Some improvements for borderline cases

- fit_with_errors for saem()
- test_log_parms for mean_degparms() and saem()

1 files changed, 62 insertions, 99 deletions

diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 31c392f7..10585403 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.4.9000</span>
       </span>
     </div>
 
@@ -141,10 +141,9 @@
       <small>Source: <a href='https://github.com/jranke/mkin/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="mkin-1039000" class="section level1">
-<h1 class="page-header" data-toc-text="1.0.3.9000">
-<a href="#mkin-1039000" class="anchor"></a>mkin 1.0.3.9000<small> Unreleased </small>
-</h1>
+    <div id="mkin-1049000" class="section level1">
+<h1 class="page-header" data-toc-text="1.0.4.9000">
+<a href="#mkin-1049000" class="anchor"></a>mkin 1.0.4.9000</h1>
 <div id="general" class="section level2">
 <h2 class="hasAnchor">
 <a href="#general" class="anchor"></a>General</h2>
@@ -159,29 +158,35 @@
 <li><p>Reintroduce the interface to the current development version of saemix, in particular:</p></li>
 <li><p>‘saemix_model’ and ‘saemix_data’: Helper functions to set up nonlinear mixed-effects models for mmkin row objects</p></li>
 <li><p>‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods</p></li>
+<li><p>‘mean_degparms’: New argument ‘test_log_parms’ that makes the function only consider log-transformed parameters where the untransformed parameters pass the t-test for a certain confidence level. This can be used to check more plausible parameters for ‘saem’</p></li>
 </ul>
 </div>
 </div>
-    <div id="mkin-103" class="section level1">
+    <div id="mkin-104-unreleased" class="section level1">
+<h1 class="page-header" data-toc-text="1.0.4">
+<a href="#mkin-104-unreleased" class="anchor"></a>mkin 1.0.4 (Unreleased)</h1>
+<ul>
+<li><p>‘plot.mixed.mmkin’: Reset graphical parameters on exit</p></li>
+<li><p>All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters</p></li>
+</ul>
+</div>
+    <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>
@@ -190,10 +195,9 @@
 <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-1" class="section level2">
 <h2 class="hasAnchor">
 <a href="#general-1" class="anchor"></a>General</h2>
@@ -221,8 +225,7 @@
 </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>
@@ -237,8 +240,7 @@
 </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>
@@ -246,8 +248,7 @@
 </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>
@@ -256,16 +257,14 @@
 </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>
@@ -277,8 +276,7 @@
 </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>
@@ -286,8 +284,7 @@
 </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>
@@ -298,8 +295,7 @@
 </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>
@@ -307,8 +303,7 @@
 </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>
@@ -327,8 +322,7 @@
 </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>
@@ -346,8 +340,7 @@
 </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>
@@ -363,8 +356,7 @@
 </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>
@@ -373,8 +365,7 @@
 </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>
@@ -382,8 +373,7 @@
 </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>
@@ -391,8 +381,7 @@
 </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>
@@ -404,8 +393,7 @@
 </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>
@@ -413,8 +401,7 @@
 </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>
@@ -422,8 +409,7 @@
 </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>
@@ -432,16 +418,14 @@
 </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>
@@ -451,8 +435,7 @@
 </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>
@@ -463,8 +446,7 @@
 </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>
@@ -477,8 +459,7 @@
 </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>
@@ -489,8 +470,7 @@
 </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>
@@ -528,8 +508,7 @@
 </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>
@@ -549,8 +528,7 @@
 </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>
@@ -572,8 +550,7 @@
 </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">
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@@ -593,8 +570,7 @@
 </div>
     <div id="mkin-09-39-2015-06-26" class="section level1">
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-<a href="#mkin-09-39-2015-06-26" class="anchor"></a>mkin 0.9-39 (2015-06-26)<small> 2015-06-26 </small>
-</h1>
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@@ -614,8 +590,7 @@
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 <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>
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@@ -635,8 +610,7 @@
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 <h1 class="page-header" data-toc-text="0.9-36">
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@@ -657,8 +631,7 @@
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 <h1 class="page-header" data-toc-text="0.9-35">
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@@ -689,8 +662,7 @@
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 <h1 class="page-header" data-toc-text="0.9-34">
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 <h1 class="page-header" data-toc-text="0.9-33">
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-</h1>
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 <h1 class="page-header" data-toc-text="0.9-32">
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@@ -781,8 +751,7 @@
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 <h1 class="page-header" data-toc-text="0.9-31">
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-</h1>
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 <h2 class="hasAnchor">
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@@ -793,8 +762,7 @@
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 <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>
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@@ -825,8 +793,7 @@
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     <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>
@@ -835,8 +802,7 @@
 </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>
@@ -845,8 +811,7 @@
 </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>
@@ -869,8 +834,7 @@
 </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>
@@ -879,8 +843,7 @@
 </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>