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-rw-r--r--docs/articles/FOCUS_D.html6
-rw-r--r--docs/articles/FOCUS_L.html32
-rw-r--r--docs/articles/web_only/benchmarks.html22
-rw-r--r--docs/index.html5
-rw-r--r--docs/news/index.html143
-rw-r--r--docs/pkgdown.yml2
-rw-r--r--docs/reference/Rplot001.pngbin13995 -> 27554 bytes
-rw-r--r--docs/reference/Rplot002.pngbin13648 -> 59342 bytes
8 files changed, 83 insertions, 127 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index f3a56065..08acf58b 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -187,8 +187,8 @@
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div>
<pre><code>## mkin version used for fitting: 1.0.3
## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 13:46:23 2021
-## Date of summary: Mon Feb 15 13:46:23 2021
+## Date of fit: Mon Feb 15 17:50:27 2021
+## Date of summary: Mon Feb 15 17:50:28 2021
##
## Equations:
## d_parent/dt = - k_parent * parent
@@ -196,7 +196,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 401 model solutions performed in 0.162 s
+## Fitted using 401 model solutions performed in 0.161 s
##
## Error model: Constant variance
##
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 53e4e1d3..ab9739bc 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -128,8 +128,8 @@
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></code></pre></div>
<pre><code>## mkin version used for fitting: 1.0.3
## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 13:46:25 2021
-## Date of summary: Mon Feb 15 13:46:25 2021
+## Date of fit: Mon Feb 15 17:50:30 2021
+## Date of summary: Mon Feb 15 17:50:30 2021
##
## Equations:
## d_parent/dt = - k_parent * parent
@@ -234,8 +234,8 @@
## doubtful</code></pre>
<pre><code>## mkin version used for fitting: 1.0.3
## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 13:46:26 2021
-## Date of summary: Mon Feb 15 13:46:26 2021
+## Date of fit: Mon Feb 15 17:50:31 2021
+## Date of summary: Mon Feb 15 17:50:31 2021
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -346,8 +346,8 @@
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
<pre><code>## mkin version used for fitting: 1.0.3
## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 13:46:26 2021
-## Date of summary: Mon Feb 15 13:46:26 2021
+## Date of fit: Mon Feb 15 17:50:31 2021
+## Date of summary: Mon Feb 15 17:50:31 2021
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -427,8 +427,8 @@
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
<pre><code>## mkin version used for fitting: 1.0.3
## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 13:46:27 2021
-## Date of summary: Mon Feb 15 13:46:27 2021
+## Date of fit: Mon Feb 15 17:50:32 2021
+## Date of summary: Mon Feb 15 17:50:32 2021
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -533,8 +533,8 @@
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
<pre><code>## mkin version used for fitting: 1.0.3
## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 13:46:27 2021
-## Date of summary: Mon Feb 15 13:46:28 2021
+## Date of fit: Mon Feb 15 17:50:32 2021
+## Date of summary: Mon Feb 15 17:50:32 2021
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -646,15 +646,15 @@
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
<pre><code>## mkin version used for fitting: 1.0.3
## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 13:46:28 2021
-## Date of summary: Mon Feb 15 13:46:28 2021
+## Date of fit: Mon Feb 15 17:50:33 2021
+## Date of summary: Mon Feb 15 17:50:33 2021
##
## Equations:
## d_parent/dt = - k_parent * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 142 model solutions performed in 0.031 s
+## Fitted using 142 model solutions performed in 0.03 s
##
## Error model: Constant variance
##
@@ -711,15 +711,15 @@
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
<pre><code>## mkin version used for fitting: 1.0.3
## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 13:46:28 2021
-## Date of summary: Mon Feb 15 13:46:28 2021
+## Date of fit: Mon Feb 15 17:50:33 2021
+## Date of summary: Mon Feb 15 17:50:33 2021
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 224 model solutions performed in 0.047 s
+## Fitted using 224 model solutions performed in 0.046 s
##
## Error model: Constant variance
##
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index d7b81f20..9908c224 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -229,8 +229,8 @@
</tr>
<tr class="odd">
<td align="left">1.0.3</td>
-<td align="right">1.722</td>
-<td align="right">3.419</td>
+<td align="right">1.881</td>
+<td align="right">3.504</td>
</tr>
</tbody>
</table>
@@ -297,9 +297,9 @@
</tr>
<tr class="odd">
<td align="left">1.0.3</td>
-<td align="right">1.402</td>
-<td align="right">6.343</td>
-<td align="right">2.802</td>
+<td align="right">1.430</td>
+<td align="right">6.344</td>
+<td align="right">2.798</td>
</tr>
</tbody>
</table>
@@ -393,12 +393,12 @@
</tr>
<tr class="odd">
<td align="left">1.0.3</td>
-<td align="right">0.771</td>
-<td align="right">1.251</td>
-<td align="right">1.464</td>
-<td align="right">3.074</td>
-<td align="right">1.940</td>
-<td align="right">2.831</td>
+<td align="right">0.763</td>
+<td align="right">1.244</td>
+<td align="right">1.457</td>
+<td align="right">3.054</td>
+<td align="right">1.923</td>
+<td align="right">2.839</td>
</tr>
</tbody>
</table>
diff --git a/docs/index.html b/docs/index.html
index 88f118ea..82aab7f3 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -191,11 +191,12 @@
<p>Many inspirations for improvements of mkin resulted from doing kinetic evaluations of degradation data for my clients while working at Harlan Laboratories and at Eurofins Regulatory AG, and now as an independent consultant.</p>
<p>Funding was received from the Umweltbundesamt in the course of the projects</p>
<ul>
-<li>Grant Number 112407 (Testing and validation of modelling software as an alternative to ModelMaker 4.0, 2014-2015)</li>
+<li>Project Number 27452 (Testing and validation of modelling software as an alternative to ModelMaker 4.0, 2014-2015)</li>
<li>Project Number 56703 (Optimization of gmkin for routine use in the Umweltbundesamt, 2015)</li>
+<li>Project Number 92570 (Update of Project Number 27452, 2017-2018)</li>
<li>Project Number 112407 (Testing the feasibility of using an error model according to Rocke and Lorenzato for more realistic parameter estimates in the kinetic evaluation of degradation data, 2018-2019)</li>
<li>Project Number 120667 (Development of objective criteria for the evaluation of the visual fit in the kinetic evaluation of degradation data, 2019-2020)</li>
-<li>Project 146839 (Checking the feasibility of using mixed-effects models for the derivation of kinetic modelling parameters from degradation studies, 2020-2021)</li>
+<li>Project Number 146839 (Checking the feasibility of using mixed-effects models for the derivation of kinetic modelling parameters from degradation studies, 2020-2021)</li>
</ul>
</div>
<div id="references" class="section level2">
diff --git a/docs/news/index.html b/docs/news/index.html
index 82fb92bd..1428dc78 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -141,26 +141,23 @@
<small>Source: <a href='https://github.com/jranke/mkin/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
- <div id="mkin-103" class="section level1">
+ <div id="mkin-103-2021-02-15" class="section level1">
<h1 class="page-header" data-toc-text="1.0.3">
-<a href="#mkin-103" class="anchor"></a>mkin 1.0.3<small> Unreleased </small>
-</h1>
+<a href="#mkin-103-2021-02-15" class="anchor"></a>mkin 1.0.3 (2021-02-15)</h1>
<ul>
<li>Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages</li>
</ul>
</div>
