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authorJohannes Ranke <jranke@uni-bremen.de>2019-06-04 15:09:28 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2019-06-04 15:09:28 +0200
commit95178837d3f91e84837628446b5fd468179af2b9 (patch)
tree8b162d5a22b28b59ca9c6bb27bf8f9dfbeaefbae /docs/news
parent9a96391589fef9f80f9c6c4881cc48a509cb75f2 (diff)
Additional algorithm "d_c", more tests, docs
The new algorithm tries direct optimization of the likelihood, as well as a three step procedure. In this way, we consistently get the model with the highest likelihood for SFO, DFOP and HS for all 12 new test datasets.
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diff --git a/docs/news/index.html b/docs/news/index.html
index 11414ed3..df6d53db 100644
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+++ b/docs/news/index.html
@@ -60,7 +60,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span>
</span>
</div>
@@ -122,13 +122,14 @@
</div>
- <div id="mkin-0-9-49-4-2019-05-08" class="section level1">
+ <div id="mkin-0-9-49-5-2019-06-04" class="section level1">
<h1 class="page-header">
-<a href="#mkin-0-9-49-4-2019-05-08" class="anchor"></a>mkin 0.9.49.4 (2019-05-08)<small> Unreleased </small>
+<a href="#mkin-0-9-49-5-2019-06-04" class="anchor"></a>mkin 0.9.49.5 (2019-06-04)<small> Unreleased </small>
</h1>
<ul>
-<li><p>Direct 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</p></li>
-<li><p>The argument ‘reweight.method’ to mkinfit and mmkin is now obsolete, use ‘error_model’ instead</p></li>
+<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 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>
+<li><p>Add a test that checks if we get the best known AIC for parent only fits to 12 test datasets. Add these test datasets for this purpose.</p></li>
<li><p>New function ‘mkinerrplot’. This function is also used for residual plots in ‘plot.mmkin’ if the argument ‘resplot = “errmod”’ is given, and in ‘plot.mkinfit’ if ‘show_errplot’ is set to TRUE.</p></li>
<li><p>Remove dependency on FME, only use nlminb for optimisation</p></li>
<li><p>Use the numDeriv package to calculate hessians</p></li>
@@ -136,6 +137,7 @@
<li><p>The code for manual weighting was removed</p></li>
<li><p>The fitting time reported in the summary now includes the calculation of the hessians</p></li>
<li><p>Adapt tests</p></li>
+<li><p>Fix an error in the FOCUS chi2 error level calculations that occurred if parameters were specified in parms.ini that were not in the model. A warning was already issued, but when fitting via mmkin this could easily go unnoticed.</p></li>
</ul>
</div>
<div id="mkin-0-9-48-1-2019-03-04" class="section level1">
@@ -696,7 +698,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#mkin-0-9-49-4-2019-05-08">0.9.49.4</a></li>
+ <li><a href="#mkin-0-9-49-5-2019-06-04">0.9.49.5</a></li>
<li><a href="#mkin-0-9-48-1-2019-03-04">0.9.48.1</a></li>
<li><a href="#mkin-0-9-47-5-2018-09-14">0.9.47.5</a></li>
<li><a href="#mkin-0-9-47-3">0.9.47.3</a></li>
@@ -740,7 +742,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
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