Update DESCRIPTION, improve NEWS

Static documentation rebuilt by pkgdown

1 files changed, 10 insertions, 10 deletions

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-    <div id="mkin-0-9-49-5-2019-06-04" class="section level1">
+    <div id="mkin-0-9-49-5-2019-07-03" class="section level1">
 <h1 class="page-header">
-<a href="#mkin-0-9-49-5-2019-06-04" class="anchor"></a>mkin 0.9.49.5 (2019-06-04)<small> Unreleased </small>
+<a href="#mkin-0-9-49-5-2019-07-03" class="anchor"></a>mkin 0.9.49.5 (2019-07-03)<small> Unreleased </small>
 </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 tries direct minimization and a three step procedure, and returns the model with the highest likelihood.</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 ‘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>
 <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>
-<li><p>Add a benchmark vignette to document the impact on performance. For very simple fits, the new code is a bit slower, presumably because of the time it takes to calculate the hessian matrices with and without parameter transformation</p></li>
-<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>Remove dependency on FME, only use nlminb for optimisation (‘Port’ algorithm). I cannot remember cases where one of the other optimisation algorithms was preferable, except that I sometime used Levenberg-Marquardt for speed in cases where I did not expect to get trapped in a local minimum.</p></li>
+<li><p>Use the numDeriv package to calculate hessians. This results in slightly different confidence intervals, takes a bit longer, but is apparently more robust</p></li>
+<li><p>Add a simple benchmark vignette to document the impact on performance.</p></li>
+<li><p>The code for manual weighting was removed. This functionality might get added again at a later time.</p></li>
+<li><p>The fitting time reported in the summary now includes the time used for 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>
+<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 in parallel via mmkin this could go unnoticed.</p></li>
 </ul>
 </div>
     <div id="mkin-0-9-48-1-2019-03-04" class="section level1">
@@ -698,7 +698,7 @@
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
-        <li><a href="#mkin-0-9-49-5-2019-06-04">0.9.49.5</a></li>
+        <li><a href="#mkin-0-9-49-5-2019-07-03">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>