List random effects correlations in output if any

Update docs

1 files changed, 39 insertions, 18 deletions

diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index e2b44bf5..6127ebc6 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -90,7 +90,11 @@
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.2.2" id="mkin-122">mkin 1.2.2<a class="anchor" aria-label="anchor" href="#mkin-122"></a></h2>
 <ul><li><p>‘R/mhmkin.R’: Allow an ‘illparms.mhmkin’ object or a list with suitable dimensions as value of the argument ‘no_random_effects’, making it possible to exclude random effects that were ill-defined in simpler variants of the set of degradation models. Remove the possibility to exclude random effects based on separate fits, as it did not work well.</p></li>
-<li><p>‘R/summary.saem.mmkin.R’: List all initial parameter values in the summary, including random effects and error model parameters. Avoid redundant warnings that occurred in the calculation of correlations of the fixed effects in the case that the Fisher information matrix could not be inverted.</p></li>
+<li><p>‘R/summary.saem.mmkin.R’: List all initial parameter values in the summary, including random effects and error model parameters. Avoid redundant warnings that occurred in the calculation of correlations of the fixed effects in the case that the Fisher information matrix could not be inverted. List correlations of random effects if specified by the user in the covariance model.</p></li>
+<li><p>‘R/parplot.R’: Possibility to select the top ‘llquant’ fraction of the fits for the parameter plots, and improved legend text.</p></li>
+<li><p>‘R/illparms.R’: Also check if confidence intervals for slope parameters in covariate models include zero. Only implemented for fits obtained with the saemix backend.</p></li>
+<li><p>‘R/parplot.R’: Make the function work also in the case that some of the multistart runs failed.</p></li>
+<li><p>‘R/intervals.R’: Include correlations of random effects in the model in case there are any.</p></li>
 </ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.2.1" id="mkin-121-2022-11-19">mkin 1.2.1 (2022-11-19)<a class="anchor" aria-label="anchor" href="#mkin-121-2022-11-19"></a></h2>
@@ -140,7 +144,8 @@
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.0.5" id="mkin-105-2021-09-15">mkin 1.0.5 (2021-09-15)<a class="anchor" aria-label="anchor" href="#mkin-105-2021-09-15"></a></h2>
-<ul><li>‘dimethenamid_2018’: Correct the data for the Borstel soil. The five observations from Staudenmaier (2013) that were previously stored as “Borstel 2” are actually just a subset of the 16 observations in “Borstel 1” which is now simply “Borstel”</li></ul></div>
+<ul><li>‘dimethenamid_2018’: Correct the data for the Borstel soil. The five observations from Staudenmaier (2013) that were previously stored as “Borstel 2” are actually just a subset of the 16 observations in “Borstel 1” which is now simply “Borstel”</li>
+</ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.0.4" id="mkin-104-2021-04-20">mkin 1.0.4 (2021-04-20)<a class="anchor" aria-label="anchor" href="#mkin-104-2021-04-20"></a></h2>
 <ul><li><p>All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters</p></li>
@@ -149,10 +154,12 @@
 </ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.0.3" id="mkin-103-2021-02-15">mkin 1.0.3 (2021-02-15)<a class="anchor" aria-label="anchor" href="#mkin-103-2021-02-15"></a></h2>
-<ul><li>Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages</li></ul></div>
+<ul><li>Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages</li>
+</ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.0.2" id="mkin-102-unreleased">mkin 1.0.2 (Unreleased)<a class="anchor" aria-label="anchor" href="#mkin-102-unreleased"></a></h2>
-<ul><li>‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’</li></ul></div>
+<ul><li>‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’</li>
+</ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.0.1" id="mkin-101-2021-02-10">mkin 1.0.1 (2021-02-10)<a class="anchor" aria-label="anchor" href="#mkin-101-2021-02-10"></a></h2>
 <ul><li><p>‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults</p></li>
