User:Timothee Flutre/Notebook/Postdoc/2011/11/16
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==About statistical modeling==  ==About statistical modeling==  
  * '''  +  * '''intro courses''': 
+  ** "OpenIntro Statistics" by Diez, Barr and CetinkayaRundel (free [http://www.openintro.org/stat/textbook.php textbook])  
+  ** "Statistics Done Wrong" by Alex Reinhart (free [http://www.refsmmat.com/statistics/ textbook])  
+  ** "Mixed effects models for the population approach" by Marc Lavielle and the POPIX team at INRIA (free [http://popix.lixoft.net/index.php?title=Home_page wiki])  
+  ** "Graphical Models" by Zoubin Ghahramani (2012, free [http://videolectures.net/mlss2012_ghahramani_graphical_models/ video & slides])  
+  ** [http://swirlstats.com/ swirl] and [http://mosaicweb.org/ mosaic], R packages to learn stats and R simultaneously and interactively  
+  
+  * '''advanced courses''':  
** "Advanced Data Analysis from an Elementary Point of View" by Cosma Shalizi (free [http://www.stat.cmu.edu/~cshalizi/ADAfaEPoV/ book])  ** "Advanced Data Analysis from an Elementary Point of View" by Cosma Shalizi (free [http://www.stat.cmu.edu/~cshalizi/ADAfaEPoV/ book])  
  ** "A First Course in Bayesian Statistical Methods" by Peter Hoff ([http://www.amazon.com/gp/product/0387922997 book])  +  ** "A First Course in Bayesian Statistical Methods" by Peter Hoff (2010, [http://www.amazon.com/gp/product/0387922997 book]) 
  ** "Bayesian Data Analysis" by Andrew Gelman (free [http://www.stat.columbia.edu/~gelman/book/slides slides], [http://www.amazon.com/dp/1439840954 book])  +  ** "Bayesian Data Analysis" by Andrew Gelman & co (2013, free [http://www.stat.columbia.edu/~gelman/book/slides slides], [http://www.amazon.com/dp/1439840954 3rd edition] of the book) 
+  ** "Statistical Decision Theory and Bayesian Analysis" by James Berger (1993, [https://www.springer.com/statistics/statistical+theory+and+methods/book/9780387960982 2nd edition] of the book)  
* '''mathematical aspects''':  * '''mathematical aspects''':  
** "Introduction to Linear Algebra" by Gilbert Strang (free [http://ocw.mit.edu/courses/mathematics/1806linearalgebraspring2010/ videos], [http://www.amazon.com/dp/0980232716 book])  ** "Introduction to Linear Algebra" by Gilbert Strang (free [http://ocw.mit.edu/courses/mathematics/1806linearalgebraspring2010/ videos], [http://www.amazon.com/dp/0980232716 book])  
  ** "Matrix Differential Calculus with Applications in Statistics and Econometrics" by Magnus and Neudecker (free [http://www.janmagnus.nl/misc/mdc20073rdedition pdf]  +  ** "Matrix Differential Calculus with Applications in Statistics and Econometrics" by Magnus and Neudecker (2007, free [http://www.janmagnus.nl/misc/mdc20073rdedition pdf] for the 3rd edition) 
* '''practical, computational aspects''':  * '''practical, computational aspects''':  
  ** "How to share data with a statistician" by Jeff Leek (  +  ** "How to share data with a statistician" by Jeff Leek ([https://github.com/jtleek/datasharing procedure] on GitHub), see also the [http://simplystatistics.org/2014/02/03/thethreetablesforgenomicscollaborations/ advice] on genomics metadata by Raphael Irrizary and "statistical consulting" by Karl Broman ([http://www.biostat.wisc.edu/~kbroman/teaching/misc/consulting.pdf slides]) 
** "Exploratory Data Analysis with R" by Jennifer Bryan (free [http://www.stat.ubc.ca/~jenny/STAT545A/2012lectures/ course])  ** "Exploratory Data Analysis with R" by Jennifer Bryan (free [http://www.stat.ubc.ca/~jenny/STAT545A/2012lectures/ course])  
** "Tutorial on Big Data with Python" by Marcel Caraciolo (free