Conflict of interest

April 13, 2015
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Conflict of interest

Disclaimer: I'm fully aware of the obvious conflict of interest here, but also I think that this looks really good, so I'll write about it anyway.This post is to highlight that Marta's and Michela's book on Spatial and Spatio-temporal Bayesian Mod...

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Quantifying uncertainty

April 13, 2015
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The primary way to quantify uncertainty is to use probability. Subject to certain axioms that aim to capture common-sense rules for quantifying uncertainty, probability theory is essentially the only way. (This is Cox’s theorem.) Other methods, such as fuzzy logic, may be useful, though they must violate common sense (at least as defined by Cox’s theorem) […]

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Why do we communicate probability calculations so poorly, even when we know how to do it better?

April 13, 2015
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Haynes Goddard writes: I thought to do some reading in psychology on why Bayesian probability seems so counterintuitive, and making it difficult for many to learn and apply. Indeed, that is the finding of considerable research in psychology. It turns out that it is counterintuitive because of the way it is presented, following no doubt […] The post Why do we communicate probability calculations so poorly, even when we know…

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Genomics Case Studies Online Courses Start in Two Weeks (4/27)

April 13, 2015
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The last month of the HarvardX Data Analysis for Genomics series start on 4/27. We will cover case studies on RNAseq, Variant calling, ChipSeq and DNA methylation. Faculty includes Shirley Liu, Mike Love, Oliver Hoffman and the HSPH Bioinformatics Core. Although taking the previous courses on the series will help, the four case study courses

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DO loop = 1 TO 600;

April 13, 2015
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DO loop = 1 TO 600;

Today is my 600th blog post for The DO Loop. I have written about many topics that are related to statistical programming, math, statistics, simulation, numerical analysis, matrix computations, and more. The right sidebar of my blog contains a tag cloud that links to many topics. What topics do you, […]

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I still think you can manufacture an unfair coin

April 13, 2015
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In Gelman and Nolan’s paper “You Can Load a Die, But You Can’t Bias a Coin” The American Statistician, November 2002, Vol. 56, No. 4 it is argued you can’t easily produce a coin that is biased when flipped (and caught). A numb...

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a vignette on Metropolis

April 12, 2015
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a vignette on Metropolis

Over the past week, I wrote a short introduction to the Metropolis-Hastings algorithm, mostly in the style of our Introduction to Monte Carlo with R book, that is, with very little theory and worked-out illustrations on simple examples. (And partly over the Atlantic on my flight to New York and Columbia.) This vignette is intended […]

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How (Not) to Interpret That p-Value

April 12, 2015
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How (Not) to Interpret That p-Value

Thanks to my colleague, Linda Welling, for bringing this post to my attention: Still Not Significant.I just love it! (Take some of the comments with a grain of salt, though.) © 2015, David E. Giles

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Power is of two kinds (or: Gandhi, power, fear, love, and statistics)

April 12, 2015
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Power is of two kinds (or: Gandhi, power, fear, love, and statistics)

In the chapter of DBDA2E on Goals, Power, and Sample Size (p. 384), I quoted the Mahatma Gandhi:"Power is of two kinds. One is obtained by the fear of punishment and the other by arts of love. Power based on love is a thousand times more effective and ...

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Cefamandole: PK after IV with six subjects in JAGS

April 12, 2015
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Cefamandole: PK after IV with six subjects in JAGS

After last week's post on Theoph I noticed the MEMSS library contained more PK data sets. The Cefamandole data is an IV data set with six subjects. It is somewhat challenging, since there seem to be several elimination rates.DataData are displayed...

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The wings of a programmer

April 12, 2015
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The wings of a programmer

Programmers think programming is really hard.  Non-programmers think it’s even harder than that. Figure 1: The perceived difficulty of programming.  Why is programming so arduous? There are a few reasons.  Here is one. Wings Programming is exacting, programming needs creativity. These are absolutely at odds with each other. One wing wants the programmer to respect every […] The post The wings of a programmer appeared first on Burns Statistics.

