309f346ced085a (diff)
Bump version, update NEWS and rebuild pkdown docsv0.9.46
-rw-r--r--DESCRIPTION4
-rw-r--r--NEWS.md14
-rw-r--r--build.log2
-rw-r--r--check.log2
-rw-r--r--docs/index.html2
-rw-r--r--docs/news/index.html19
-rw-r--r--docs/reference/DFOP.solution-2.pngbin6375 -> 6748 bytes
-rw-r--r--docs/reference/DFOP.solution.html2
-rw-r--r--docs/reference/Extract.mmkin.html14
-rw-r--r--docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html2
-rw-r--r--docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html2
-rw-r--r--docs/reference/FOCUS_2006_HS_ref_A_to_F.html2
-rw-r--r--docs/reference/FOCUS_2006_SFO_ref_A_to_F.html2
-rw-r--r--docs/reference/FOCUS_2006_datasets.html2
-rw-r--r--docs/reference/FOMC.solution-2.pngbin6406 -> 6774 bytes
-rw-r--r--docs/reference/FOMC.solution.html2
-rw-r--r--docs/reference/HS.solution-2.pngbin6153 -> 6548 bytes
-rw-r--r--docs/reference/HS.solution.html2
-rw-r--r--docs/reference/IORE.solution-2.pngbin6168 -> 6536 bytes
-rw-r--r--docs/reference/SFO.solution-2.pngbin6424 -> 6779 bytes
-rw-r--r--docs/reference/SFO.solution.html2
-rw-r--r--docs/reference/SFORB.solution-2.pngbin6788 -> 7164 bytes
-rw-r--r--docs/reference/SFORB.solution.html2
-rw-r--r--docs/reference/add_err-4.pngbin26860 -> 28621 bytes
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-rw-r--r--docs/reference/index.html2
-rw-r--r--docs/reference/mccall81_245T.html20
-rw-r--r--docs/reference/mkinerrmin.html2
-rw-r--r--docs/reference/mkinfit.html72
-rw-r--r--docs/reference/mkinmod.html4
-rw-r--r--docs/reference/mkinparplot-4.pngbin5360 -> 5812 bytes
-rw-r--r--docs/reference/mkinpredict.html6
-rw-r--r--docs/reference/mkinresplot-4.pngbin5255 -> 5508 bytes
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-rw-r--r--docs/reference/plot.mkinfit-10.pngbin18197 -> 19456 bytes
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-rw-r--r--docs/reference/summary.mkinfit.html12
-rw-r--r--docs/reference/synthetic_data_for_UBA.html10
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-rw-r--r--docs/reference/transform_odeparms.html40
52 files changed, 141 insertions, 108 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 36a54b55..e18c3fea 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: mkin
Type: Package
Title: Kinetic Evaluation of Chemical Degradation Data
-Version: 0.9.45.2
-Date: 2017-07-21
+Version: 0.9.46
+Date: 2017-07-29
Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
email = "jranke@uni-bremen.de"),
person("Katrin", "Lindenberger", role = "ctb"),
diff --git a/NEWS.md b/NEWS.md
index ac36f39b..818a85be 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,17 @@
+# mkin 0.9.46 (2017-07-24)
+
+- Remove `test_FOMC_ill-defined.R` as it is too platform dependent
+
+# mkin 0.9.45.2 (2017-07-24)
+
+- Rename `twa` to `max_twa_parent` to avoid conflict with `twa` from my `pfm` package
+
+- Update URLs in documentation
+
+- Limit test code to one core to pass on windows
+
+- Switch from `microbenchmark` to `rbenchmark` as the former is not supported on all platforms
+
# mkin 0.9.45.1 (2016-12-20)
## New features
diff --git a/build.log b/build.log
index 4cdccab4..2d06c4dc 100644
--- a/build.log
+++ b/build.log
@@ -6,5 +6,5 @@
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
-* building ‘mkin_0.9.45.2.tar.gz’
+* building ‘mkin_0.9.46.tar.gz’
diff --git a/check.log b/check.log
index 2876f64a..6db43c99 100644
--- a/check.log
+++ b/check.log
@@ -5,7 +5,7 @@
* using options ‘--no-tests --as-cran’
* checking for file ‘mkin/DESCRIPTION’ ... OK
* checking extension type ... Package
-* this is package ‘mkin’ version ‘0.9.45.2’
+* this is package ‘mkin’ version ‘0.9.45.3’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
diff --git a/docs/index.html b/docs/index.html
index 7ac6f226..9898d6f5 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -134,7 +134,7 @@
<h2 class="hasAnchor">
<a href="#credits-and-historical-remarks" class="anchor"></a>Credits and historical remarks</h2>
<p><code>mkin</code> would not be possible without the underlying software stack consisting of R and the packages <a href="https://cran.r-project.org/package=deSolve">deSolve</a> and <a href="https://cran.r-project.org/package=FME">FME</a>, to say the least.</p>
-<p>It could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). <code>mkin</code> greatly profits from and largely follows the work done by the <a href="http://focus.jrc.ec.europa.eu/dk">FOCUS Degradation Kinetics Workgroup</a>, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.</p>
+<p>It could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). <code>mkin</code> greatly profits from and largely follows the work done by the <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">FOCUS Degradation Kinetics Workgroup</a>, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.</p>