@@ -207,7 +214,8 @@
 </ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9.49.11" id="mkin-094911-2020-04-20">mkin 0.9.49.11 (2020-04-20)<a class="anchor" aria-label="anchor" href="#mkin-094911-2020-04-20"></a></h2>
-<ul><li>Increase a test tolerance to make it pass on all CRAN check machines</li></ul></div>
+<ul><li>Increase a test tolerance to make it pass on all CRAN check machines</li>
+</ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9.49.10" id="mkin-094910-2020-04-18">mkin 0.9.49.10 (2020-04-18)<a class="anchor" aria-label="anchor" href="#mkin-094910-2020-04-18"></a></h2>
 <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>
@@ -322,7 +330,8 @@
 </ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9.46" id="mkin-0946-2017-07-24">mkin 0.9.46 (2017-07-24)<a class="anchor" aria-label="anchor" href="#mkin-0946-2017-07-24"></a></h2>
-<ul><li>Remove <code>test_FOMC_ill-defined.R</code> as it is too platform dependent</li></ul></div>
+<ul><li>Remove <code>test_FOMC_ill-defined.R</code> as it is too platform dependent</li>
+</ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9.45.2" id="mkin-09452-2017-07-24">mkin 0.9.45.2 (2017-07-24)<a class="anchor" aria-label="anchor" href="#mkin-09452-2017-07-24"></a></h2>
 <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>
@@ -334,7 +343,8 @@
 <h2 class="page-header" data-toc-text="0.9.45.1" id="mkin-09451-2016-12-20">mkin 0.9.45.1 (2016-12-20)<a class="anchor" aria-label="anchor" href="#mkin-09451-2016-12-20"></a></h2>
 <div class="section level3">
 <h3 id="new-features-0-9-45-1">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-45-1"></a></h3>
-<ul><li>A <code>twa</code> function, calculating maximum time weighted average concentrations for the parent (SFO, FOMC and DFOP).</li></ul></div>
+<ul><li>A <code>twa</code> function, calculating maximum time weighted average concentrations for the parent (SFO, FOMC and DFOP).</li>
+</ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9.45" id="mkin-0945-2016-12-08">mkin 0.9.45 (2016-12-08)<a class="anchor" aria-label="anchor" href="#mkin-0945-2016-12-08"></a></h2>
@@ -349,7 +359,8 @@
 <h2 class="page-header" data-toc-text="0.9.44" id="mkin-0944-2016-06-29">mkin 0.9.44 (2016-06-29)<a class="anchor" aria-label="anchor" href="#mkin-0944-2016-06-29"></a></h2>
 <div class="section level3">
 <h3 id="bug-fixes-0-9-44">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-44"></a></h3>
-<ul><li>The test <code>test_FOMC_ill-defined</code> failed on several architectures, so the test is now skipped</li></ul></div>
+<ul><li>The test <code>test_FOMC_ill-defined</code> failed on several architectures, so the test is now skipped</li>
+</ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9.43" id="mkin-0943-2016-06-28">mkin 0.9.43 (2016-06-28)<a class="anchor" aria-label="anchor" href="#mkin-0943-2016-06-28"></a></h2>
@@ -383,7 +394,8 @@
 <h2 class="page-header" data-toc-text="0.9.42" id="mkin-0942-2016-03-25">mkin 0.9.42 (2016-03-25)<a class="anchor" aria-label="anchor" href="#mkin-0942-2016-03-25"></a></h2>
 <div class="section level3">
 <h3 id="major-changes-0-9-42">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-42"></a></h3>
-<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>
+<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 class="section level3">
 <h3 id="minor-changes-0-9-42">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-9-42"></a></h3>
 <ul><li><p>Add plots to <code>compiled_models</code> vignette</p></li>
@@ -403,18 +415,21 @@
 <div class="section level3">
 <h3 id="bug-fixes-0-9-41">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-41"></a></h3>
 <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></ul></div>
+<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>
+</ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9-40" id="mkin-09-40-2015-07-21">mkin 0.9-40 (2015-07-21)<a class="anchor" aria-label="anchor" href="#mkin-09-40-2015-07-21"></a></h2>
 <div class="section level3">
 <h3 id="bug-fixes-0-9-40">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-40"></a></h3>
 <ul><li>