- <div id="mkin-102" class="section level1">
+ <div id="mkin-102-unreleased" class="section level1">
<h1 class="page-header" data-toc-text="1.0.2">
-<a href="#mkin-102" class="anchor"></a>mkin 1.0.2<small> Unreleased </small>
-</h1>
+<a href="#mkin-102-unreleased" class="anchor"></a>mkin 1.0.2 (Unreleased)</h1>
<ul>
<li>‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’</li>
</ul>
</div>
- <div id="mkin-101" class="section level1">
+ <div id="mkin-101-2021-02-10" class="section level1">
<h1 class="page-header" data-toc-text="1.0.1">
-<a href="#mkin-101" class="anchor"></a>mkin 1.0.1<small> 2021-02-10 </small>
-</h1>
+<a href="#mkin-101-2021-02-10" class="anchor"></a>mkin 1.0.1 (2021-02-10)</h1>
<ul>
<li><p>‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults</p></li>
<li><p>‘logLik.mkinfit’: Improve example code to avoid warnings and show convenient syntax</p></li>
@@ -169,10 +166,9 @@
<li><p>Increase test tolerance for some parameter comparisons that also proved to be platform dependent</p></li>
</ul>
</div>
- <div id="mkin-100" class="section level1">
+ <div id="mkin-100-2021-02-03" class="section level1">
<h1 class="page-header" data-toc-text="1.0.0">
-<a href="#mkin-100" class="anchor"></a>mkin 1.0.0<small> 2021-02-03 </small>
-</h1>
+<a href="#mkin-100-2021-02-03" class="anchor"></a>mkin 1.0.0 (2021-02-03)</h1>
<div id="general" class="section level2">
<h2 class="hasAnchor">
<a href="#general" class="anchor"></a>General</h2>
@@ -200,8 +196,7 @@
</div>
<div id="mkin-09503-2020-10-08" class="section level1">
<h1 class="page-header" data-toc-text="0.9.50.3">
-<a href="#mkin-09503-2020-10-08" class="anchor"></a>mkin 0.9.50.3 (2020-10-08)<small> 2020-10-08 </small>
-</h1>
+<a href="#mkin-09503-2020-10-08" class="anchor"></a>mkin 0.9.50.3 (2020-10-08)</h1>
<ul>
<li><p>‘parms’: Add a method for mmkin objects</p></li>
<li><p>‘mmkin’ and ‘confint(method = ’profile’): Use all cores detected by parallel::detectCores() per default</p></li>
@@ -216,8 +211,7 @@
</div>
<div id="mkin-09502-2020-05-12" class="section level1">
<h1 class="page-header" data-toc-text="0.9.50.2">
-<a href="#mkin-09502-2020-05-12" class="anchor"></a>mkin 0.9.50.2 (2020-05-12)<small> 2020-05-12 </small>
-</h1>
+<a href="#mkin-09502-2020-05-12" class="anchor"></a>mkin 0.9.50.2 (2020-05-12)</h1>
<ul>
<li><p>Increase tolerance for a platform specific test results on the Solaris test machine on CRAN</p></li>
<li><p>Updates and corrections (using the spelling package) to the documentation</p></li>
@@ -225,8 +219,7 @@
</div>
<div id="mkin-09501-2020-05-11" class="section level1">
<h1 class="page-header" data-toc-text="0.9.50.1">
-<a href="#mkin-09501-2020-05-11" class="anchor"></a>mkin 0.9.50.1 (2020-05-11)<small> 2020-05-11 </small>
-</h1>
+<a href="#mkin-09501-2020-05-11" class="anchor"></a>mkin 0.9.50.1 (2020-05-11)</h1>
<ul>
<li><p>Support SFORB with formation fractions</p></li>
<li><p>‘mkinmod’: Make ‘use_of_ff’ = “max” the default</p></li>
@@ -235,16 +228,14 @@
</div>
<div id="mkin-094911-2020-04-20" class="section level1">
<h1 class="page-header" data-toc-text="0.9.49.11">
-<a href="#mkin-094911-2020-04-20" class="anchor"></a>mkin 0.9.49.11 (2020-04-20)<small> 2020-04-20 </small>
-</h1>
+<a href="#mkin-094911-2020-04-20" class="anchor"></a>mkin 0.9.49.11 (2020-04-20)</h1>
<ul>
<li>Increase a test tolerance to make it pass on all CRAN check machines</li>
</ul>
</div>
<div id="mkin-094910-2020-04-18" class="section level1">
<h1 class="page-header" data-toc-text="0.9.49.10">
-<a href="#mkin-094910-2020-04-18" class="anchor"></a>mkin 0.9.49.10 (2020-04-18)<small> 2020-04-18 </small>
-</h1>
+<a href="#mkin-094910-2020-04-18" class="anchor"></a>mkin 0.9.49.10 (2020-04-18)</h1>
<ul>
<li><p>‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods</p></li>
