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-rw-r--r--docs/news/index.html115
1 files changed, 60 insertions, 55 deletions
diff --git a/docs/news/index.html b/docs/news/index.html
index 2e7f0e34..667c5c1f 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -25,12 +25,14 @@
<script src="../pkgdown.js"></script>
<!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
+
+
</head>
<body>
@@ -70,6 +72,9 @@
<li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
+ <li>
+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
</ul>
</li>
<li>
@@ -102,10 +107,10 @@
<div class="contents">
<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>
+<a href="#mkin-0-9-45-1-2016-12-20" 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>
+<a href="#new-features" class="anchor"></a>New features</h2>
<ul>
<li>A <code>twa</code> function, calculating maximum time weighted average concentrations for the parent (SFO, FOMC and DFOP).</li>
</ul>
@@ -113,10 +118,10 @@
</div>
<div id="mkin-0-9-45-2016-12-08" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-45-2016-12-08" class="anchor"> </a>mkin 0.9.45 (2016-12-08)</h1>
+<a href="#mkin-0-9-45-2016-12-08" 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>
+<a href="#minor-changes" class="anchor"></a>Minor changes</h2>
<ul>
<li><p><code>plot.mkinfit</code> and <code>plot.mmkin</code>: If the plotting device is <code>tikz</code>, LaTeX markup is being used for the chi2 error in the graphs.</p></li>
<li><p>Use <code>pkgdown</code>, the successor of <code>staticdocs</code> for generating static HTML documentation. Include example output and graphs also for <code>dontrun</code> sections.</p></li>
@@ -126,10 +131,10 @@
</div>
<div id="mkin-0-9-44-2016-06-29" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-44-2016-06-29" class="anchor"> </a>mkin 0.9.44 (2016-06-29)</h1>
+<a href="#mkin-0-9-44-2016-06-29" 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>
+<a href="#bug-fixes" class="anchor"></a>Bug fixes</h2>
<ul>
<li>The test <code>test_FOMC_ill-defined</code> failed on several architectures, so the test is now skipped</li>
</ul>
@@ -137,10 +142,10 @@
</div>
<div id="mkin-0-9-43-2016-06-28" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-43-2016-06-28" class="anchor"> </a>mkin 0.9.43 (2016-06-28)</h1>
+<a href="#mkin-0-9-43-2016-06-28" 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>
+<a href="#major-changes" class="anchor"></a>Major changes</h2>
<ul>
<li><p>The title was changed to <code>Kinetic evaluations of chemical degradation data</code></p></li>
<li><p><code>plot.mkinfit</code>: Add the possibility to show fits (and residual plots if requested) separately for the observed variables</p></li>
@@ -152,7 +157,7 @@
</div>
<div id="minor-changes-1" class="section level2">
<h2 class="hasAnchor">
-<a href="#minor-changes-1" class="anchor"> </a>Minor changes</h2>
+<a href="#minor-changes-1" class="anchor"></a>Minor changes</h2>
<ul>
<li><p>Remove an outdated reference to the inline package in the <code>compiled_models</code> vignette</p></li>
<li><p><code>mkinfit</code>: Do not error out in cases where the fit converges, but the Jacobian for the untransformed model cost can not be estimated. Give a warning instead and return NA for the t-test results.</p></li>
@@ -164,7 +169,7 @@
</div>
<div id="bug-fixes-1" class="section level2">
<h2 class="hasAnchor">
-<a href="#bug-fixes-1" class="anchor"> </a>Bug fixes</h2>
+<a href="#bug-fixes-1" class="anchor"></a>Bug fixes</h2>
<ul>
<li><p><code>endpoints</code>: When the name of a substance degrading to a metabolite (e.g. a parent compound) used in the model formulation ended in the letter <code>f</code>, some rate parameters could be listed as formation fractions with mixed up names. These would also appear in the summary.</p></li>
<li><p><code>mkinfit</code>: Check for all observed variables when checking if the user tried to fix formation fractions when fitting them using ilr transformation.</p></li>
@@ -175,17 +180,17 @@
</div>
<div id="mkin-0-9-42-2016-03-25" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-42-2016-03-25" class="anchor"> </a>mkin 0.9.42 (2016-03-25)</h1>
