Merge branch 'main' into custom_lsoda_call

1 files changed, 28 insertions, 8 deletions

diff --git a/docs/news/index.html b/docs/news/index.html
index faaab288..f6883766 100644
--- a/docs/news/index.html
+++ b/docs/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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.1</span>
       </span>
     </div>
 
@@ -44,19 +44,25 @@
       <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
     </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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </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>
     <li>
-      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul></li>
 <li>
@@ -82,13 +88,27 @@
     </div>
 
     <div class="section level2">
-<h2 class="page-header" data-toc-text="1.1.2" id="mkin-112">mkin 1.1.2<a class="anchor" aria-label="anchor" href="#mkin-112"></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>
-<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/saem.R’: ‘logLik’ and ‘update’ methods for ‘saem.mmkin’ objects.</p></li>
-<li><p>‘R/convergence.R’: New generic to show convergence information with methods for ‘mmkin’ and ‘mhmkin’ objects.</p></li>
+<h2 class="page-header" data-toc-text="1.2.1" id="mkin-121-unreleased">mkin 1.2.1 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-121-unreleased"></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>
+<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/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>
+<li><p>‘R/tex_listings.R’: Conveniently include summaries of fit objects in R markdown documents that are compiled to LaTeX.</p></li>
 </ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.1.1" id="mkin-111-2022-07-12">mkin 1.1.1 (2022-07-12)<a class="anchor" aria-label="anchor" href="#mkin-111-2022-07-12"></a></h2>