update vignettes & bibliography

_data/biblio.yml

@@ -987,8 +987,9 @@
   author: "J. Li, E. L. Ionides, A. A. King, M. Pascual, and N. Ning"
   year: "2024"
   title: "Inference on spatiotemporal dynamics for coupled biological populations"
-  journal: "Journal of The Royal Society Interface"
+  journal: "J R Soc Interface"
   volume: "21"
+  number: "216"
   pages: "20240217"
   doi: "https://doi.org/10.1098/rsif.2024.0217"
 
@@ -1245,9 +1246,9 @@
   author: "M. A. E. Peters, A. A. King, and N. Wale"
   year: "2024"
   title: "Red blood cell dynamics during malaria infection challenge the assumptions of mathematical models of infection dynamics"
-  journal: "bioRxiv"
-  eprint: "2024.01.10.575051"
-  doi: "https://doi.org/10.1101/2024.01.10.575051"
+  journal: "Frontiers in Malaria"
+  volume: "2"
+  doi: "https://doi.org/10.3389/fmala.2024.1365770"
 
 - key: PonsSalort2018a
   author: "M. Pons-Salort and N. C. Grassly"
@@ -1549,6 +1550,15 @@
   pages: "1976"
   doi: "https://doi.org/10.3201/eid2707.210118"
 
+- key: Wen2024
+  author: "L. Wen, Y. Yin, Q. Li, Z. Peng, and D. He"
+  year: "2024"
+  title: "Modeling the co-circulation of influenza and COVID-19 in Hong Kong, China"
+  journal: "Advances in Continuous and Discrete Models"
+  volume: "2024"
+  number: "1"
+  doi: "https://doi.org/10.1186/s13662-024-03830-7"
+
 - key: Wheeler2023
   author: "J. Wheeler, A. Rosengart, Z. Jiang, K. Tan, N. Treutle, and E. Ionides"
   year: "2023"

_includes/menu.html

@@ -2,11 +2,11 @@
   <li><a id="about" href="{{site.baseurl}}/index.html">About</a></li>
   <li><a id="install" href="{{site.baseurl}}/install.html">Installation</a></li>
   <li><a id="faq" href="{{site.baseurl}}/FAQ.html">FAQ</a></li>
-  <li><a id="manual" href="{{site.baseurl}}/manual/" target="_blank">Manual</a></li>
+  <li><a id="manual" href="{{site.baseurl}}/manual/">Manual</a></li>
   <li><a id="docs" href="{{site.baseurl}}/docs.html">Documentation</a></li>
-  <li><a id="discussions" href="https://github.com/kingaa/pomp/discussions" target="_blank">Discussions</a></li>
-  <li><a id="issues" href="https://github.com/kingaa/pomp/issues" target="_blank">Issues</a></li>
-  <li><a id="source" href="https://github.com/kingaa/pomp/" target="_blank">Source</a></li>
+  <li><a id="discussions" href="https://github.com/kingaa/pomp/discussions">Discussions</a></li>
+  <li><a id="issues" href="https://github.com/kingaa/pomp/issues">Issues</a></li>
+  <li><a id="source" href="https://github.com/kingaa/pomp/">Source</a></li>
   <li><a id="biblio" href="{{site.baseurl}}/biblio.html">Bibliography</a></li>
   <li><a id="news" href="{{site.baseurl}}/blog.html">News</a></li>
 </ul>

vignettes/FAQ.Rmd

@@ -61,7 +61,7 @@ source("https://kingaa.github.io/scripts/diagnostics.R")
 ## What's the proper way to cite **pomp**? {#cite-pomp}
 
 ```{r echo=FALSE,results="asis"}
-print(citation("pomp"),bibtex=FALSE)
+citation("pomp") |> print(bibtex=FALSE)
 ```
 
 You can get this information by executing `citation("pomp")` in an **R** session.

vignettes/R_v_C.html

@@ -277,18 +277,18 @@ <h2>Comparing the implementations</h2>
 <p>Using each implementation, we’ll now run a number of simulations and compare the amount of time required.</p>
 <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true"></a><span class="kw">system.time</span>(<span class="kw">simulate</span>(gompertz,<span class="dt">nsim=</span><span class="dv">10000</span>,<span class="dt">format=</span><span class="st">&quot;arrays&quot;</span>))</span></code></pre></div>
 <pre><code>##    user  system elapsed 
-##   7.387   0.087   7.473</code></pre>
+##   4.669   0.004   4.674</code></pre>
 <div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true"></a><span class="kw">system.time</span>(<span class="kw">simulate</span>(Gompertz,<span class="dt">nsim=</span><span class="dv">10000</span>,<span class="dt">format=</span><span class="st">&quot;arrays&quot;</span>))</span></code></pre></div>
 <pre><code>##    user  system elapsed 
-##   0.167   0.000   0.167</code></pre>
+##   0.138   0.001   0.139</code></pre>
 <div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true"></a><span class="kw">system.time</span>(<span class="kw">pfilter</span>(gompertz,<span class="dt">Np=</span><span class="dv">10000</span>))</span></code></pre></div>
 <pre><code>##    user  system elapsed 
-##   6.478   0.054   6.532</code></pre>
+##   5.151   0.001   5.155</code></pre>
 <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true"></a><span class="kw">system.time</span>(<span class="kw">pfilter</span>(Gompertz,<span class="dt">Np=</span><span class="dv">10000</span>))</span></code></pre></div>
 <pre><code>##    user  system elapsed 
-##   0.199   0.007   0.207</code></pre>
+##   0.176   0.002   0.178</code></pre>
 <hr />
-<p>This document was produced using <strong>pomp</strong> version 5.7.1.0 and <strong>R</strong> version 4.3.3.</p>
+<p>This document was produced using <strong>pomp</strong> version 5.10 and <strong>R</strong> version 4.4.1.</p>
 </div>
 
 

vignettes/upgrade_guide.html

@@ -759,7 +759,7 @@ <h3>SIR model</h3>
 <span id="cb16-7"><a href="#cb16-7" aria-hidden="true"></a>  ...</span>
 <span id="cb16-8"><a href="#cb16-8" aria-hidden="true"></a>) -&gt;<span class="st"> </span>sir2C</span></code></pre></div>
 <hr />
-<p>This document was produced using <strong>pomp</strong> version 5.7.1.0 and <strong>R</strong> version 4.3.3.</p>
+<p>This document was produced using <strong>pomp</strong> version 5.10 and <strong>R</strong> version 4.4.1.</p>
 </div>
 </div>