+<a href="#mkin-0-9-42-2016-03-25" 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>
+<a href="#major-changes-1" class="anchor"></a>Major changes</h2>
<ul>
<li>Add the argument <code>from_max_mean</code> to <code>mkinfit</code>, for fitting only the decline from the maximum observed value for models with a single observed variable</li>
</ul>
</div>
<div id="minor-changes-2" class="section level2">
<h2 class="hasAnchor">
-<a href="#minor-changes-2" class="anchor"> </a>Minor changes</h2>
+<a href="#minor-changes-2" class="anchor"></a>Minor changes</h2>
<ul>
<li><p>Add plots to <code>compiled_models</code> vignette</p></li>
<li><p>Give an explanatory error message when mkinmod fails due to a missing definition of a target variable</p></li>
@@ -195,10 +200,10 @@
</div>
<div id="mkin-0-9-41-2015-11-09" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-41-2015-11-09" class="anchor"> </a>mkin 0.9-41 (2015-11-09)</h1>
+<a href="#mkin-0-9-41-2015-11-09" 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>
+<a href="#minor-changes-3" class="anchor"></a>Minor changes</h2>
<ul>
<li><p>Add an R6 class <code>mkinds</code> representing datasets with a printing method</p></li>
<li><p>Add a printing method for mkinmod objects</p></li>
@@ -208,7 +213,7 @@
</div>
<div id="bug-fixes-2" class="section level2">
<h2 class="hasAnchor">
-<a href="#bug-fixes-2" class="anchor"> </a>Bug fixes</h2>
+<a href="#bug-fixes-2" class="anchor"></a>Bug fixes</h2>
<ul>
<li>
<code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36</li>
@@ -217,10 +222,10 @@
</div>
<div id="mkin-0-9-40-2015-07-21" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-40-2015-07-21" class="anchor"> </a>mkin 0.9-40 (2015-07-21)</h1>
+<a href="#mkin-0-9-40-2015-07-21" 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>
+<a href="#bug-fixes-3" class="anchor"></a>Bug fixes</h2>
<ul>
<li>
<code><a href="../reference/endpoints.html">endpoints()</a></code>: For DFOP and SFORB models, where <code>optimize()</code> is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as <code>optimize()</code> sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient.</li>
@@ -228,7 +233,7 @@
</div>
<div id="internal-changes" class="section level2">
<h2 class="hasAnchor">
-<a href="#internal-changes" class="anchor"> </a>Internal changes</h2>
+<a href="#internal-changes" class="anchor"></a>Internal changes</h2>
<ul>
<li>
<code>DESCRIPTION</code>, <code>NAMESPACE</code>, <code>R/*.R</code>: Import (from) stats, graphics and methods packages, and qualify some function calls for non-base packages installed with R to avoid NOTES made by R CMD check –as-cran with upcoming R versions.</li>
@@ -237,10 +242,10 @@
</div>
<div id="mkin-0-9-39-2015-06-26" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-39-2015-06-26" class="anchor"> </a>mkin 0.9-39 (2015-06-26)</h1>
+<a href="#mkin-0-9-39-2015-06-26" 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>
+<a href="#major-changes-2" class="anchor"></a>Major changes</h2>
<ul>
<li><p>New function <code><a href="../reference/mmkin.html">mmkin()</a></code>: This function takes a character vector of model shorthand names, or alternatively a list of mkinmod models, as well as a list of dataset as main arguments. It returns a matrix of mkinfit objects, with a row for each model and a column for each dataset. A subsetting method with single brackets is available. Fitting the models in parallel using the <code>parallel</code> package is supported.</p></li>
<li><p>New function <code><a href="../reference/plot.mmkin.html">plot.mmkin()</a></code>: Plots single-row or single-column <code>mmkin</code> objects including residual plots.</p></li>
@@ -248,7 +253,7 @@
</div>
<div id="bug-fixes-4" class="section level2">
<h2 class="hasAnchor">
-<a href="#bug-fixes-4" class="anchor"> </a>Bug fixes</h2>
+<a href="#bug-fixes-4" class="anchor"></a>Bug fixes</h2>
<ul>
<li>
<code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Fix the x axis scaling for rate constants and formation fractions that got confused by the introduction of the t-values of transformed parameters.</li>
@@ -257,10 +262,10 @@
</div>
<div id="mkin-0-9-38-2015-06-24" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-38-2015-06-24" class="anchor"> </a>mkin 0.9-38 (2015-06-24)</h1>