Python [https://github.com/marcelcaraciolo/bigdatatutorial notebooks])  ** "Tutorial on Big Data with Python" by Marcel Caraciolo (free Python [https://github.com/marcelcaraciolo/bigdatatutorial notebooks])  
  ** interpreted languages: obviously [http://openwetware.org/wiki/User:Timothee_Flutre/Notebook/Postdoc/2011/11/07 R], but more and more Python ([  +  ** interpreted languages: obviously [http://openwetware.org/wiki/User:Timothee_Flutre/Notebook/Postdoc/2011/11/07 R], but more and more Python ([https://en.wikipedia.org/wiki/Scipy SciPy] for NumPy, Matplotlib, and pandas, but see also [https://en.wikipedia.org/wiki/Scikitlearn scikitlearn] and [http://statsmodels.sourceforge.net/ statsmodels]), as well as others ([https://en.wikipedia.org/wiki/Julia_%28programming_language%29 Julia]) 
** C/C++: [http://en.wikipedia.org/wiki/GNU_Scientific_Library GSL], [http://en.wikipedia.org/wiki/Armadillo_%28C++_library%29 Armadillo], [http://en.wikipedia.org/wiki/Eigen_(C%2B%2B_library) Eigen], [http://www.rcpp.org/ Rcpp], [http://mcstan.org/ Stan]  ** C/C++: [http://en.wikipedia.org/wiki/GNU_Scientific_Library GSL], [http://en.wikipedia.org/wiki/Armadillo_%28C++_library%29 Armadillo], [http://en.wikipedia.org/wiki/Eigen_(C%2B%2B_library) Eigen], [http://www.rcpp.org/ Rcpp], [http://mcstan.org/ Stan]  
  ** editor: [https://openwetware.org/wiki/User:Timothee_Flutre/Notebook/Postdoc/2012/07/25 Emacs]  +  ** editor: obviously [https://openwetware.org/wiki/User:Timothee_Flutre/Notebook/Postdoc/2012/07/25 Emacs] (languageagnostic, orgmode, etc), but also [https://en.wikipedia.org/wiki/RStudio Rstudio] (Ronly...) and [https://en.wikipedia.org/wiki/Ipython IPython] (Pythononly...) 
* '''visualizing, plotting''':  * '''visualizing, plotting''':  
** "Visualizing uncertainty about the future" by Spiegelhalter et al. (Science 2011, [http://dx.doi.org/10.1126/science.1191181 DOI])  ** "Visualizing uncertainty about the future" by Spiegelhalter et al. (Science 2011, [http://dx.doi.org/10.1126/science.1191181 DOI])  
** "Let's practice what we preach: turning tables into graphs" by Gelman et al. (The American Statistician 2002, [http://dx.doi.org/10.1198/000313002317572790 DOI])  ** "Let's practice what we preach: turning tables into graphs" by Gelman et al. (The American Statistician 2002, [http://dx.doi.org/10.1198/000313002317572790 DOI])  
+  ** "Top ten worst graphs" by Karl Broman ([http://www.biostat.wisc.edu/~kbroman/topten_worstgraphs/ webpage])  
+  ** "EDA: Investigate, Visualize, and Summarize Data Using Ra" (on [https://www.udacity.com/course/ud651 Udacity], free courseware available)  
* '''philosophy, history, pragmatism''':  * '''philosophy, history, pragmatism''':  
  ** "Mathematical Models and Reality: A Constructivist Perspective" by Christian Hennig (Foundations of Science  +  ** "Statistical analysis and the illusion of objectivity" by Berger and Berry (American Scientist 1988, [http://dx.doi.org/10.1016/02782316(88)900576 DOI], [http://www.medicine.mcgill.ca/epidemiology/joseph/courses/EPIB675/Berger.Berry.pdf pdf]) 
+  ** "Bayesian methods: general background" by E. T. Jaynes (1985, free [http://bayes.wustl.edu/etj/articles/general.background.pdf pdf]) and "Where do we stand on maximum entropy?" by E. T. Jaynes (1978, free [http://bayes.wustl.edu/etj/articles/stand.on.entropy.pdf pdf])  
+  ** "The Philosophy of Statistics" by Lindley (JRSSD 2000, [http://dx.doi.org/10.1111/14679884.00238 DOI])  
+  ** "What is statistics?" by Feinberg (An.Rev.Stat.Appl. 2014, [http://dx.doi.org/10.1146/annurevstatistics022513115703 DOI])  