<p>Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based on the MatLab runtime environment.</p>
<p>The companion package <a href="http://kinfit.r-forge.r-project.org/kinfit_static/index.html">kinfit</a> (now deprecated) was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&amp;root=kinfit&amp;revision=2">started in 2008</a> and <a href="https://cran.r-project.org/src/contrib/Archive/kinfit/">first published</a> on CRAN on 01 May 2010.</p>
<p>The first <code>mkin</code> code was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&amp;root=kinfit&amp;revision=8">published on 11 May 2010</a> and the <a href="https://cran.r-project.org/src/contrib/Archive/mkin">first CRAN version</a> on 18 May 2010.</p>
diff --git a/docs/news/index.html b/docs/news/index.html
index 667c5c1f..b4f97681 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -105,6 +105,23 @@
</div>
<div class="contents">
+ <div id="mkin-0-9-46-2017-07-24" class="section level1">
+<h1 class="hasAnchor">
+<a href="#mkin-0-9-46-2017-07-24" class="anchor"></a>mkin 0.9.46 (2017-07-24)</h1>
+<ul>
+<li>Remove <code>test_FOMC_ill-defined.R</code> as it is too platform dependent</li>
+</ul>
+</div>
+ <div id="mkin-0-9-45-2-2017-07-24" class="section level1">
+<h1 class="hasAnchor">
+<a href="#mkin-0-9-45-2-2017-07-24" class="anchor"></a>mkin 0.9.45.2 (2017-07-24)</h1>
+<ul>
+<li><p>Rename <code>twa</code> to <code>max_twa_parent</code> to avoid conflict with <code>twa</code> from my <code>pfm</code> package</p></li>
+<li><p>Update URLs in documentation</p></li>
+<li><p>Limit test code to one core to pass on windows</p></li>
+<li><p>Switch from <code>microbenchmark</code> to <code>rbenchmark</code> as the former is not supported on all platforms</p></li>
+</ul>
+</div>
<div id="mkin-0-9-45-1-2016-12-20" class="section level1">
<h1 class="hasAnchor">
<a href="#mkin-0-9-45-1-2016-12-20" class="anchor"></a>mkin 0.9.45.1 (2016-12-20)</h1>
@@ -538,6 +555,8 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
+ <li><a href="#mkin-0-9-46-2017-07-24">0.9.46</a></li>
+ <li><a href="#mkin-0-9-45-2-2017-07-24">0.9.45.2</a></li>
<li><a href="#mkin-0-9-45-1-2016-12-20">0.9.45.1</a></li>
<li><a href="#mkin-0-9-45-2016-12-08">0.9.45</a></li>
<li><a href="#mkin-0-9-44-2016-06-29">0.9.44</a></li>
diff --git a/docs/reference/DFOP.solution-2.png b/docs/reference/DFOP.solution-2.png
index 91efcebb..0902b9df 100644
--- a/docs/reference/DFOP.solution-2.png
+++ b/docs/reference/DFOP.solution-2.png
Binary files differ
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index 3dbacdc1..30b9d057 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -146,7 +146,7 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p>
+ <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 135297cd..5d4eca29 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -398,7 +398,7 @@
#&gt; {
#&gt; assign("calls", calls + 1, inherits = TRUE)
#&gt; if (trace_parms)
-#&gt; cat(P, "\n")
+#&gt; cat(P, "\\n")
#&gt; if (length(state.ini.optim) &gt; 0) {
#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
@@ -420,7 +420,7 @@
#&gt; if (mC$model &lt; cost.old) {
#&gt; if (!quiet)
#&gt; cat("Model cost at call ", calls, ": ", mC$model,
-#&gt; "\n")
+#&gt; "\\n")
#&gt; if (plot) {
#&gt; outtimes_plot = seq(min(observed$time), max(observed$time),
#&gt; length.out = 100)
@@ -447,8 +447,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x5554250&gt;
-#&gt; &lt;environment: 0x4eb4b18&gt;
+#&gt; &lt;bytecode: 0x560110508c60&gt;
+#&gt; &lt;environment: 0x56010f8d8c30&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -470,8 +470,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x5073868&gt;
-#&gt; &lt;environment: 0x4eb4b18&gt;
+#&gt; &lt;bytecode: 0x56010fede550&gt;
+#&gt; &lt;environment: 0x56010f8d8c30&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -534,7 +534,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Fri May 5 12:44:53 2017"
+#&gt; [1] "Sat Jul 29 15:14:04 2017"
#&gt;
#&gt; attr(,"class")
#&gt; [1] "mkinfit" "modFit"
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 703dc472..d79aaff6 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -132,7 +132,7 @@ in this fit.</p>
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p>
+ <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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 eec595f0..e0da5a8d 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -131,7 +131,7 @@ in this fit.</p>
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p>
+ <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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 c2a90311..720073f2 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -132,7 +132,7 @@ in this fit.</p>
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p>