+<a href="#mkin-0-9-38-2015-06-24" 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>
+<a href="#minor-changes-4" class="anchor"></a>Minor changes</h2>
<ul>
<li><p><code>vignettes/compiled_models.html</code>: Show the performance improvement factor actually obtained when building the vignette, as well as mkin version, some system info and the CPU model used for building the vignette.</p></li>
<li><p><code>GNUMakefile</code>,<code>vignettes/*</code>: Clean up vignette generation and include table of contents in HTML vignettes.</p></li>
@@ -268,7 +273,7 @@
</div>
<div id="bug-fixes-5" class="section level2">
<h2 class="hasAnchor">
-<a href="#bug-fixes-5" class="anchor"> </a>Bug fixes</h2>
+<a href="#bug-fixes-5" class="anchor"></a>Bug fixes</h2>
<ul>
<li>
<code><a href="../reference/mkinmod.html">mkinmod()</a></code>: When generating the C code for the derivatives, only declare the time variable when it is needed and remove the ‘-W-no-unused-variable’ compiler flag as the C compiler used in the CRAN checks on Solaris does not know it.</li>
@@ -277,10 +282,10 @@
</div>
<div id="mkin-0-9-36-2015-06-21" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-36-2015-06-21" class="anchor"> </a>mkin 0.9-36 (2015-06-21)</h1>
+<a href="#mkin-0-9-36-2015-06-21" 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>
+<a href="#major-changes-3" class="anchor"></a>Major changes</h2>
<ul>
<li><p><code><a href="../reference/summary.mkinfit.html">summary.mkinfit()</a></code>: A one-sided t-test for significant difference of untransformed parameters from zero is now always shown, based on the assumption of normal distribution for estimators of all untransformed parameters. Use with caution, as this assumption is unrealistic e.g. for rate constants in these nonlinear kinetic models.</p></li>
<li><p>If a compiler (gcc) is installed, use a version of the differential equation model compiled from C code, which is a huge performance boost for models where only the deSolve method works.</p></li>
@@ -290,7 +295,7 @@
</div>
<div id="minor-changes-5" class="section level2">
<h2 class="hasAnchor">
-<a href="#minor-changes-5" class="anchor"> </a>Minor changes</h2>
+<a href="#minor-changes-5" class="anchor"></a>Minor changes</h2>
<ul>
<li>Added a simple showcase vignette with an evaluation of FOCUS example dataset D</li>
</ul>
@@ -298,17 +303,17 @@
</div>
<div id="mkin-0-9-35-2015-05-15" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-35-2015-05-15" class="anchor"> </a>mkin 0.9-35 (2015-05-15)</h1>
+<a href="#mkin-0-9-35-2015-05-15" 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>
+<a href="#major-changes-4" class="anchor"></a>Major changes</h2>
<ul>
<li>Switch from RUnit to testthat for testing</li>
</ul>
</div>
<div id="bug-fixes-6" class="section level2">
<h2 class="hasAnchor">
-<a href="#bug-fixes-6" class="anchor"> </a>Bug fixes</h2>
+<a href="#bug-fixes-6" class="anchor"></a>Bug fixes</h2>
<ul>
<li><p><code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit</p></li>
<li><p><code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Fix printing the summary for the case that the number of iterations is not available</p></li>
@@ -318,7 +323,7 @@
</div>
<div id="new-features-1" class="section level2">
<h2 class="hasAnchor">
-<a href="#new-features-1" class="anchor"> </a>New features</h2>
+<a href="#new-features-1" class="anchor"></a>New features</h2>
<ul>
<li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: Report successful termination when quiet = FALSE. This is helpful for more difficult problems fitted with reweight.method = obs, as no progress is often indicated during the reweighting.</p></li>
<li><p>A first test using results established in the expertise written for the German Federal Environmental Agency (UBA) was added.</p></li>
@@ -329,10 +334,10 @@
</div>
<div id="mkin-0-9-34-2014-11-22" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-34-2014-11-22" class="anchor"> </a>mkin 0.9-34 (2014-11-22)</h1>
+<a href="#mkin-0-9-34-2014-11-22" 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>
+<a href="#new-features-2" class="anchor"></a>New features</h2>
