diff --git a/.github/workflows/Doxygen.yml b/.github/workflows/Doxygen.yml index 4845ed227..6eca303ca 100644 --- a/.github/workflows/Doxygen.yml +++ b/.github/workflows/Doxygen.yml @@ -37,6 +37,9 @@ jobs: # Installs libjs-mathjax for rendering mathematical notation in Doxygen documentation - run: sudo apt-get install -y libjs-mathjax + # Install perl for bibtex + - run: sudo apt-get install -y perl + # Runs a single command using the runners shell - name: Doxygen Action uses: mattnotmitt/doxygen-action@1.9.8 diff --git a/Doc/Doxyfile b/Doc/Doxyfile index ac949063a..900fd2f8d 100644 --- a/Doc/Doxyfile +++ b/Doc/Doxyfile @@ -670,7 +670,7 @@ LAYOUT_FILE = # search path. Do not use file names with spaces, bibtex cannot handle them. See # also \cite for info how to create references. -CITE_BIB_FILES = bibliography.bib +CITE_BIB_FILES = ../Doc/bibliography.bib #--------------------------------------------------------------------------- # Configuration options related to warning and progress messages diff --git a/Doc/bibliography.bib b/Doc/bibliography.bib index d97d04fb8..af131af2b 100755 --- a/Doc/bibliography.bib +++ b/Doc/bibliography.bib @@ -1,165 +1,162 @@ @article{gelman1996posterior, - title = {Posterior predictive assessment of model fitness via realized discrepancies}, - author = {Gelman, A. and Meng, X. L. and Stern, H.}, - journal = {Statistica Sinica}, - pages = {733--760}, - year = {1996}, - publisher = {JSTOR}, - url = {http://www.stat.columbia.edu/~gelman/research/published/A6n41.pdf} + author = "Gelman, A. and Meng, X. L. and Stern, H.", + title = "{Posterior predictive assessment of model fitness via realized discrepancies}", + journal = "Statistica Sinica", + pages = "733--760", + year = "1996", + publisher = "JSTOR", + url = "http://www.stat.columbia.edu/~gelman/research/published/A6n41.pdf" } @inproceedings{Conway:2011in, - author = {Conway, J. S.}, - title = {Incorporating Nuisance Parameters in Likelihoods for Multisource Spectra}, - booktitle = {PHYSTAT 2011}, - eprint = {1103.0354}, - archivePrefix= {arXiv}, - primaryClass = {physics.data-an}, - doi = {10.5170/CERN-2011-006.115}, - pages = {115--120}, - year = {2011} + author = "Conway, J. S.", + title = "{Incorporating Nuisance Parameters in Likelihoods for Multisource Spectra}", + booktitle = "PHYSTAT 2011", + eprint = "1103.0354", + archivePrefix = "arXiv", + primaryClass = "physics.data-an", + doi = "10.5170/CERN-2011-006.115", + pages = "115--120", + year = "2011" } @article{Arguelles:2019izp, - author = {Argüelles, Carlos A. and Schneider, Austin and Yuan, Tianlu}, - title = {A binned likelihood for stochastic models}, - eprint = {1901.04645}, - archivePrefix= {arXiv}, - primaryClass = {physics.data-an}, - doi = {10.1007/JHEP06(2019)030}, - journal = {JHEP}, - volume = {06}, - pages = {030}, - year = {2019} + author = "Argüelles, Carlos A. and Schneider, Austin and Yuan, Tianlu", + title = "{A binned likelihood for stochastic models}", + eprint = "1901.04645", + archivePrefix = "arXiv", + primaryClass = "physics.data-an", + doi = "10.1007/JHEP06(2019)030", + journal = "JHEP", + volume = "06", + pages = "030", + year = "2019" } @article{Dembinski:2022ios, - author = {Dembinski, Hans Peter and Abdelmotteleb, Ahmed}, - title = {A new maximum-likelihood method for template fits}, - eprint = {2206.12346}, - archivePrefix= {arXiv}, - primaryClass = {stat.ME}, - doi = {10.1140/epjc/s10052-022-11019-z}, - journal = {Eur. Phys. J. C}, - volume = {82}, - number = {11}, - pages = {1043}, - year = {2022} + author = "Dembinski, Hans Peter and Abdelmotteleb, Ahmed", + title = "{A new maximum-likelihood method for template fits}", + eprint = "2206.12346", + archivePrefix = "arXiv", + primaryClass = "stat.ME", + doi = "10.1140/epjc/s10052-022-11019-z", + journal = "Eur. Phys. J. C", + volume = "82", + number = "11", + pages = "1043", + year = "2022" } @misc{Fang2014GewekeDiagnostics, - author = {Qijun Fang}, - title = {A Brief Introduction to Geweke’s Diagnostics}, - howpublished = {\url{https://math.arizona.edu/~piegorsch/675/GewekeDiagnostics.pdf}}, - note = {STAT 675, University of Arizona}, - year = {2014}, - month = {May}, - day = {7} + author = "Qijun Fang", + title = "{A Brief Introduction to Geweke’s Diagnostics}", + howpublished = "\url{https://math.arizona.edu/~piegorsch/675/GewekeDiagnostics.pdf}", + note = "STAT 675, University of Arizona", + year = "2014", + month = "May", + day = "7" } @mastersthesis{karlsbakk2011, - author = {Jarle Karlsbakk}, - title = {Likelihood Inference and Comparison of Time-Inhomogeneous Markov Processes}, - school = {Stockholm University, Department of Mathematics}, - year = {2011}, - type = {Master's Thesis}, - note = {Accessed: 2024-09-08}, - url = {https://www2.math.su.se/matstat/reports/master/2011/rep2/report.pdf}, - chapter = {3.1} + author = "Jarle Karlsbakk", + title = "{Likelihood Inference and Comparison of Time-Inhomogeneous Markov Processes}", + school = "Stockholm University, Department of Mathematics", + year = "2011", + type = "Master's Thesis", + url = "https://www2.math.su.se/matstat/reports/master/2011/rep2/report.pdf", + chapter = "3.1" } @article{Dunkley:2004sv, - author = {Dunkley, Joanna and Bucher, Martin and Ferreira, Pedro G. and Moodley, Kavilan and Skordis, Constantinos}, - title = {Fast and reliable MCMC for cosmological parameter estimation}, - eprint = {astro-ph/0405462}, - archivePrefix= {arXiv}, - doi = {10.1111/j.1365-2966.2004.08464.x}, - journal = {Mon. Not. Roy. Astron. Soc.}, - volume = {356}, - pages = {925--936}, - year = {2005} + author = "Dunkley, Joanna and Bucher, Martin and Ferreira, Pedro G. and Moodley, Kavilan and Skordis, Constantinos", + title = "{Fast and reliable MCMC for cosmological parameter estimation}", + eprint = "astro-ph/0405462", + archivePrefix = "arXiv", + doi = "10.1111/j.1365-2966.2004.08464.x", + journal = "Mon. Not. Roy. Astron. Soc.", + volume = "356", + pages = "925--936", + year = "2005" } @manual{StanManual, - title = {Stan Reference Manual: Effective Sample Size}, - author = {{Stan Development Team}}, - year = {2018}, - note = {Version 2.18}, - url = {https://mc-stan.org/docs/2_18/reference-manual/effective-sample-size-section.html} + title = "{Stan Reference Manual: Effective Sample Size}", + author = "{Stan Development Team}", + year = "2018", + note = "Version 2.18", + url = "https://mc-stan.org/docs/2_18/reference-manual/effective-sample-size-section.html" } @misc{hanson2008mcmc, - author = {Kenneth M. Hanson}, - title = {Tutorial on Markov Chain Monte Carlo}, - year = {2008}, - note = {Revised 14/05/08, LA-UR-05-5680}, - howpublished = {Presented at the 29th International Workshop on Bayesian Inference and Maximum Entropy Methods in Science and Technology, Gif-sur-Yvette, France, July 8–13, 2009}, - url = {https://kmh-lanl.hansonhub.com/talks/maxent00b.pdf}, - institution = {Los Alamos National Laboratory} + author = "Kenneth M. Hanson", + title = "{Tutorial on Markov Chain Monte Carlo}", + year = "2008", + note = "Revised 14/05/08, LA-UR-05-5680", + howpublished = "Presented at the 29th International Workshop on Bayesian Inference and Maximum Entropy Methods in Science and Technology, Gif-sur-Yvette, France, July 8–13, 2009", + url = "https://kmh-lanl.hansonhub.com/talks/maxent00b.pdf", + institution = "Los Alamos National Laboratory" } @article{roberts2009adaptive, - author = {Gareth O. Roberts and Jeffrey S. Rosenthal}, - title = {Examples of Adaptive MCMC}, - journal = {Journal of Computational and Graphical Statistics}, - volume = {18}, - number = {2}, - year = {2009}, - pages = {349--367}, - url = {http://www.jstor.org/stable/25651249}, - note = {Accessed: 2024-09-08} + author = "Gareth O. Roberts and Jeffrey S. Rosenthal", + title = "{Examples of Adaptive MCMC}", + journal = "Journal of Computational and Graphical Statistics", + volume = "18", + number = "2", + year = "2009", + pages = "349--367", + url = "http://www.jstor.org/stable/25651249", } @article{James:2004xla, - author = {James, Fred and