+ <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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 24070b9c..b12abf8c 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -130,7 +130,7 @@ in this fit.</p>
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p>
+ <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 93901bfa..65bc572a 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -123,7 +123,7 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p>
+ <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
diff --git a/docs/reference/FOMC.solution-2.png b/docs/reference/FOMC.solution-2.png
index 0efe8f07..a673bc0e 100644
--- a/docs/reference/FOMC.solution-2.png
+++ b/docs/reference/FOMC.solution-2.png
Binary files differ
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 67a37b4f..9af30b7a 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -152,7 +152,7 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p>
+ <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<p>Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A
new model based on spatial variability. <em>Environmental Science and
Technology</em> <b>24</b>, 1032-1038</p>
diff --git a/docs/reference/HS.solution-2.png b/docs/reference/HS.solution-2.png
index 0bdb37a9..2e516447 100644
--- a/docs/reference/HS.solution-2.png
+++ b/docs/reference/HS.solution-2.png
Binary files differ
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 3d608a2f..8f6bbbe2 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -147,7 +147,7 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p>
+ <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
diff --git a/docs/reference/IORE.solution-2.png b/docs/reference/IORE.solution-2.png
index df268b64..a83d49c7 100644
--- a/docs/reference/IORE.solution-2.png
+++ b/docs/reference/IORE.solution-2.png
Binary files differ
diff --git a/docs/reference/SFO.solution-2.png b/docs/reference/SFO.solution-2.png
index 78c083c3..9626091f 100644
--- a/docs/reference/SFO.solution-2.png
+++ b/docs/reference/SFO.solution-2.png
Binary files differ
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 08928135..ef9b8eb7 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -136,7 +136,7 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p>
+ <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
diff --git a/docs/reference/SFORB.solution-2.png b/docs/reference/SFORB.solution-2.png
index 9625debf..63a50bf9 100644
--- a/docs/reference/SFORB.solution-2.png
+++ b/docs/reference/SFORB.solution-2.png
Binary files differ
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index 112e157d..ebe67733 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -149,7 +149,7 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p>
+ <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
diff --git a/docs/reference/add_err-4.png b/docs/reference/add_err-4.png
index f3d04134..8bbd1758 100644
--- a/docs/reference/add_err-4.png
+++ b/docs/reference/add_err-4.png
Binary files differ
diff --git a/docs/reference/add_err-6.png b/docs/reference/add_err-6.png
index 05b27247..2a4fe33f 100644
--- a/docs/reference/add_err-6.png
+++ b/docs/reference/add_err-6.png
Binary files differ
diff --git a/docs/reference/add_err-8.png b/docs/reference/add_err-8.png
index b0182d2a..49c4a5f0 100644
--- a/docs/reference/add_err-8.png
+++ b/docs/reference/add_err-8.png
Binary files differ
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 2d58eeeb..bf7cd233 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -102,7 +102,7 @@
<div class="page-header">
<h1>
Reference
- <small>version&nbsp;0.9.45.2</small>
+ <small>version&nbsp;0.9.46</small>
</h1>
</div>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 9a681191..0111deb3 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -135,10 +135,10 @@
<span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>),
<span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:45:02 2017
-#&gt; Date of summary: Fri May 5 12:45:02 2017
+ <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:14:14 2017
+#&gt; Date of summary: Sat Jul 29 15:14:14 2017
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -148,7 +148,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 612 model solutions performed in 3.576 s
+#&gt; Fitted with method Port using 612 model solutions performed in 3.558 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -225,10 +225,10 @@
<span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
<span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
<span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:45:04 2017
-#&gt; Date of summary: Fri May 5 12:45:04 2017
+ <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:14:15 2017
+#&gt; Date of summary: Sat Jul 29 15:14:15 2017