<ul>
<li><p>Add the convenience function <code><a href="../reference/mkinsub.html">mkinsub()</a></code> for creating the lists used in <code><a href="../reference/mkinmod.html">mkinmod()</a></code></p></li>
<li><p>Add the possibility to fit indeterminate order rate equation (IORE) models using an analytical solution (parent only) or a numeric solution. Paths from IORE compounds to metabolites are supported when using formation fractions (use_of_ff = ‘max’). Note that the numerical solution (method.ode = ‘deSolve’) of the IORE differential equations sometimes fails due to numerical problems.</p></li>
@@ -341,7 +346,7 @@
</div>
<div id="minor-changes-6" class="section level2">
<h2 class="hasAnchor">
-<a href="#minor-changes-6" class="anchor"> </a>Minor changes</h2>
+<a href="#minor-changes-6" class="anchor"></a>Minor changes</h2>
<ul>
<li><p>The formatting of differential equations in the summary was further improved</p></li>
<li><p>Always include 0 on y axis when plotting during the fit</p></li>
@@ -350,10 +355,10 @@
</div>
<div id="mkin-0-9-33-2014-10-22" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-33-2014-10-22" class="anchor"> </a>mkin 0.9-33 (2014-10-22)</h1>
+<a href="#mkin-0-9-33-2014-10-22" 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>
+<a href="#new-features-3" class="anchor"></a>New features</h2>
<ul>
<li><p>The initial value (state.ini) for the observed variable with the highest observed residue is set to 100 in case it has no time zero observation and <code>state.ini = "auto"</code></p></li>
<li><p>A basic unit test for <code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code> was written</p></li>
@@ -361,7 +366,7 @@
</div>
<div id="bug-fixes-7" class="section level2">
<h2 class="hasAnchor">
-<a href="#bug-fixes-7" class="anchor"> </a>Bug fixes</h2>
+<a href="#bug-fixes-7" class="anchor"></a>Bug fixes</h2>
<ul>
<li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: The internally fitted parameter for <code>g</code> was named <code>g_ilr</code> even when <code>transform_fractions=FALSE</code></p></li>
<li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: The initial value (state.ini) for the parent compound was not set when the parent was not the (only) variable with the highest value in the observed data.</p></li>
@@ -371,7 +376,7 @@
</div>
<div id="minor-changes-7" class="section level2">
<h2 class="hasAnchor">
-<a href="#minor-changes-7" class="anchor"> </a>Minor changes</h2>
+<a href="#minor-changes-7" class="anchor"></a>Minor changes</h2>
<ul>
<li><p>The formatting of differential equations in the summary was improved by wrapping overly long lines</p></li>
<li><p>The FOCUS_Z vignette was rebuilt with the above improvement and using a width of 70 to avoid output outside of the grey area</p></li>
@@ -382,10 +387,10 @@
</div>
<div id="mkin-0-9-32-2014-07-24" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-32-2014-07-24" class="anchor"> </a>mkin 0.9-32 (2014-07-24)</h1>
+<a href="#mkin-0-9-32-2014-07-24" 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>
+<a href="#new-features-4" class="anchor"></a>New features</h2>
<ul>
<li><p>The number of degrees of freedom is difficult to define in the case of ilr transformation of formation fractions. Now for each source compartment the number of ilr parameters (=number of optimised parameters) is divided by the number of pathways to metabolites (=number of affected data series) which leads to fractional degrees of freedom in some cases.</p></li>
<li><p>The default for the initial value for the first state value is now taken from the mean of the observations at time zero, if available.</p></li>
@@ -397,7 +402,7 @@
</div>
<div id="bug-fixes-8" class="section level2">
<h2 class="hasAnchor">
-<a href="#bug-fixes-8" class="anchor"> </a>Bug fixes</h2>
+<a href="#bug-fixes-8" class="anchor"></a>Bug fixes</h2>
<ul>
<li><p>Avoid plotting an artifical 0 residual at time zero in <code>mkinresplot</code></p></li>
<li><p>In the determination of the degrees of freedom in <code>mkinerrmin</code>, formation fractions were accounted for multiple times in the case of parallel formation of metabolites. See the new feature described above for the solution.</p></li>