<li><p>‘mean_degparms, nlme_data, nlme_function’: Three new functions to facilitate building nlme models from mmkin row objects</p></li>
@@ -256,8 +247,7 @@
</div>
<div id="mkin-09499-2020-03-31" class="section level1">
<h1 class="page-header" data-toc-text="0.9.49.9">
-<a href="#mkin-09499-2020-03-31" class="anchor"></a>mkin 0.9.49.9 (2020-03-31)<small> 2020-03-31 </small>
-</h1>
+<a href="#mkin-09499-2020-03-31" class="anchor"></a>mkin 0.9.49.9 (2020-03-31)</h1>
<ul>
<li><p>‘mkinmod’: Use pkgbuild::has_compiler instead of Sys.which(‘gcc’), as the latter will often fail even if Rtools are installed</p></li>
<li><p>‘mkinds’: Use roxygen for documenting fields and methods of this R6 class</p></li>
@@ -265,8 +255,7 @@
</div>
<div id="mkin-09498-2020-01-09" class="section level1">
<h1 class="page-header" data-toc-text="0.9.49.8">
-<a href="#mkin-09498-2020-01-09" class="anchor"></a>mkin 0.9.49.8 (2020-01-09)<small> 2020-01-09 </small>
-</h1>
+<a href="#mkin-09498-2020-01-09" class="anchor"></a>mkin 0.9.49.8 (2020-01-09)</h1>
<ul>
<li><p>‘aw’: Generic function for calculating Akaike weights, methods for mkinfit objects and mmkin columns</p></li>
<li><p>‘loftest’: Add a lack-of-fit test</p></li>
@@ -277,8 +266,7 @@
</div>
<div id="mkin-09497-2019-11-01" class="section level1">
<h1 class="page-header" data-toc-text="0.9.49.7">
-<a href="#mkin-09497-2019-11-01" class="anchor"></a>mkin 0.9.49.7 (2019-11-01)<small> 2019-11-02 </small>
-</h1>
+<a href="#mkin-09497-2019-11-01" class="anchor"></a>mkin 0.9.49.7 (2019-11-01)</h1>
<ul>
<li><p>Fix a bug introduced in 0.9.49.6 that occurred if the direct optimisation yielded a higher likelihood than the three-step optimisation in the d_3 algorithm, which caused the fitted parameters of the three-step optimisation to be returned instead of the parameters of the direct optimisation</p></li>
<li><p>Add a ‘nobs’ method for mkinfit objects, enabling the default ‘BIC’ method from the stats package. Also, add a ‘BIC’ method for mmkin column objects.</p></li>
@@ -286,8 +274,7 @@
</div>
<div id="mkin-09496-2019-10-31" class="section level1">
<h1 class="page-header" data-toc-text="0.9.49.6">
-<a href="#mkin-09496-2019-10-31" class="anchor"></a>mkin 0.9.49.6 (2019-10-31)<small> 2019-10-31 </small>
-</h1>
+<a href="#mkin-09496-2019-10-31" class="anchor"></a>mkin 0.9.49.6 (2019-10-31)</h1>
<ul>
<li><p>Implement a likelihood ratio test as a method for ‘lrtest’ from the lmtest package</p></li>
<li><p>Add an ‘update’ method for mkinfit objects which remembers fitted parameters if appropriate</p></li>
@@ -306,8 +293,7 @@
</div>
<div id="mkin-09495-2019-07-04" class="section level1">
<h1 class="page-header" data-toc-text="0.9.49.5">
-<a href="#mkin-09495-2019-07-04" class="anchor"></a>mkin 0.9.49.5 (2019-07-04)<small> 2019-07-04 </small>
-</h1>
+<a href="#mkin-09495-2019-07-04" class="anchor"></a>mkin 0.9.49.5 (2019-07-04)</h1>
<ul>
<li><p>Several algorithms for minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable. The default algorithm ‘d_3’ tries direct minimization and a three-step procedure, and returns the model with the highest likelihood.</p></li>
<li><p>The argument ‘reweight.method’ to mkinfit and mmkin is now obsolete, use ‘error_model’ and ‘error_model_algorithm’ instead</p></li>
@@ -325,8 +311,7 @@
</div>
<div id="mkin-09481-2019-03-04" class="section level1">
<h1 class="page-header" data-toc-text="0.9.48.1">
-<a href="#mkin-09481-2019-03-04" class="anchor"></a>mkin 0.9.48.1 (2019-03-04)<small> 2019-03-04 </small>
-</h1>
+<a href="#mkin-09481-2019-03-04" class="anchor"></a>mkin 0.9.48.1 (2019-03-04)</h1>
<ul>
<li><p>Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects</p></li>
<li><p>Add the function ‘AIC.mmkin’ to make it easy to compare columns of mmkin objects</p></li>
@@ -342,8 +327,7 @@
</div>
<div id="mkin-09475-2018-09-14" class="section level1">
<h1 class="page-header" data-toc-text="0.9.47.5">