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -238,7 +238,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.461 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.431 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 678750cd..67b7a35e 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -146,7 +146,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p>
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p>
+ <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 875bd1dd..cdf7c7ef 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -377,17 +377,17 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:45:06 2017
-#&gt; Date of summary: Fri May 5 12:45:06 2017
+<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:14:18 2017
+#&gt; Date of summary: Sat Jul 29 15:14:18 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 64 model solutions performed in 0.206 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.141 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -456,7 +456,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.912 0.000 0.915 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.888 0.000 0.890 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -535,7 +535,7 @@
#&gt; Model cost at call 153 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; user system elapsed
-#&gt; 0.792 0.000 0.793 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.728 0.000 0.729 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -576,10 +576,10 @@
<span class='co'># Weighted fits, including IRLS</span>
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:45:17 2017
-#&gt; Date of summary: Fri May 5 12:45:17 2017
+<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:14:28 2017
+#&gt; Date of summary: Sat Jul 29 15:14:28 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -697,10 +697,10 @@
#&gt; 100 m1 33.13 3.198e+01 1.148e+00
#&gt; 120 m1 25.15 2.879e+01 -3.640e+00
#&gt; 120 m1 33.31 2.879e+01 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:45:19 2017
-#&gt; Date of summary: Fri May 5 12:45:19 2017
+<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:14:30 2017
+#&gt; Date of summary: Sat Jul 29 15:14:30 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -708,7 +708,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 468 model solutions performed in 1.925 s
+#&gt; Fitted with method Port using 468 model solutions performed in 1.914 s
#&gt;
#&gt; Weighting: none then iterative reweighting method obs
#&gt;
@@ -818,10 +818,10 @@
#&gt; 100 m1 33.13 3.199e+01 1.140e+00 2.722
#&gt; 120 m1 25.15 2.881e+01 -3.659e+00 2.722
#&gt; 120 m1 33.31 2.881e+01 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:45:20 2017
-#&gt; Date of summary: Fri May 5 12:45:20 2017
+<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:14:31 2017
+#&gt; Date of summary: Sat Jul 29 15:14:31 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -829,7 +829,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.699 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.692 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -940,10 +940,10 @@
#&gt; 120 m1 25.15 28.824128 -3.674128
#&gt; 120 m1 33.31 28.824128 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>,
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:45:21 2017
-#&gt; Date of summary: Fri May 5 12:45:21 2017
+<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:14:32 2017
+#&gt; Date of summary: Sat Jul 29 15:14:32 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -951,7 +951,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.767 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.701 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1062,10 +1062,10 @@
<span class='no'>errors</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='no'>dw</span>$<span class='no'>err.man</span> <span class='kw'>&lt;-</span> <span class='no'>errors</span>[<span class='no'>FOCUS_2006_D</span>$<span class='no'>name</span>]
<span class='no'>f.w.man</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:45:22 2017
-#&gt; Date of summary: Fri May 5 12:45:22 2017
+<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:14:33 2017
+#&gt; Date of summary: Sat Jul 29 15:14:33 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1073,7 +1073,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 297 model solutions performed in 1.276 s
+#&gt; Fitted with method Port using 297 model solutions performed in 1.223 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1184,10 +1184,10 @@
#&gt; 120 m1 25.15 28.760616 -3.610616 2
#&gt; 120 m1 33.31 28.760616 4.549384 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:45:25 2017
-#&gt; Date of summary: Fri May 5 12:45:25 2017
+<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:14:36 2017