@@ -408,7 +413,7 @@
</div>
<div id="minor-changes-8" class="section level2">
<h2 class="hasAnchor">
-<a href="#minor-changes-8" class="anchor"> </a>Minor changes</h2>
+<a href="#minor-changes-8" class="anchor"></a>Minor changes</h2>
<ul>
<li><p>Vignettes were rebuilt to reflect the changes in the summary method.</p></li>
<li><p>Algorithm <code>Pseudo</code> was excluded because it needs user-defined parameter limits which are not supported.</p></li>
@@ -418,10 +423,10 @@
</div>
<div id="mkin-0-9-31-2014-07-14" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-31-2014-07-14" class="anchor"> </a>mkin 0.9-31 (2014-07-14)</h1>
+<a href="#mkin-0-9-31-2014-07-14" 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>
+<a href="#bug-fixes-9" class="anchor"></a>Bug fixes</h2>
<ul>
<li>The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in <code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code> used by the summary function.</li>
</ul>
@@ -429,17 +434,17 @@
</div>
<div id="mkin-0-9-30-2014-07-11" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-30-2014-07-11" class="anchor"> </a>mkin 0.9-30 (2014-07-11)</h1>
+<a href="#mkin-0-9-30-2014-07-11" 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>
+<a href="#new-features-5" class="anchor"></a>New features</h2>
<ul>
<li>It is now possible to use formation fractions in combination with turning off the sink in <code><a href="../reference/mkinmod.html">mkinmod()</a></code>.</li>
</ul>
</div>
<div id="major-changes-5" class="section level2">
<h2 class="hasAnchor">
-<a href="#major-changes-5" class="anchor"> </a>Major changes</h2>
+<a href="#major-changes-5" class="anchor"></a>Major changes</h2>
<ul>
<li><p>The original and the transformed parameters now have different names (e.g. <code>k_parent</code> and <code>log_k_parent</code>. They also differ in how many they are when we have formation fractions but no pathway to sink.</p></li>
<li><p>The order of some of the information blocks in <code>print.summary.mkinfit.R()</code> has been ordered in a more logical way.</p></li>
@@ -447,7 +452,7 @@
</div>
<div id="minor-changes-9" class="section level2">
<h2 class="hasAnchor">
-<a href="#minor-changes-9" class="anchor"> </a>Minor changes</h2>
+<a href="#minor-changes-9" class="anchor"></a>Minor changes</h2>
<ul>
<li><p>The vignette FOCUS_Z has been simplified to use formation fractions with turning off the sink, and slightly amended to use the new versions of DT50 values calculated since mkin 0.9-29.</p></li>
<li><p>All vignettes have been rebuilt so they reflect all changes.</p></li>
@@ -460,7 +465,7 @@
</div>
<div id="mkin-0-9-29-2014-06-27" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-29-2014-06-27" class="anchor"> </a>mkin 0.9-29 (2014-06-27)</h1>
+<a href="#mkin-0-9-29-2014-06-27" 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>
@@ -469,7 +474,7 @@
</div>
<div id="mkin-0-9-28-2014-05-20" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-28-2014-05-20" class="anchor"> </a>mkin 0.9-28 (2014-05-20)</h1>
+<a href="#mkin-0-9-28-2014-05-20" 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>
@@ -478,7 +483,7 @@
</div>
<div id="mkin-0-9-27-2014-05-10" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-27-2014-05-10" class="anchor"> </a>mkin 0.9-27 (2014-05-10)</h1>
+<a href="#mkin-0-9-27-2014-05-10" class="anchor"></a>mkin 0.9-27 (2014-05-10)</h1>
<ul>
<li><p>Fork the GUI into a separate package <a href="http://github.com/jranke/gmkin">gmkin</a></p></li>
<li><p>DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information</p></li>
@@ -501,7 +506,7 @@
</div>
<div id="mkin-0-9-24-2013-11-06" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-24-2013-11-06" class="anchor"> </a>mkin 0.9-24 (2013-11-06)</h1>
+<a href="#mkin-0-9-24-2013-11-06" 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>
@@ -510,7 +515,7 @@
</div>
<div id="mkin-0-9-22-2013-10-26" class="section level1">
<h1 class="hasAnchor">
-<a href="#mkin-0-9-22-2013-10-26" class="anchor"> </a>mkin 0.9-22 (2013-10-26)</h1>
+<a href="#mkin-0-9-22-2013-10-26" 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>

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