Add Bayesian experimentation triptych

examples/references.bib

@@ -102,6 +102,12 @@ @article{bonilla2007multioutput
   year          = {2007},
   url           = {https://papers.nips.cc/paper/2007/hash/66368270ffd51418ec58bd793f2d9b1b-Abstract.html}
 }
+@book{borenstein2009meta,
+  title         = {Introduction to Meta-Analysis},
+  author        = {Borenstein, Michael and Hedges, Larry V. and Higgins, Julian P. T. and Rothstein, Hannah R.},
+  year          = {2009},
+  publisher     = {John Wiley \& Sons}
+}
 @book{breen1996regression,
   title         = {Regression models: Censored, sample selected, or truncated data},
   author        = {Breen, Richard and others},
@@ -164,6 +170,16 @@ @article{ChernozhukovDoubleML
   year          = {2018},
   doi           = {https://doi.org/10.1111/ectj.12097}
 }
+@article{cinellihazlett2020omitted,
+  title         = {Making sense of sensitivity: extending omitted variable bias},
+  author        = {Cinelli, Carlos and Hazlett, Chad},
+  journal       = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
+  volume        = {82},
+  number        = {1},
+  pages         = {39--67},
+  year          = {2020},
+  doi           = {10.1111/rssb.12348}
+}
 @book{coles2001gev,
   title         = {An introduction to statistical modeling of extreme values},
   author        = {Coles, Stuart},
@@ -259,6 +275,15 @@ @book{facure2023causal
   year          = {2023},
   publisher     = {O'Reilly}
 }
+@techreport{fda2026bayesian,
+  title         = {Use of Bayesian Methodology in Clinical Trials of Drug and Biological Products: Guidance for Industry (Draft Guidance)},
+  author        = {{U.S. Food and Drug Administration}},
+  institution   = {Center for Drug Evaluation and Research (CDER) and Center for Biologics Evaluation and Research (CBER)},
+  type          = {Draft Guidance},
+  year          = {2026},
+  month         = jan,
+  note          = {Distributed for comment purposes only}
+}
 @book{fox2010bayesian,
   title         = {Bayesian item response modeling: Theory and applications},
   author        = {Fox, Jean-Paul},
@@ -373,6 +398,16 @@ @book{hernan2020whatif
   year          = {2020},
   publisher     = {Chapman \& Hall/CRC}
 }
+@article{higgins2009meta,
+  title         = {A re-evaluation of random-effects meta-analysis},
+  author        = {Higgins, Julian P. T. and Thompson, Simon G. and Spiegelhalter, David J.},
+  journal       = {Journal of the Royal Statistical Society: Series A (Statistics in Society)},
+  volume        = {172},
+  number        = {1},
+  pages         = {137--159},
+  year          = {2009},
+  doi           = {10.1111/j.1467-985X.2008.00552.x}
+}
 @article{hoffman2014nuts,
   title         = {The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo},
   author        = {Hoffman, Matthew and Gelman, Andrew},
@@ -441,6 +476,16 @@ @article{iacobucci2017mean
   year          = {2017},
   publisher     = {Springer}
 }
+@article{imbens2003sensitivity,
+  title         = {Sensitivity to exogeneity assumptions in program evaluation},
+  author        = {Imbens, Guido W.},
+  journal       = {American Economic Review},
+  volume        = {93},
+  number        = {2},
+  pages         = {126--132},
+  year          = {2003},
+  doi           = {10.1257/000282803321946921}
+}
 @book{ivezić2014astroMLtext,
   author        = {\v{Z}eljko Ivezi\'{c} and Andrew J. Connolly and Jacob T. VanderPlas and Alexander Gray},
   doi           = {10.1515/9781400848911},
@@ -731,16 +776,16 @@ @online{numpyroBirthdays
   title         = {Example: Hilbert space approximation for Gaussian processes},
   url           = {https://num.pyro.ai/en/stable/examples/hsgp.html}
 }
-@online{numpyroBirthdays,
-  title         = {Example: Hilbert space approximation for Gaussian processes},
-  url           = {https://num.pyro.ai/en/stable/examples/hsgp.html}