+#&gt; Date of summary: Sat Jul 29 15:14:36 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1195,7 +1195,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 628 model solutions performed in 2.626 s
+#&gt; Fitted with method Port using 628 model solutions performed in 2.578 s
#&gt;
#&gt; Weighting: manual then iterative reweighting method obs
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index de9815d4..5703b188 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -182,7 +182,7 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p>
+ <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for
Evaluating and Calculating Degradation Kinetics in Environmental
Media</p>
@@ -205,7 +205,7 @@
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
-#&gt; /usr/lib/R/bin/R CMD SHLIB file70ea30edf42a.c 2&gt; file70ea30edf42a.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file519167a14b3a.c 2&gt; file519167a14b3a.c.err.txt
#&gt; Program source:
#&gt; 1: #include &lt;R.h&gt;
#&gt; 2:
diff --git a/docs/reference/mkinparplot-4.png b/docs/reference/mkinparplot-4.png
index 8b32f554..c9f4aadb 100644
--- a/docs/reference/mkinparplot-4.png
+++ b/docs/reference/mkinparplot-4.png
Binary files differ
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 327a7d8d..b3453e6c 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -299,17 +299,17 @@
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.004 0.000 0.004 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.004 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.004 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.000 0.000 0.001 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.032 0.000 0.033 </div></pre>
+#&gt; 0.032 0.000 0.032 </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mkinresplot-4.png b/docs/reference/mkinresplot-4.png
index 7dbd7522..5f3a65e3 100644
--- a/docs/reference/mkinresplot-4.png
+++ b/docs/reference/mkinresplot-4.png
Binary files differ
diff --git a/docs/reference/mmkin-15.png b/docs/reference/mmkin-15.png
index f50a6185..e8a23a55 100644
--- a/docs/reference/mmkin-15.png
+++ b/docs/reference/mmkin-15.png
Binary files differ
diff --git a/docs/reference/mmkin-17.png b/docs/reference/mmkin-17.png
index 72cfc5e7..01bb3ae3 100644
--- a/docs/reference/mmkin-17.png
+++ b/docs/reference/mmkin-17.png
Binary files differ
diff --git a/docs/reference/mmkin-19.png b/docs/reference/mmkin-19.png
index 0b315b1a..b5ac70f7 100644
--- a/docs/reference/mmkin-19.png
+++ b/docs/reference/mmkin-19.png
Binary files differ
diff --git a/docs/reference/mmkin-21.png b/docs/reference/mmkin-21.png
index b98940ff..7e15e1b3 100644
--- a/docs/reference/mmkin-21.png
+++ b/docs/reference/mmkin-21.png
Binary files differ
diff --git a/docs/reference/mmkin-23.png b/docs/reference/mmkin-23.png
index 5ca52efb..45e8efc1 100644
--- a/docs/reference/mmkin-23.png
+++ b/docs/reference/mmkin-23.png
Binary files differ
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index fe10c88f..d649563f 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -168,8 +168,8 @@
#&gt; <span class='warning'>Convergence code is 1</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation by method Port did not converge.</span>
#&gt; <span class='warning'>Convergence code is 1</span></div><div class='input'>
<span class='no'>time_default</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 16.092 0.132 11.761 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 25.004 0.000 25.000 </div><div class='input'>
+#&gt; 15.992 0.188 11.440 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
+#&gt; 24.576 0.000 24.578 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
#&gt; 0.7340479 0.2659521 0.7505687 0.2494313
diff --git a/docs/reference/plot.mkinfit-10.png b/docs/reference/plot.mkinfit-10.png
index 09bb687c..87d3351d 100644
--- a/docs/reference/plot.mkinfit-10.png
+++ b/docs/reference/plot.mkinfit-10.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png
index 1e90d789..cb52d4ac 100644
--- a/docs/reference/plot.mkinfit-4.png
+++ b/docs/reference/plot.mkinfit-4.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png
index 1dfbbe4c..8e0faa21 100644
--- a/docs/reference/plot.mkinfit-6.png
+++ b/docs/reference/plot.mkinfit-6.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-8.png b/docs/reference/plot.mkinfit-8.png
index e4ab674a..129f1445 100644
--- a/docs/reference/plot.mkinfit-8.png
+++ b/docs/reference/plot.mkinfit-8.png
Binary files differ
diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png
index a26e413f..7739e3b0 100644
--- a/docs/reference/plot.mmkin-2.png
+++ b/docs/reference/plot.mmkin-2.png
Binary files differ
diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png
index f23ed172..e2eb3aae 100644
--- a/docs/reference/plot.mmkin-4.png