-<a href="#mkin-09475-2018-09-14" class="anchor"></a>mkin 0.9.47.5 (2018-09-14)<small> 2018-09-14 </small>
-</h1>
+<a href="#mkin-09475-2018-09-14" class="anchor"></a>mkin 0.9.47.5 (2018-09-14)</h1>
<ul>
<li><p>Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows</p></li>
<li><p>Move two vignettes to a location where they will not be built on CRAN (to avoid more NOTES from long execution times)</p></li>
@@ -352,8 +336,7 @@
</div>
<div id="mkin-09473" class="section level1">
<h1 class="page-header" data-toc-text="0.9.47.3">
-<a href="#mkin-09473" class="anchor"></a>mkin 0.9.47.3<small> Unreleased </small>
-</h1>
+<a href="#mkin-09473" class="anchor"></a>mkin 0.9.47.3</h1>
<ul>
<li><p>‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’. Add ‘manual’ to possible arguments for ‘weight’</p></li>
<li><p>Test that FOCUS_2006_C can be evaluated with DFOP and reweight.method = ‘tc’</p></li>
@@ -361,8 +344,7 @@
</div>
<div id="mkin-09472-2018-07-19" class="section level1">
<h1 class="page-header" data-toc-text="0.9.47.2">
-<a href="#mkin-09472-2018-07-19" class="anchor"></a>mkin 0.9.47.2 (2018-07-19)<small> 2018-07-19 </small>
-</h1>
+<a href="#mkin-09472-2018-07-19" class="anchor"></a>mkin 0.9.47.2 (2018-07-19)</h1>
<ul>
<li><p>‘sigma_twocomp’: Rename ‘sigma_rl’ to ‘sigma_twocomp’ as the Rocke and Lorenzato model assumes lognormal distribution for large y. Correct references to the Rocke and Lorenzato model accordingly.</p></li>
<li><p>‘mkinfit’: Use 1.1 as starting value for N parameter of IORE models to obtain convergence in more difficult cases. Show parameter names when ‘trace_parms’ is ‘TRUE’.</p></li>
@@ -370,8 +352,7 @@
</div>
<div id="mkin-09471-2018-02-06" class="section level1">
<h1 class="page-header" data-toc-text="0.9.47.1">
-<a href="#mkin-09471-2018-02-06" class="anchor"></a>mkin 0.9.47.1 (2018-02-06)<small> 2018-02-06 </small>
-</h1>
+<a href="#mkin-09471-2018-02-06" class="anchor"></a>mkin 0.9.47.1 (2018-02-06)</h1>
<ul>
<li><p>Skip some tests on CRAN and winbuilder to avoid timeouts</p></li>
<li><p>‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014</p></li>
@@ -383,8 +364,7 @@
</div>
<div id="mkin-09463-2017-11-16" class="section level1">
<h1 class="page-header" data-toc-text="0.9.46.3">
-<a href="#mkin-09463-2017-11-16" class="anchor"></a>mkin 0.9.46.3 (2017-11-16)<small> 2017-11-16 </small>
-</h1>
+<a href="#mkin-09463-2017-11-16" class="anchor"></a>mkin 0.9.46.3 (2017-11-16)</h1>
<ul>
<li><p><code>README.md</code>, <code>vignettes/mkin.Rmd</code>: URLs were updated</p></li>
<li><p><code>synthetic_data_for_UBA</code>: Add the code used to generate the data in the interest of reproducibility</p></li>
@@ -392,8 +372,7 @@
</div>
<div id="mkin-09462-2017-10-10" class="section level1">
<h1 class="page-header" data-toc-text="0.9.46.2">
-<a href="#mkin-09462-2017-10-10" class="anchor"></a>mkin 0.9.46.2 (2017-10-10)<small> 2017-10-10 </small>
-</h1>
+<a href="#mkin-09462-2017-10-10" class="anchor"></a>mkin 0.9.46.2 (2017-10-10)</h1>
<ul>
<li><p>Converted the vignette FOCUS_Z from tex/pdf to markdown/html</p></li>
<li><p><code>DESCRIPTION</code>: Add ORCID</p></li>
@@ -401,8 +380,7 @@
</div>
<div id="mkin-09461-2017-09-14" class="section level1">
<h1 class="page-header" data-toc-text="0.9.46.1">
-<a href="#mkin-09461-2017-09-14" class="anchor"></a>mkin 0.9.46.1 (2017-09-14)<small> 2017-09-14 </small>
-</h1>
+<a href="#mkin-09461-2017-09-14" class="anchor"></a>mkin 0.9.46.1 (2017-09-14)</h1>
<ul>
<li><p><code>plot.mkinfit</code>: Fix scaling of residual plots for the case of separate plots for each observed variable</p></li>
<li><p><code>plot.mkinfit</code>: Use all data points of the fitted curve for y axis scaling for the case of separate plots for each observed variable</p></li>
@@ -411,16 +389,14 @@
</div>