+  ** "Mathematical Models and Reality: A Constructivist Perspective" by Christian Hennig (Foundations of Science 2010, [http://dx.doi.org/10.1007/s106990099167x DOI])  
** "Philosophy and the practice of Bayesian statistics" by Andrew Gelman and Cosma Shalizi (British Journal of Mathematical and Statistical Psychology 2013, [http://dx.doi.org/10.1111/j.20448317.2011.02037.x DOI])  ** "Philosophy and the practice of Bayesian statistics" by Andrew Gelman and Cosma Shalizi (British Journal of Mathematical and Statistical Psychology 2013, [http://dx.doi.org/10.1111/j.20448317.2011.02037.x DOI])  
** "Statistical Inference : the Big Picture" by Robert Kass (Statistical Science 2011, [http://dx.doi.org/10.1214/10STS337 DOI], free [http://arxiv.org/pdf/1106.2895v2.pdf pdf] on arXiv)  ** "Statistical Inference : the Big Picture" by Robert Kass (Statistical Science 2011, [http://dx.doi.org/10.1214/10STS337 DOI], free [http://arxiv.org/pdf/1106.2895v2.pdf pdf] on arXiv)  
** "In Praise of Simplicity not Mathematistry! Ten Simple Powerful Ideas for the Statistical Scientist" by Roderick Little (JASA 2013, [http://dx.doi.org/10.1080/01621459.2013.787932 DOI])  ** "In Praise of Simplicity not Mathematistry! Ten Simple Powerful Ideas for the Statistical Scientist" by Roderick Little (JASA 2013, [http://dx.doi.org/10.1080/01621459.2013.787932 DOI])  
  ** "Des spécificités de l’approche bayésienne et de ses justifications en statistique inférentielle"  +  ** "Des spécificités de l’approche bayésienne et de ses justifications en statistique inférentielle" par Christian Robert (chapitre 2013, [http://hal.archivesouvertes.fr/docs/00/87/01/24/PDF/Bayes.pdf pdf] gratuit sur HAL) 
* '''classics''':  * '''classics''':  
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* '''litterature, community''':  * '''litterature, community''':  
  ** Annals of Statistics, JRSSB, JASA, Annals of Applied Statistics, Bayesian Analysis, JMRL, NIPS  +  ** [http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.aos Annals of Statistics], [http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)14679868 JRSSB], [http://www.tandfonline.com/toc/uasa20/current JASA], [http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.aoas Annals of Applied Statistics], [http://ba.stat.cmu.edu/ Bayesian Analysis], [http://jmlr.org/ JMRL], [http://books.nips.cc/ NIPS] 
  ** Biometrics, Biostatistics  +  ** [http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)15410420 Biometrics], [http://biostatistics.oxfordjournals.org/ Biostatistics], [http://biomet.oxfordjournals.org/ Biometrika] 
  ** Statistical Science, The American Statistician  +  ** [http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.ss Statistical Science], [http://amstat.tandfonline.com/loi/tas#.UsrQx47_7Gg The American Statistician], [http://www.annualreviews.org/journal/statistics Annual Review of Statistics and its Application] 
** see also on [http://projecteuclid.org/ Project Euclid] and [http://arxiv.org/archive/stat arXiv]  ** see also on [http://projecteuclid.org/ Project Euclid] and [http://arxiv.org/archive/stat arXiv]  
** blogs: [http://andrewgelman.com/ Andrew Gelman], [http://xianblog.wordpress.com/ Christian Robert], [http://normaldeviate.wordpress.com/ Larry Wasserman]  ** blogs: [http://andrewgelman.com/ Andrew Gelman], [http://xianblog.wordpress.com/ Christian Robert], [http://normaldeviate.wordpress.com/ Larry Wasserman]  
+  ** links with society: [http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291467985X JRSSA], Statistique et Société (free [http://publicationssfds.fr/index.php/stat_soc/index pdfs])  
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