+++ b/docs/reference/plot.mmkin-4.png
Binary files differ
diff --git a/docs/reference/plot.mmkin-6.png b/docs/reference/plot.mmkin-6.png
index dc24d92f..3bbd390a 100644
--- a/docs/reference/plot.mmkin-6.png
+++ b/docs/reference/plot.mmkin-6.png
Binary files differ
diff --git a/docs/reference/schaefer07_complex_case-4.png b/docs/reference/schaefer07_complex_case-4.png
index b87ccb82..b90185a1 100644
--- a/docs/reference/schaefer07_complex_case-4.png
+++ b/docs/reference/schaefer07_complex_case-4.png
Binary files differ
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index dbed926d..f20e3948 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -177,21 +177,21 @@
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p>
+ <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:46:20 2017
-#&gt; Date of summary: Fri May 5 12:46:20 2017
+ <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:15:30 2017
+#&gt; Date of summary: Sat Jul 29 15:15:30 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 35 model solutions performed in 0.082 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.084 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index d8ff3a1e..173af92e 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -156,10 +156,10 @@
<span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
<span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><img src='synthetic_data_for_UBA_2014-10.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:46:23 2017
-#&gt; Date of summary: Fri May 5 12:46:23 2017
+<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><img src='synthetic_data_for_UBA_2014-10.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:15:33 2017
+#&gt; Date of summary: Sat Jul 29 15:15:34 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -168,7 +168,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 381 model solutions performed in 2.203 s
+#&gt; Fitted with method Port using 381 model solutions performed in 2.241 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/synthetic_data_for_UBA_2014-10.png b/docs/reference/synthetic_data_for_UBA_2014-10.png
index b98940ff..7e15e1b3 100644
--- a/docs/reference/synthetic_data_for_UBA_2014-10.png
+++ b/docs/reference/synthetic_data_for_UBA_2014-10.png
Binary files differ
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index c14740c2..bbf15a41 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -170,10 +170,10 @@
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:46:24 2017
-#&gt; Date of summary: Fri May 5 12:46:24 2017
+<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:15:35 2017
+#&gt; Date of summary: Sat Jul 29 15:15:35 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -181,7 +181,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.61 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.608 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -247,10 +247,10 @@
#&gt; m1 131.761 437.70</div><div class='input'>
<span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:46:26 2017
-#&gt; Date of summary: Fri May 5 12:46:26 2017
+<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:15:36 2017
+#&gt; Date of summary: Sat Jul 29 15:15:36 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -258,7 +258,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 352 model solutions performed in 1.437 s
+#&gt; Fitted with method Port using 352 model solutions performed in 1.401 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -337,10 +337,10 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>fit.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:46:27 2017
-#&gt; Date of summary: Fri May 5 12:46:27 2017
+<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:15:37 2017
+#&gt; Date of summary: Sat Jul 29 15:15:37 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -348,7 +348,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 185 model solutions performed in 0.776 s
+#&gt; Fitted with method Port using 185 model solutions performed in 0.772 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -421,10 +421,10 @@
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>fit.ff.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.45.2
-#&gt; R version: 3.4.0
-#&gt; Date of fit: Fri May 5 12:46:28 2017
-#&gt; Date of summary: Fri May 5 12:46:28 2017
+<span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.46
+#&gt; R version: 3.4.1
+#&gt; Date of fit: Sat Jul 29 15:15:38 2017
+#&gt; Date of summary: Sat Jul 29 15:15:38 2017
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -432,7 +432,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 104 model solutions performed in 0.433 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.416 s
#&gt;
#&gt; Weighting: none
#&gt;

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