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“Another bad chart for you to criticize”

April 12, 2015
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“Another bad chart for you to criticize”

Perhaps in response to my lament, “People used to send me ugly graphs, now I get these things,” Stuart Buck sends me an email with the above comment and a link to this “Graphic of the day” produced by some uncredited designer at Thomson Reuters: From a statistical perspective, this graph is a disaster in […] The post “Another bad chart for you to criticize” appeared first on Statistical Modeling,…

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Another stylized fact bites the dust

April 11, 2015
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According to economist Henry Farber (link from Dan Goldstein): In a seminal paper, Camerer, Babcock, Loewenstein, and Thaler (1997) find that the wage elasticity of daily hours of work New York City (NYC) taxi drivers is negative and conclude that their labor supply behavior is consistent with target earning (having reference dependent preferences). I replicate […] The post Another stylized fact bites the dust appeared first on Statistical Modeling, Causal…

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Summer Internship at Novartis: Stan PK/PD Modeling

April 11, 2015
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Summer Internship at Novartis:  Stan PK/PD Modeling

This looks like a great way to spend a summer: Summer Internship at Novartis Integrated Quantitative Sciences Here’s the job description: Bayesian modeling tools with Stan: Create re-usable tools for the Bayesian modeling of pharmacometrics data that can integrate diverse data sources (including pre-clinical, in-silico model predictions, etc.). Using the latest Stan’s facilities (http://mc-stan.org) develop […] The post Summer Internship at Novartis: Stan PK/PD Modeling appeared first on Statistical Modeling,…

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Modeling Categories with Breadth and Depth

April 11, 2015
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Modeling Categories with Breadth and Depth

Religion is a categorical variable with followers differentiated by their degree of devotion. Liberals and conservatives check their respective boxes when surveyed, although moderates from each group sometimes seem more alike than their more extreme co...

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Translational Bioinformatics Year In Review

April 10, 2015
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Translational Bioinformatics Year In Review

Per tradition, Russ Altman gave his "Translational Bioinformatics: The Year in Review" presentation at the close of the AMIA Joint Summit on Translational Bioinformatics in San Francisco on March 26th.  This year, papers came from six key areas (a...

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A silly little error, of the sort that I make every day

April 10, 2015
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A silly little error, of the sort that I make every day

Ummmm, running Stan, testing out a new method we have that applies EP-like ideas to perform inference with aggregate data—it’s really cool, I’ll post more on it once we’ve tried everything out and have a paper that’s in better shape—anyway, I’m starting with a normal example, a varying-intercept, varying-slope model where the intercepts have population […] The post A silly little error, of the sort that I make every day…

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A silly little error, of the sort that I make every day

April 10, 2015
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A silly little error, of the sort that I make every day

Ummmm, running Stan, testing out a new method we have that applies EP-like ideas to perform inference with aggregate data—it’s really cool, I’ll post more on it once we’ve tried everything out and have a paper that’s in better shape—anyway, I’m starting with a normal example, a varying-intercept, varying-slope model where the intercepts have population […] The post A silly little error, of the sort that I make every day…

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R User Group Recap: Heatmaps and Using the caret Package

April 10, 2015
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R User Group Recap: Heatmaps and Using the caret Package

At our most recent R user group meeting we were delighted to have presentations from Mark Lawson and Steve Hoang, both bioinformaticians at Hemoshear. All of the code used in both demos is in our Meetup’s GitHub repo.Making heatmaps in RSteve started...

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Mistaken identity

April 10, 2015
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Someone I know sent me the following email: The person XX [pseudonym redacted] who posts on your blog is almost certainly YY [name redacted]. So he is referencing his own work and trying to make it sound like it is a third party endorsing it. Not sure why but it bugs me. He is an […] The post Mistaken identity appeared first on Statistical Modeling, Causal Inference, and Social Science.

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All about that "bias, bias, bias" (it’s no trouble)

April 10, 2015
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All about that "bias, bias, bias" (it’s no trouble)

At some point, everyone who fiddles around with Bayes factors with point nulls notices something that, at first blush, seems strange: small effect sizes seem “biased” toward the null hypothesis. In null hypothesis significance testing, power simply increases when you change the true effect size. With Bayes factors, there is a non-monotonicity where increasing the sample size will slightly increase the degree to which a small effect size favors the…

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Index to first 50 posts

April 10, 2015
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Index to first 50 posts

This is the 50th post to this blog. For my 25th post I provided a catalogue of my first 25 posts, and as promised then, I now provide a similar index for posts 25 to 50. 25. Catalogue of my first 25 blog posts 26. Multivariate data analysis (using R): a course and some lecture … Continue reading Index to first 50 posts

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Index to first 50 posts

April 10, 2015
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Index to first 50 posts

This is the 50th post to this blog. For my 25th post I provided a catalogue of my first 25 posts, and as promised then, I now provide a similar index for posts 25 to 50. 25. Catalogue of my first 25 blog posts 26. Multivariate data analysis (using R): a course and some lecture … Continue reading Index to first 50 posts

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