-<code><a href="../reference/endpoints.html">endpoints()</a></code>: For DFOP and SFORB models, where <code><a href="https://rdrr.io/r/stats/optimize.html" class="external-link">optimize()</a></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><a href="https://rdrr.io/r/stats/optimize.html" class="external-link">optimize()</a></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></ul></div>
+<code><a href="../reference/endpoints.html">endpoints()</a></code>: For DFOP and SFORB models, where <code><a href="https://rdrr.io/r/stats/optimize.html" class="external-link">optimize()</a></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><a href="https://rdrr.io/r/stats/optimize.html" class="external-link">optimize()</a></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>
+</ul></div>
 <div class="section level3">
 <h3 id="internal-changes-0-9-40">Internal changes<a class="anchor" aria-label="anchor" href="#internal-changes-0-9-40"></a></h3>
 <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></ul></div>
+<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>
+</ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9-39" id="mkin-09-39-2015-06-26">mkin 0.9-39 (2015-06-26)<a class="anchor" aria-label="anchor" href="#mkin-09-39-2015-06-26"></a></h2>
@@ -426,7 +441,8 @@
 <div class="section level3">
 <h3 id="bug-fixes-0-9-39">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-39"></a></h3>
 <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></ul></div>
+<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>
+</ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9-38" id="mkin-09-38-2015-06-24">mkin 0.9-38 (2015-06-24)<a class="anchor" aria-label="anchor" href="#mkin-09-38-2015-06-24"></a></h2>
@@ -438,7 +454,8 @@
 <div class="section level3">
 <h3 id="bug-fixes-0-9-38">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-38"></a></h3>
 <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></ul></div>
+<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>
+</ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9-36" id="mkin-09-36-2015-06-21">mkin 0.9-36 (2015-06-21)<a class="anchor" aria-label="anchor" href="#mkin-09-36-2015-06-21"></a></h2>
@@ -451,13 +468,15 @@
 </ul></div>
 <div class="section level3">
 <h3 id="minor-changes-0-9-36">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-9-36"></a></h3>
-<ul><li>Added a simple showcase vignette with an evaluation of FOCUS example dataset D</li></ul></div>
+<ul><li>Added a simple showcase vignette with an evaluation of FOCUS example dataset D</li>
+</ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9-35" id="mkin-09-35-2015-05-15">mkin 0.9-35 (2015-05-15)<a class="anchor" aria-label="anchor" href="#mkin-09-35-2015-05-15"></a></h2>
 <div class="section level3">
 <h3 id="major-changes-0-9-35">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-35"></a></h3>
-<ul><li>Switch from RUnit to testthat for testing</li></ul></div>
+<ul><li>Switch from RUnit to testthat for testing</li>
+</ul></div>
 <div class="section level3">
 <h3 id="bug-fixes-0-9-35">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-35"></a></h3>
 <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>
@@ -539,13 +558,15 @@
 <h2 class="page-header" data-toc-text="0.9-31" id="mkin-09-31-2014-07-14">mkin 0.9-31 (2014-07-14)<a class="anchor" aria-label="anchor" href="#mkin-09-31-2014-07-14"></a></h2>
 <div class="section level3">
 <h3 id="bug-fixes-0-9-31">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-31"></a></h3>
-<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></div>
+<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></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9-30" id="mkin-09-30-2014-07-11">mkin 0.9-30 (2014-07-11)<a class="anchor" aria-label="anchor" href="#mkin-09-30-2014-07-11"></a></h2>
 <div class="section level3">
 <h3 id="new-features-0-9-30">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-30"></a></h3>
-<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>
+<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 class="section level3">
 <h3 id="major-changes-0-9-30">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-30"></a></h3>
 <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>