-}
-@online{orduz2024Birthdays,
-  title         = {Time Series Modeling with HSGP: Baby Births Example},
-  author        = {Orduz, Juan},
-  url           = {https://juanitorduz.github.io/birthdays/},
-  urldate       = {2024-01-02},
-  year          = {2024}
+@article{ohagan2005assurance,
+  title         = {Assurance in clinical trial design},
+  author        = {O'Hagan, Anthony and Stevens, John W. and Campbell, Michael J.},
+  journal       = {Pharmaceutical Statistics},
+  volume        = {4},
+  number        = {3},
+  pages         = {187--201},
+  year          = {2005},
+  publisher     = {Wiley Online Library},
+  doi           = {10.1002/pst.175}
 }
 @online{orduz2024Birthdays,
   title         = {Time Series Modeling with HSGP: Baby Births Example},
@@ -808,21 +853,6 @@ @article{penrose1985
   year          = {1985},
   pages         = {189}
 }
-@article{penrose1985,
-  title         = {{GENERALIZED} {BODY} {COMPOSITION} {PREDICTION} {EQUATION} {FOR} {MEN} {USING} {SIMPLE} {MEASUREMENT} {TECHNIQUES}},
-  volume        = {17},
-  issn          = {0195-9131},
-  url           = {https://journals.lww.com/acsm-msse/citation/1985/04000/generalized_body_composition_prediction_equation.37.aspx},
-  abstract      = {An abstract is unavailable. This article is available as a PDF only.},
-  language      = {en-US},
-  number        = {2},
-  urldate       = {2023-10-17},
-  journal       = {Medicine \& Science in Sports \& Exercise},
-  author        = {Penrose, K. W. and Nelson, A. G. and Fisher, A. G.},
-  month         = apr,
-  year          = {1985},
-  pages         = {189}
-}
 @misc{quiroga2022bart,
   title         = {Bayesian additive regression trees for probabilistic programming},
   author        = {Quiroga, Miriana and Garay, Pablo G and Alonso, Juan M. and Loyola, Juan Martin and Martin, Osvaldo A},
@@ -862,17 +892,6 @@ @article{riutort2022PracticalHilbertSpaceApproximate
   volume        = {33},
   year          = {2022}
 }
-@article{riutort2022PracticalHilbertSpaceApproximate,
-  author        = {Riutort-Mayol, Gabriel and B{\"u}rkner, Paul-Christian and Andersen, Michael R. and Solin, Arno and Vehtari, Aki},
-  doi           = {10.1007/s11222-022-10167-2},
-  journal       = {Statistics and Computing},
-  number        = {1},
-  pages         = {17},
-  title         = {Practical Hilbert space approximate Bayesian Gaussian processes for probabilistic programming},
-  url           = {https://doi.org/10.1007/s11222-022-10167-2},
-  volume        = {33},
-  year          = {2022}
-}
 @book{roback2021beyond,
   title         = {Beyond multiple linear regression: Applied generalized linear models and multilevel models in R},
   author        = {Roback, P., and Legler, J.},
@@ -884,6 +903,13 @@ @online{rochford2018
   author        = {Austin Rochford},
   url           = {https://austinrochford.com/posts/2018-11-10-monotonic-predictors.html}
 }
+@book{rosenbaum2002observational,
+  title         = {Observational Studies},
+  author        = {Rosenbaum, Paul R.},
+  year          = {2002},
+  publisher     = {Springer},
+  edition       = {2nd}
+}
 @book{rousseeuw2005robust,
   author        = {Rousseeuw, Peter J. and Leroy, Annick M.},
   title         = {Robust Regression and Outlier Detection},
@@ -892,6 +918,16 @@ @book{rousseeuw2005robust
   year          = {2005},
   isbn          = {978-0-471-48855-2}
 }
+@incollection{rubin1981estimation,
+  title         = {Estimation in parallel randomized experiments},
+  author        = {Rubin, Donald B.},
+  journal       = {Journal of Educational Statistics},
+  volume        = {6},
+  number        = {4},
+  pages         = {377--401},
+  year          = {1981},
+  doi           = {10.3102/10769986006004377}
+}
 @misc{säilynoja2025,
   title         = {Recommendations for visual predictive checks in Bayesian workflow},