Winkler, Matthias}, - title = {MINUIT User's Guide}, - month = {June}, - year = {2004} + author = "James, Fred and Winkler, Matthias", + title = "{MINUIT User's Guide}", + month = "June", + year = "2004" } @book{jeffreys1998theory, - author = {H. Jeffreys}, - title = {The Theory of Probability}, - publisher = {UOP Oxford}, - year = {1998}, - doi = {10.2307/3619118} + author = "H. Jeffreys", + title = "{The Theory of Probability}", + publisher = "UOP Oxford", + year = "1998", + doi = "10.2307/3619118" } @book{press1992numerical, - author = {William H. Press and Saul A. Teukolsky and William T. Vetterling and Brian P. Flannery}, - title = {Numerical Recipes in C: The Art of Scientific Computing}, - edition = {Second Edition}, - publisher = {Cambridge University Press}, - year = {1992}, - note = {William H. Press: Harvard-Smithsonian Center for Astrophysics, Saul A. Teukolsky: Department of Physics, Cornell University, William T. Vetterling: Polaroid Corporation, Brian P. Flannery: EXXON Research and Engineering Company} + author = "William H. Press and Saul A. Teukolsky and William T. Vetterling and Brian P. Flannery", + title = "{Numerical Recipes in C: The Art of Scientific Computing}", + edition = "Second Edition", + publisher = "Cambridge University Press", + year = "1992", + note = "William H. Press: Harvard-Smithsonian Center for Astrophysics, Saul A. Teukolsky: Department of Physics, Cornell University, William T. Vetterling: Polaroid Corporation, Brian P. Flannery: EXXON Research and Engineering Company" } @misc{gabry2024visual, - author = {Jonah Gabry and Martin Modr{\'a}k}, - title = {Visual MCMC diagnostics using the bayesplot package}, - year = {2024}, - month = {January}, - day = {30}, - howpublished = {\url{https://mc-stan.org/bayesplot/articles/visual-mcmc-diagnostics.html}}, - note = {Source: vignettes/visual-mcmc-diagnostics.Rmd} + author = "Jonah Gabry and Martin Modr{\'a}k", + title = "{Visual MCMC diagnostics using the bayesplot package}", + year = "2024", + month = "January", + day = "30", + howpublished = "\url{https://mc-stan.org/bayesplot/articles/visual-mcmc-diagnostics.html}", + note = "Source: vignettes/visual-mcmc-diagnostics.Rmd" } @misc{chakraborty2019estimating, - author = {Saptarshi Chakraborty and Suman K. Bhattacharya and Kshitij Khare}, - title = {Estimating accuracy of the MCMC variance estimator: a central limit theorem for batch means estimators}, - year = {2019}, - eprint = {1911.00915}, - archivePrefix= {arXiv}, - primaryClass = {stat.CO}, - url = {https://doi.org/10.48550/arXiv.1911.00915} + author = "Saptarshi Chakraborty and Suman K. Bhattacharya and Kshitij Khare", + title = "{Estimating accuracy of the MCMC variance estimator: a central limit theorem for batch means estimators}", + year = "2019", + eprint = "1911.00915", + archivePrefix = "arXiv", + primaryClass = "stat.CO", + url = "https://doi.org/10.48550/arXiv.1911.00915" } @misc{rossetti2024batch, - author = {Manuel D. Rossetti}, - title = {The Batch Means Method}, - booktitle = {Simulation Modeling and Arena, 2nd Edition}, - year = {2024}, - chapter = {5.4}, - url = {https://rossetti.github.io/RossettiArenaBook/ch5-BatchMeansMethod.html}, - note = {Accessed: 2024-09-08} + author = "Manuel D. Rossetti", + title = "{The Batch Means Method}", + booktitle = "Simulation Modeling and Arena, 2nd Edition", + year = "2024", + chapter = "5.4", + url = "https://rossetti.github.io/RossettiArenaBook/ch5-BatchMeansMethod.html", } diff --git a/cmake/Templates/Doxyfile.in b/cmake/Templates/Doxyfile.in index 9a938834b..d5ac8285b 100644 --- a/cmake/Templates/Doxyfile.in +++ b/cmake/Templates/Doxyfile.in @@ -670,7 +670,7 @@ LAYOUT_FILE = # search path. Do not use file names with spaces, bibtex cannot handle them. See # also \cite for info how to create references. -CITE_BIB_FILES = bibliography.bib +CITE_BIB_FILES = ../Doc/bibliography.bib #--------------------------------------------------------------------------- # Configuration options related to warning and progress messages