From 26a4b9e03fe0f3d8e777ad52f97685a98ff4462e Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 16 Nov 2022 15:18:10 +0100
Subject: Update docs

---
 docs/dev/news/index.html | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'docs/dev/news/index.html')

diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 8448ebc8..3353922b 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -89,13 +89,13 @@
 
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.2.0" id="mkin-120-unreleased">mkin 1.2.0 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-120-unreleased"></a></h2>
-<ul><li><p>‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.</p></li>
+<ul><li><p>‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.</p></li>
+<li><p>‘R/saem.R’: Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions.</p></li>
+<li><p>‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’, ‘mhmkin’ and ‘multistart’ objects.</p></li>
+<li><p>‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.</p></li>
 <li><p>‘R/mhmkin.R’: ‘anova.mhmkin’ for conveniently comparing the resulting fits.</p></li>
 <li><p>‘R/illparms.R’: New generic to show ill-defined parameters with methods for ‘mkinfit’, ‘mmkin’, ‘saem.mmkin’ and ‘mhmkin’ objects.</p></li>
 <li><p>‘R/multistart.R’: New method for testing multiple start parameters for hierarchical model fits, with function ‘llhist’ and new generic ‘parplot’ for diagnostics, and new generics ‘which.best’ and ‘best’ for extracting the fit with the highest likelihood</p></li>
-<li><p>‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.</p></li>
-<li><p>‘R/saem.R’: Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions.</p></li>
-<li><p>‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’, ‘mhmkin’ and ‘multistart’ objects.</p></li>
 <li><p>‘R/summary.mmkin.R’: Summary method for mmkin objects.</p></li>
 <li><p>‘R/saem.R’: Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported.</p></li>
 <li><p>‘R/read_spreadsheet.R’: Conveniently read in data from a spreadsheet file.</p></li>
-- 
cgit v1.2.1


From af7c6de4db9981ac814362c441fbac22c8faa2d7 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 24 Nov 2022 09:02:26 +0100
Subject: Start online docs of the development version

---
 docs/dev/news/index.html | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

(limited to 'docs/dev/news/index.html')

diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 3353922b..50afb3e9 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -17,7 +17,7 @@
       </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">1.2.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -88,7 +88,19 @@
     </div>
 
     <div class="section level2">
-<h2 class="page-header" data-toc-text="1.2.0" id="mkin-120-unreleased">mkin 1.2.0 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-120-unreleased"></a></h2>
+<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></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>
+<ul><li><p>‘{data,R}/ds_mixed.rda’: Include the test data in the package instead of generating it in ‘tests/testthat/setup_script.R’. Refactor the generating code to make it consistent and update tests.</p></li>
+<li><p>‘tests/testthat/setup_script.R’: Excluded another ill-defined random effect for the DFOP fit with ‘saem’, in an attempt to avoid a platform dependence that surfaced on Fedora systems on the CRAN check farm</p></li>
+<li><p>‘tests/testthat/test_mixed.R’: Round parameters found by saemix to two significant digits before printing, to also help to avoid platform dependence of tests</p></li>
+<li><p>‘R/saem.R’: Fix a bug that prevented that ‘error.ini’ is passed to ‘saemix_model’, and set default to c(1, 1) to avoid changing test results</p></li>
+<li><p>‘R/parplot.R’: Show initial values for error model parameters</p></li>
+<li><p>‘R/loglik.mkinfit.R’: Add ‘nobs’ attribute to the resulting ‘logLik’ object, in order to make test_AIC.R succeed on current R-devel</p></li>
+</ul></div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="1.2.0" id="mkin-120-2022-11-17">mkin 1.2.0 (2022-11-17)<a class="anchor" aria-label="anchor" href="#mkin-120-2022-11-17"></a></h2>
 <ul><li><p>‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.</p></li>
 <li><p>‘R/saem.R’: Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions.</p></li>
 <li><p>‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’, ‘mhmkin’ and ‘multistart’ objects.</p></li>
-- 
cgit v1.2.1


From 9a1136dc5550663b352239502a39a07601959644 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 2 Dec 2022 08:00:40 +0100
Subject: Update online docs

---
 docs/dev/news/index.html | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'docs/dev/news/index.html')

diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 50afb3e9..c9663964 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -89,7 +89,9 @@
 
     <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></ul></div>
+<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</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>
 <ul><li><p>‘{data,R}/ds_mixed.rda’: Include the test data in the package instead of generating it in ‘tests/testthat/setup_script.R’. Refactor the generating code to make it consistent and update tests.</p></li>
-- 
cgit v1.2.1


From e3057a3a71dbbd9028e192885d17a92607428296 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 2 Dec 2022 14:09:07 +0100
Subject: Update online docs

---
 docs/dev/news/index.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'docs/dev/news/index.html')

diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index c9663964..e2b44bf5 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -90,7 +90,7 @@
     <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</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>
 </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>
-- 
cgit v1.2.1


From a54bd290bc3884d0000c52c1b29bc557825d9eae Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 15 Dec 2022 14:50:28 +0100
Subject: List random effects correlations in output if any

Update docs
---
 docs/dev/news/index.html | 57 +++++++++++++++++++++++++++++++++---------------
 1 file changed, 39 insertions(+), 18 deletions(-)

(limited to 'docs/dev/news/index.html')

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>
-- 
cgit v1.2.1


From 24eb77216700cf8b2f2bde3abad84c1f83f9e32a Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 9 Jan 2023 06:22:04 +0100
Subject: Prebuilt PDF vignettes, summary_listing

---
 docs/dev/news/index.html | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'docs/dev/news/index.html')

diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 6127ebc6..060135bf 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -89,7 +89,9 @@
 
     <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>
+<ul><li><p>‘inst/rmarkdown/templates/hier’: R markdown template to facilitate the application of hierarchical kinetic models.</p></li>
+<li><p>‘inst/testdata/lambda-cyhalothrin_soil_efsa_2014.xlsx’: Example spreadsheet for use with ‘read_spreadsheet()’.</p></li>
+<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. 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>
@@ -649,7 +651,7 @@
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>
-- 
cgit v1.2.1


From 9aa186eaf43d3c86a99fd08c310cefbc5dfe0612 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 28 Jan 2023 17:40:31 +0100
Subject: Build online HTML versions of prebuilt vignettes

Also, give some structure to the menu for selecting articles
---
 docs/dev/news/index.html | 31 ++++++++++++++++++++++++-------
 1 file changed, 24 insertions(+), 7 deletions(-)

(limited to 'docs/dev/news/index.html')

diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 060135bf..d8fcbfe9 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -23,7 +23,7 @@
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav"><li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../reference/index.html">Reference</a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
@@ -34,6 +34,8 @@
   <ul class="dropdown-menu" role="menu"><li>
       <a href="../articles/mkin.html">Introduction to mkin</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li>
     <li>
       <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
     </li>
@@ -41,22 +43,29 @@
       <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
     </li>
     <li>
-      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li>
     <li>
-      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+      <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
     </li>
     <li>
-      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+      <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
     </li>
     <li>
-      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+      <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
     </li>
     <li>
-      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+    </li>
+    <li class="divider">
+    <li class="dropdown-header">Performance</li>
+    <li>
+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
       <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
@@ -64,6 +73,14 @@
     <li>
       <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Miscellaneous</li>
+    <li>
+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+    </li>
   </ul></li>
 <li>
   <a href="../news/index.html">News</a>
-- 
cgit v1.2.1