   author        = {Teemu S\"{a}ilynoja and Andrew R. Johnson and Osvaldo A. Martin and Aki Vehtari},
@@ -940,16 +976,11 @@ @article{solin2020Hilbert
   volume        = {30},
   year          = {2020}
 }
-@article{solin2020Hilbert,
-  author        = {Solin, Arno and S{\"a}rkk{\"a}, Simo},
-  doi           = {10.1007/s11222-019-09886-w},
-  journal       = {Statistics and Computing},
-  number        = {2},
-  pages         = {419--446},
-  title         = {Hilbert space methods for reduced-rank Gaussian process regression},
-  url           = {https://doi.org/10.1007/s11222-019-09886-w},
-  volume        = {30},
-  year          = {2020}
+@book{spiegelhalter2004bayesian,
+  title         = {Bayesian Approaches to Clinical Trials and Health-Care Evaluation},
+  author        = {Spiegelhalter, David J. and Abrams, Keith R. and Myles, Jonathan P.},
+  year          = {2004},
+  publisher     = {John Wiley \& Sons}
 }
 @article{spiller2013spotlights,
   title         = {Spotlights, floodlights, and the magic number zero: Simple effects tests in moderated regression},
@@ -1040,6 +1071,16 @@ @inproceedings{vanderplas2012astroML
   doi           = {10.1109/CIDU.2012.6382200},
   year          = {2012}
 }
+@article{vanderweele2017sensitivity,
+  title         = {Sensitivity analysis in observational research: introducing the {E}-value},
+  author        = {VanderWeele, Tyler J. and Ding, Peng},
+  journal       = {Annals of Internal Medicine},
+  volume        = {167},
+  number        = {4},
+  pages         = {268--274},
+  year          = {2017},
+  doi           = {10.7326/M16-2607}
+}
 @book{vehkalahti2019multivariate,
   title         = {Multivariate Analysis for the Behavioral Sciences},
   author        = {Vehkalahti, K. and Everitt, B.S.},
@@ -1055,13 +1096,6 @@ @online{vehtari2022Birthdays
   urldate       = {2022-03-07},
   year          = {2022}
 }
-@online{vehtari2022Birthdays,
-  title         = {Bayesian workflow book - Birthdays},
-  author        = {Vehtari, Aki},
-  url           = {https://avehtari.github.io/casestudies/Birthdays/birthdays.html},
-  urldate       = {2022-03-07},
-  year          = {2022}
-}
 @book{venables2002mass,
   author        = {Venables, W. N. and Ripley, B. D.},
   title         = {Modern Applied Statistics with {S}},
@@ -1132,19 +1166,6 @@ @article{Yao_2022
   doi           = {10.1214/21-BA1287},
   url           = {https://doi.org/10.1214/21-BA1287}
 }
-@article{Yao_2022,
-  author        = {Yuling Yao and Gregor Pir\v{s} and Aki Vehtari and Andrew Gelman},
-  title         = {{Bayesian Hierarchical Stacking: Some Models Are (Somewhere) Useful}},
-  volume        = {17},
-  journal       = {Bayesian Analysis},
-  number        = {4},
-  publisher     = {International Society for Bayesian Analysis},
-  pages         = {1043 -- 1071},
-  keywords      = {Bayesian hierarchical modeling, conditional prediction, covariate shift, model averaging, prior construction, stacking},
-  year          = {2022},
-  doi           = {10.1214/21-BA1287},
-  url           = {https://doi.org/10.1214/21-BA1287}
-}
 @article{yuan2009bayesian,
   title         = {Bayesian mediation analysis.},
   author        = {Yuan, Ying and MacKinnon, David P},

pixi.toml

@@ -3,19 +3,19 @@ authors = ["Chris Fonnesbeck <fonnesbeck@gmail.com>"]
 channels = ["conda-forge"]
 description = "Add a short description here"
 name = "pymc-examples"
-platforms = ["linux-64"]
+platforms = ["linux-64", "osx-arm64"]
 version = "0.1.0"
 
 [tasks]
 
 [dependencies]
 python = ">=3.13.9,<3.14"
-pymc = ">=5.26.1,<6"
+pymc = ">=6.0,<7"
 jupyter = ">=1.1.1,<2"
 ipykernel = ">=7.1.0,<8"
 ipywidgets = ">=8.1.8,<9"
 numpy = ">=2.3.5,<3"
-arviz = ">=0.22.0,<0.23"
+arviz = ">=1.0,<2"
 numpyro = ">=0.19.0,<0.20"
 seaborn = ">=0.13.2,<0.14"
 matplotlib = ">=3.10.8,<4"