update tutorials and references

index.Rmd

@@ -48,18 +48,21 @@ Papers using **spatPomp** include the following:
   [doi](https://doi.org/10.5705/ss.202022.0188).
   [arxiv](https://arxiv.org/abs/2206.03837).
   [code](https://github.com/ionides/ibpf_article).
-- Li, J., E. L. Ionides, A. A., King, M. Pascual and N. Ning (2024). Inference on spatiotemporal dynamics for networks of biological populations.
+- Li, J., E. L. Ionides, A. A., King, M. Pascual and N. Ning (2024). Inference on spatiotemporal dynamics for coupled biological populations. _Journal of the Royal Society Interface_ 21(216), 20240217.
+  [doi](https://doi.org/10.1098/rsif.2024.0217).
   [arxiv](https://arxiv.org/abs/2311.06702).
   [code](https://github.com/jifanli/metapop_article).
+  [software](https://github.com/jifanli/metapoppkg)
 - Ning, N. and Ionides, E. L. (2023). Iterated block particle filter for high-dimensional parameter learning: Beating the curse of dimensionality. _Journal of Machine Learning Research_ 24(82), 1-76.
 [pdf](https://jmlr.org/papers/v24/21-1253.pdf). 
 [arxiv](https://arxiv.org/abs/2110.10745v3"><i>arxiv</i></a>).
 - Wheeler, J., Rosengart, A. L., Jiang, Z., Tan, K., Treutle, N. and Ionides, E. L. (2024).
   Informing policy via dynamic models: Cholera in Haiti.
-  To appear in _PLOS Computational Biology_.
+  _PLOS Computational Biology_ 20(4), e1012032.
+  [doi](https://doi.org/10.1371/journal.pcbi.1012032).
   [arxiv](https://doi.org/10.48550/arXiv.2301.08979).
   [code](https://github.com/jeswheel/haiti_article).
   [software](https://github.com/jeswheel/haitipkg).
-- Zhang, B., Huang, W., Pei, S., Zeng, J., Shen, W., Wang, D., Wang, G., Chen, T., Yang, L., Cheng, P., Wang, D., Shu, Y., & Du, X. (2022). Mechanisms for the circulation of influenza A (H3N2) in China: A spatiotemporal modelling study. _PLoS Pathogens_, 18(12), e1011046.
+- Zhang, B., Huang, W., Pei, S., Zeng, J., Shen, W., Wang, D., Wang, G., Chen, T., Yang, L., Cheng, P., Wang, D., Shu, Y., & Du, X. (2022). Mechanisms for the circulation of influenza A (H3N2) in China: A spatiotemporal modelling study. _PLOS Pathogens_, 18(12), e1011046.
 [doi](https://doi.org/10.1371/journal.ppat.1011046).
 

index.html

@@ -487,19 +487,19 @@ <h1 class="title toc-ignore">spatPomp, an R package for statistical
 unit-specific parameters. <em>Statistica Sinica,</em> prepublished
 online. <a href="https://doi.org/10.5705/ss.202022.0188">doi</a>. <a href="https://arxiv.org/abs/2206.03837">arxiv</a>. <a href="https://github.com/ionides/ibpf_article">code</a>.</li>
 <li>Li, J., E. L. Ionides, A. A., King, M. Pascual and N. Ning (2024).
-Inference on spatiotemporal dynamics for networks of biological
-populations. <a href="https://arxiv.org/abs/2311.06702">arxiv</a>. <a href="https://github.com/jifanli/metapop_article">code</a>.</li>
+Inference on spatiotemporal dynamics for coupled biological populations.
+<em>Journal of the Royal Society Interface</em> 21(216), 20240217. <a href="https://doi.org/10.1098/rsif.2024.0217">doi</a>. <a href="https://arxiv.org/abs/2311.06702">arxiv</a>. <a href="https://github.com/jifanli/metapop_article">code</a>. <a href="https://github.com/jifanli/metapoppkg">software</a></li>
 <li>Ning, N. and Ionides, E. L. (2023). Iterated block particle filter
 for high-dimensional parameter learning: Beating the curse of
 dimensionality. <em>Journal of Machine Learning Research</em> 24(82),
 1-76. <a href="https://jmlr.org/papers/v24/21-1253.pdf">pdf</a>. <a href="https://arxiv.org/abs/2110.10745v3%22%3E%3Ci%3Earxiv%3C/i%3E%3C/a%3E">arxiv</a>.</li>
 <li>Wheeler, J., Rosengart, A. L., Jiang, Z., Tan, K., Treutle, N. and
 Ionides, E. L. (2024). Informing policy via dynamic models: Cholera in
-Haiti. To appear in <em>PLOS Computational Biology</em>. <a href="https://doi.org/10.48550/arXiv.2301.08979">arxiv</a>. <a href="https://github.com/jeswheel/haiti_article">code</a>. <a href="https://github.com/jeswheel/haitipkg">software</a>.</li>
+Haiti. <em>PLOS Computational Biology</em> 20(4), e1012032. <a href="https://doi.org/10.1371/journal.pcbi.1012032">doi</a>. <a href="https://doi.org/10.48550/arXiv.2301.08979">arxiv</a>. <a href="https://github.com/jeswheel/haiti_article">code</a>. <a href="https://github.com/jeswheel/haitipkg">software</a>.</li>
 <li>Zhang, B., Huang, W., Pei, S., Zeng, J., Shen, W., Wang, D., Wang,
 G., Chen, T., Yang, L., Cheng, P., Wang, D., Shu, Y., &amp; Du, X.
 (2022). Mechanisms for the circulation of influenza A (H3N2) in China: A
-spatiotemporal modelling study. <em>PLoS Pathogens</em>, 18(12),
+spatiotemporal modelling study. <em>PLOS Pathogens</em>, 18(12),
 e1011046. <a href="https://doi.org/10.1371/journal.ppat.1011046">doi</a>.</li>
 </ul>