<div id="mkin-0946-2017-07-24" class="section level1">
<h1 class="page-header" data-toc-text="0.9.46">
-<a href="#mkin-0946-2017-07-24" class="anchor"></a>mkin 0.9.46 (2017-07-24)<small> 2017-07-29 </small>
-</h1>
+<a href="#mkin-0946-2017-07-24" 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-09452-2017-07-24" class="section level1">
<h1 class="page-header" data-toc-text="0.9.45.2">
-<a href="#mkin-09452-2017-07-24" class="anchor"></a>mkin 0.9.45.2 (2017-07-24)<small> 2017-07-22 </small>
-</h1>
+<a href="#mkin-09452-2017-07-24" 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>
@@ -430,8 +406,7 @@
</div>
<div id="mkin-09451-2016-12-20" class="section level1">
<h1 class="page-header" data-toc-text="0.9.45.1">
-<a href="#mkin-09451-2016-12-20" class="anchor"></a>mkin 0.9.45.1 (2016-12-20)<small> Unreleased </small>
-</h1>
+<a href="#mkin-09451-2016-12-20" class="anchor"></a>mkin 0.9.45.1 (2016-12-20)</h1>
<div id="new-features" class="section level2">
<h2 class="hasAnchor">
<a href="#new-features" class="anchor"></a>New features</h2>
@@ -442,8 +417,7 @@
</div>
<div id="mkin-0945-2016-12-08" class="section level1">
<h1 class="page-header" data-toc-text="0.9.45">
-<a href="#mkin-0945-2016-12-08" class="anchor"></a>mkin 0.9.45 (2016-12-08)<small> 2016-12-08 </small>
-</h1>
+<a href="#mkin-0945-2016-12-08" class="anchor"></a>mkin 0.9.45 (2016-12-08)</h1>
<div id="minor-changes" class="section level2">
<h2 class="hasAnchor">
<a href="#minor-changes" class="anchor"></a>Minor changes</h2>
@@ -456,8 +430,7 @@
</div>
<div id="mkin-0944-2016-06-29" class="section level1">
<h1 class="page-header" data-toc-text="0.9.44">
-<a href="#mkin-0944-2016-06-29" class="anchor"></a>mkin 0.9.44 (2016-06-29)<small> 2016-06-29 </small>
-</h1>
+<a href="#mkin-0944-2016-06-29" class="anchor"></a>mkin 0.9.44 (2016-06-29)</h1>
<div id="bug-fixes" class="section level2">
<h2 class="hasAnchor">
<a href="#bug-fixes" class="anchor"></a>Bug fixes</h2>
@@ -468,8 +441,7 @@
</div>
<div id="mkin-0943-2016-06-28" class="section level1">
<h1 class="page-header" data-toc-text="0.9.43">
-<a href="#mkin-0943-2016-06-28" class="anchor"></a>mkin 0.9.43 (2016-06-28)<small> 2016-06-28 </small>
-</h1>
+<a href="#mkin-0943-2016-06-28" class="anchor"></a>mkin 0.9.43 (2016-06-28)</h1>
<div id="major-changes" class="section level2">
<h2 class="hasAnchor">
<a href="#major-changes" class="anchor"></a>Major changes</h2>
@@ -507,8 +479,7 @@
</div>
<div id="mkin-0942-2016-03-25" class="section level1">
<h1 class="page-header" data-toc-text="0.9.42">
-<a href="#mkin-0942-2016-03-25" class="anchor"></a>mkin 0.9.42 (2016-03-25)<small> 2016-03-25 </small>
-</h1>
+<a href="#mkin-0942-2016-03-25" class="anchor"></a>mkin 0.9.42 (2016-03-25)</h1>
<div id="major-changes-1" class="section level2">
<h2 class="hasAnchor">
<a href="#major-changes-1" class="anchor"></a>Major changes</h2>
@@ -528,8 +499,7 @@
</div>
<div id="mkin-09-41-2015-11-09" class="section level1">
<h1 class="page-header" data-toc-text="0.9-41">
-<a href="#mkin-09-41-2015-11-09" class="anchor"></a>mkin 0.9-41 (2015-11-09)<small> 2015-11-09 </small>
-</h1>
+<a href="#mkin-09-41-2015-11-09" class="anchor"></a>mkin 0.9-41 (2015-11-09)</h1>
<div id="minor-changes-3" class="section level2">
<h2 class="hasAnchor">
<a href="#minor-changes-3" class="anchor"></a>Minor changes</h2>
@@ -551,8 +521,7 @@
</div>
<div id="mkin-09-40-2015-07-21" class="section level1">
<h1 class="page-header" data-toc-text="0.9-40">
-<a href="#mkin-09-40-2015-07-21" class="anchor"></a>mkin 0.9-40 (2015-07-21)<small> 2015-07-21 </small>
-</h1>
+<a href="#mkin-09-40-2015-07-21" class="anchor"></a>mkin 0.9-40 (2015-07-21)</h1>
<div id="bug-fixes-3" class="section level2">
<h2 class="hasAnchor">
<a href="#bug-fixes-3" class="anchor"></a>Bug fixes</h2>
@@ -572,8 +541,7 @@
</div>
<div id="mkin-09-39-2015-06-26" class="section level1">
