Update dirichlet mixture model notebooks (pymc-devs#212)

* Update dirichlet mixture model notebooks correct notation in text fixes and changes initialize trees and forests for dims use from_pymc3 changes * fix tags * fix citations * author name referencing error fix * fix read the docs: error * references * fix syntax error * correct reference instances * fixes * fix reference * finish updates and rerun Co-authored-by: Oriol (ZBook) <oriol.abril.pla@gmail.com>
martiningram · Jan 9, 2022 · 7af5789 · 7af5789
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diff --git a/examples/mixture_models/dirichlet_mixture_of_multinomials.ipynb b/examples/mixture_models/dirichlet_mixture_of_multinomials.ipynb
diff --git a/examples/mixture_models/dp_mix.ipynb b/examples/mixture_models/dp_mix.ipynb
diff --git a/examples/references.bib b/examples/references.bib
@@ -74,6 +74,17 @@ @article{goldberg2001eigentaste
     pages = {133--151}
 }
 
+@misc{goodhardt1984thedirichlet,
+  title={The Dirichlet: A Comprehensive Model of Buying Behaviour },
+  author={G. J. Goodhardt, A. S. C. Ehrenberg and C. Chatfield },
+  url={https://www.jstor.org/stable/2981696},
+  journal={Journal of the Royal Statistical Society. Series A (General)},
+  volume={147},
+  number={3},
+  pages={621--655},
+  year={1984}
+}
+
 @misc{harper2015movielens,
   title={The MovieLens Datasets: History and Context},
   author={Harper, F. Maxwell and Konstan, Joseph A.},
@@ -95,6 +106,18 @@ @misc{hogg2010data
       primaryClass={astro-ph.IM}
 }
 
+@article{ishwaran2002approxdirichlet,
+  author = {Hemant Ishwaran and Lancelot F James},
+  title = {Approximate Dirichlet Process Computing in Finite Normal Mixtures},
+  journal = {Journal of Computational and Graphical Statistics},
+  volume = {11},
+  number = {3},
+  pages = {508-532},
+  year  = {2002},
+  publisher = {Taylor & Francis},
+  url = {https://doi.org/10.1198/106186002411}
+}
+
 @book{ivezić2014astroMLtext,
   author = {Željko Ivezić and Andrew J. Connolly and Jacob T. VanderPlas and Alexander Gray},
   doi = {10.1515/9781400848911},
@@ -154,14 +177,22 @@ @article{lewandowski2009generating
   publisher={Elsevier}
 }
 
+@misc{madsen2005modelingdirichlet,
+  title={Modeling word burstiness using the Dirichlet distribution},
+  url={https://dl.acm.org/doi/10.1145/1102351.1102420},
+  journal={Proceedings of the 22nd international conference on Machine learning},
+  author={Rasmus E. Madsen, David Kauchak, Charles Elkan and et al.},
+  year={2005},
+  month={Aug}
+}
+
 @book{martin2018bayesian,
   title={Bayesian analysis with Python: introduction to statistical modeling and probabilistic programming using PyMC3 and ArviZ},
   author={Martin, Osvaldo},
   year={2018},
   publisher={Packt Publishing Ltd}
 }
 
-
 @book{mcelreath2018statistical,
   title={Statistical rethinking: A Bayesian course with examples in R and Stan},
   author={McElreath, Richard},
@@ -189,6 +220,15 @@ @misc{mnih2013playing
   primaryClass={cs.LG}
 }
 
+@misc{nowicka2016drimseq,
+  title={DRIMSeq: A Dirichlet-Multinomial Framework for Multivariate Count Outcomes in Genomics},
+  url={https://f1000research.com/articles/5-1356/v2},
+  journal={F1000Research},
+  author={Nowicka, Malgorzata and Robinson, Mark D.},
+  year={2016},
+  month={Dec}
+}
+
 @article{nowlan1992simplifying,
   title={Simplifying Neural Networks By Soft Weight-Sharing},
   author={Nowlan, Steven J and Hinton, Geoffrey E},
@@ -200,6 +240,23 @@ @article{nowlan1992simplifying
   publisher={MIT Press}
 }
 
+@article{ohlssen2007flexible,
+  title={Flexible random-effects models using Bayesian semi-parametric models: applications to institutional comparisons},
+  author={Ohlssen, David I and Sharples, Linda D and Spiegelhalter, David J},
+  journal={Statistics in medicine},
+  volume={26},
+  number={9},
+  pages={2088--2112},
+  year={2007},
+  publisher={Wiley Online Library}
+}
+
+@inproceedings{roy2008npbayes,
+  title={A stochastic programming perspective on nonparametric Bayes},
+  author={Daniel M. Roy, Vikash Mansinghka, Noah Goodman and Joshua Tenenbaum},
+  journal={International Conference on Machine Learning: Workshop on Nonparametric Bayesian},
+  year={2008}
+}
 
 @inproceedings{salakhutdinov2008bayesian,
   title={Bayesian Probabilistic Matrix Factorization Using Markov Chain Monte Carlo},
@@ -210,6 +267,15 @@ @inproceedings{salakhutdinov2008bayesian
   volume={25}
 }
 
+@article{sidc2021sunspot,
+  author={SILSO World Data Center},
+  address={Royal Observatory of Belgium, Avenue Circulaire 3, 1180 Brussels, Belgium},
+  title={The International Sunspot Number},
+  journal={International Sunspot Number Monthly Bulletin and online catalogue},
+  year={2020-2021},
+  adsurl={https://wwwbis.sidc.be/silso/datafiles}
+}
+
 @article{silver2016masteringgo,
   title={Mastering the game of Go with deep neural networks and tree search},
   author={D. Silver, A. Huang, C. Maddison et al.},
@@ -239,8 +305,22 @@ @misc{szegedy2014going
   eprint={1409.4842},
   archivePrefix={arXiv},
   primaryClass={cs.CV}
-  }
+}
+
+@article{roy2008npbayes,
+  title={A stochastic programming perspective on nonparametric Bayes},
+  author={Daniel M. Roy, Vikash Mansinghka, Noah Goodman and Joshua Tenenbaum},
+  journal={International Conference on Machine Learning: Workshop on Nonparametric Bayesian},
+  year={2008}
+}
 
+@incollection{teh2010dirichletprocess,
+  author={Y. W. Teh},
+  booktitle={Encyclopedia of Machine Learning},
+  publisher={Springer},
+  title={Dirichlet Processes},
+  year={2010}
+}
 
 @INPROCEEDINGS{vanderplas2012astroML,
  author={{Vanderplas}, J.T. and {Connolly}, A.J.