<h1 class="page-header" data-toc-text="0.9-39">
-<a href="#mkin-09-39-2015-06-26" class="anchor"></a>mkin 0.9-39 (2015-06-26)<small> 2015-06-26 </small>
-</h1>
+<a href="#mkin-09-39-2015-06-26" class="anchor"></a>mkin 0.9-39 (2015-06-26)</h1>
<div id="major-changes-2" class="section level2">
<h2 class="hasAnchor">
<a href="#major-changes-2" class="anchor"></a>Major changes</h2>
@@ -593,8 +561,7 @@
</div>
<div id="mkin-09-38-2015-06-24" class="section level1">
<h1 class="page-header" data-toc-text="0.9-38">
-<a href="#mkin-09-38-2015-06-24" class="anchor"></a>mkin 0.9-38 (2015-06-24)<small> 2015-06-23 </small>
-</h1>
+<a href="#mkin-09-38-2015-06-24" class="anchor"></a>mkin 0.9-38 (2015-06-24)</h1>
<div id="minor-changes-4" class="section level2">
<h2 class="hasAnchor">
<a href="#minor-changes-4" class="anchor"></a>Minor changes</h2>
@@ -614,8 +581,7 @@
</div>
<div id="mkin-09-36-2015-06-21" class="section level1">
<h1 class="page-header" data-toc-text="0.9-36">
-<a href="#mkin-09-36-2015-06-21" class="anchor"></a>mkin 0.9-36 (2015-06-21)<small> 2015-06-21 </small>
-</h1>
+<a href="#mkin-09-36-2015-06-21" class="anchor"></a>mkin 0.9-36 (2015-06-21)</h1>
<div id="major-changes-3" class="section level2">
<h2 class="hasAnchor">
<a href="#major-changes-3" class="anchor"></a>Major changes</h2>
@@ -636,8 +602,7 @@
</div>
<div id="mkin-09-35-2015-05-15" class="section level1">
<h1 class="page-header" data-toc-text="0.9-35">
-<a href="#mkin-09-35-2015-05-15" class="anchor"></a>mkin 0.9-35 (2015-05-15)<small> 2015-05-15 </small>
-</h1>
+<a href="#mkin-09-35-2015-05-15" class="anchor"></a>mkin 0.9-35 (2015-05-15)</h1>
<div id="major-changes-4" class="section level2">
<h2 class="hasAnchor">
<a href="#major-changes-4" class="anchor"></a>Major changes</h2>
@@ -668,8 +633,7 @@
</div>
<div id="mkin-09-34-2014-11-22" class="section level1">
<h1 class="page-header" data-toc-text="0.9-34">
-<a href="#mkin-09-34-2014-11-22" class="anchor"></a>mkin 0.9-34 (2014-11-22)<small> 2014-11-22 </small>
-</h1>
+<a href="#mkin-09-34-2014-11-22" class="anchor"></a>mkin 0.9-34 (2014-11-22)</h1>
<div id="new-features-2" class="section level2">
<h2 class="hasAnchor">
<a href="#new-features-2" class="anchor"></a>New features</h2>
@@ -690,8 +654,7 @@
</div>
<div id="mkin-09-33-2014-10-22" class="section level1">
<h1 class="page-header" data-toc-text="0.9-33">
-<a href="#mkin-09-33-2014-10-22" class="anchor"></a>mkin 0.9-33 (2014-10-22)<small> 2014-10-12 </small>
-</h1>
+<a href="#mkin-09-33-2014-10-22" class="anchor"></a>mkin 0.9-33 (2014-10-22)</h1>
<div id="new-features-3" class="section level2">
<h2 class="hasAnchor">
<a href="#new-features-3" class="anchor"></a>New features</h2>
@@ -723,8 +686,7 @@
</div>
<div id="mkin-09-32-2014-07-24" class="section level1">
<h1 class="page-header" data-toc-text="0.9-32">
-<a href="#mkin-09-32-2014-07-24" class="anchor"></a>mkin 0.9-32 (2014-07-24)<small> 2014-07-24 </small>
-</h1>
+<a href="#mkin-09-32-2014-07-24" class="anchor"></a>mkin 0.9-32 (2014-07-24)</h1>
<div id="new-features-4" class="section level2">
<h2 class="hasAnchor">
<a href="#new-features-4" class="anchor"></a>New features</h2>
@@ -760,8 +722,7 @@
</div>
<div id="mkin-09-31-2014-07-14" class="section level1">
<h1 class="page-header" data-toc-text="0.9-31">
-<a href="#mkin-09-31-2014-07-14" class="anchor"></a>mkin 0.9-31 (2014-07-14)<small> 2014-07-14 </small>
-</h1>
+<a href="#mkin-09-31-2014-07-14" class="anchor"></a>mkin 0.9-31 (2014-07-14)</h1>
<div id="bug-fixes-9" class="section level2">
<h2 class="hasAnchor">
<a href="#bug-fixes-9" class="anchor"></a>Bug fixes</h2>
@@ -772,8 +733,7 @@
</div>
<div id="mkin-09-30-2014-07-11" class="section level1">
<h1 class="page-header" data-toc-text="0.9-30">
-<a href="#mkin-09-30-2014-07-11" class="anchor"></a>mkin 0.9-30 (2014-07-11)<small> 2014-07-11 </small>
-</h1>
+<a href="#mkin-09-30-2014-07-11" class="anchor"></a>mkin 0.9-30 (2014-07-11)</h1>
<div id="new-features-5" class="section level2">
<h2 class="hasAnchor">
<a href="#new-features-5" class="anchor"></a>New features</h2>
@@ -804,8 +764,7 @@
</div>
<div id="mkin-09-29-2014-06-27" class="section level1">
<h1 class="page-header" data-toc-text="0.9-29">
-<a href="#mkin-09-29-2014-06-27" class="anchor"></a>mkin 0.9-29 (2014-06-27)<small> 2014-06-27 </small>
-</h1>
+<a href="#mkin-09-29-2014-06-27" class="anchor"></a>mkin 0.9-29 (2014-06-27)</h1>
<ul>
<li><p>R/mkinresplot.R: Make it possible to specify <code>xlim</code></p></li>
<li><p>R/geometric_mean.R, man/geometric_mean.Rd: Add geometric mean function</p></li>
@@ -814,8 +773,7 @@
</div>
<div id="mkin-09-28-2014-05-20" class="section level1">
<h1 class="page-header" data-toc-text="0.9-28">
-<a href="#mkin-09-28-2014-05-20" class="anchor"></a>mkin 0.9-28 (2014-05-20)<small> 2014-05-20 </small>
-</h1>
+<a href="#mkin-09-28-2014-05-20" class="anchor"></a>mkin 0.9-28 (2014-05-20)</h1>
<ul>
<li><p>Do not backtransform confidence intervals for formation fractions if more than one compound is formed, as such parameters only define the pathways as a set</p></li>
<li><p>Add historical remarks and some background to the main package vignette</p></li>
@@ -824,8 +782,7 @@
</div>
<div id="mkin-09-27-2014-05-10" class="section level1">
<h1 class="page-header" data-toc-text="0.9-27">
-<a href="#mkin-09-27-2014-05-10" class="anchor"></a>mkin 0.9-27 (2014-05-10)<small> 2014-05-10 </small>
-</h1>
+<a href="#mkin-09-27-2014-05-10" class="anchor"></a>mkin 0.9-27 (2014-05-10)</h1>
<ul>
<li><p>Fork the GUI into a separate package <a href="https://github.com/jranke/gmkin">gmkin</a></p></li>
<li><p>DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information</p></li>
@@ -848,8 +805,7 @@
</div>
<div id="mkin-09-24-2013-11-06" class="section level1">
<h1 class="page-header" data-toc-text="0.9-24">
-<a href="#mkin-09-24-2013-11-06" class="anchor"></a>mkin 0.9-24 (2013-11-06)<small> 2013-11-06 </small>
-</h1>
+<a href="#mkin-09-24-2013-11-06" class="anchor"></a>mkin 0.9-24 (2013-11-06)</h1>
<ul>
<li><p>Bugfix re-enabling the fixing of any combination of initial values for state variables</p></li>
<li><p>Default values for kinetic rate constants are not all 0.1 any more but are “salted” with a small increment to avoid numeric artefacts with the eigenvalue based solutions</p></li>
@@ -858,8 +814,7 @@
</div>
<div id="mkin-09-22-2013-10-26" class="section level1">
<h1 class="page-header" data-toc-text="0.9-22">
-<a href="#mkin-09-22-2013-10-26" class="anchor"></a>mkin 0.9-22 (2013-10-26)<small> 2013-10-26 </small>
-</h1>
+<a href="#mkin-09-22-2013-10-26" class="anchor"></a>mkin 0.9-22 (2013-10-26)</h1>
<ul>
<li><p>Get rid of the optimisation step in <code>mkinerrmin</code> - this was unnecessary. Thanks to KinGUII for the inspiration - actually this is equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally</p></li>
<li><p>Fix <code>plot.mkinfit</code> as it passed graphical arguments like main to the solver</p></li>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 847dd4c5..71325fcc 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
web_only/NAFTA_examples: NAFTA_examples.html
web_only/benchmarks: benchmarks.html
web_only/compiled_models: compiled_models.html
-last_built: 2021-02-15T13:07Z
+last_built: 2021-02-15T18:11Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
index 7f498242..762a3dd4 100644
--- a/docs/reference/Rplot001.png
+++ b/docs/reference/Rplot001.png
Binary files differ
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
index 54c31a3f..d24e35b4 100644
--- a/docs/reference/Rplot002.png
+++ b/docs/reference/Rplot002.png
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