Distrust of R

March 12, 2013
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Distrust of R

I guess I've been living in a bubble for a bit, but apparently there are a lot of people who still mistrust R. I got asked this week why I used R (and, specifically, the package rpart) to generate classification and regression trees instead of SAS Ente...

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The difference between prediction intervals and confidence intervals

March 12, 2013
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The difference between prediction intervals and confidence intervals

Prediction intervals and confidence intervals are not the same thing. Unfortunately the terms are often confused, and I am often frequently correcting the error in students’ papers and articles I am reviewing or editing. A prediction interval is an interval associated with a random variable yet to be observed, with a specified probability of the random variable lying within the interval. For example, I might give an 80% interval for…

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R to Latex packages: Coverage

March 12, 2013
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There are now quite a few R packages to turn cross-tables and fitted models into nicely formatted latex. In a previous post I showed how to use one of them to display regression tables on the fly. In this post I summarise what types of R object each of the major packages can deal with. […]

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The Beautiful Table: an Alternative Representation of Football Scores

March 12, 2013
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The Beautiful Table: an Alternative Representation of Football Scores

Designed by software engineer Jon Perry, and following the Tufte-inspired mantra "no visual treatment for the purpose of aesthetics only", The Beautiful Table [the-beautiful-table.com] provides football (soccer) standings, results and schedule, as one...

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Misunderstanding the p-value

March 12, 2013
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Misunderstanding the p-value

The New York Times has a feature in its Tuesday science section, Take a Number, to which I occasionally contribute (see here and here). Today’s column, by Nicholas Balakar, is in error. The column begins: When medical researchers report their findings, they need to know whether their result is a real effect of what they [...]

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How tall is Jon Lee Anderson?

March 12, 2013
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How tall is Jon Lee Anderson?

The second best thing about this story (from Tom Scocca) is that Anderson spells “Tweets” with a capital T. But the best thing is that Scocca is numerate—he compares numbers on the logarithmic scale: Reminding Lake that he only had 169 Twitter followers was the saddest gambit of all. Jon Lee Anderson has 17,866 followers. [...]

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Job advert

March 12, 2013
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Job advert

We finally got around to prepare everything we needed to advertise the position which will be available in the MRC grant we've been awarded last year.The project will run for 30 months and we're looking for a post-doctoral candidate to work on the Rese...

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Blowing the whistle at bubble charts

March 12, 2013
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Blowing the whistle at bubble charts

The bubble chart is one of the most hopeless data graphics ever invented. It is sometimes useful for conceptual charts but trying to express data with it is a lost cause. The Wall Street Journal used a bubble chart to...

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reports 0.1.2 Released

March 12, 2013
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reports 0.1.2 Released

I’m very pleased to announce the release of reports : An R package to assist in the workflow of writing academic articles and other reports. This is the first CRAN release of reports: http://cran.r-project.org/web/packages/reports/index.html The reports package assists in writing … Continue reading →

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If I were at #ENAR2013 today, here’s where I’d go

March 12, 2013
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This week is the annual ENAR meeting, the big biostatistics conference, in Orlando, Florida. It actually started on Sunday but I haven’t gotten around to looking at the program (obviously, I’m not there right now). Flipping through the program now, … Continue reading →

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How to use optim in R

March 12, 2013
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How to use optim in R

A friend of mine asked me the other day how she could use the function optim in R to fit data. Of course there are functions for fitting data in R and I wrote about this earlier. However, she wanted to understand how to do this from scratch using opti...

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Man versus man-plus-machine

March 12, 2013
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As you read Steve Lohr's article "Algorithms Get a Human Hand in Steering Web" (link), recall what I wrote when discussing David Brooks's piece on Big Data (link): The biggest issue with Brooks's column is the incessant use of the flawed man versus machine dichotomy. He warns: "It's foolish to swap the amazing machine in your skull for the crude machine on your desk." The machine he has in his…

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S. Stanley Young: Scientific Integrity and Transparency

March 12, 2013
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S. Stanley Young: Scientific Integrity and Transparency

Stanley Young recently shared his summary testimony with me, and has agreed to my posting it.  S. Stanley Young, PhD Assistant Director for Bioinformatics National Institute of Statistical Sciences Research Triangle Park, NC One-page Summary Young Testimony of Committee on Science, Space and Technology, 5 March 2013 Scientific Integrity and Transparency S. Stanley Young, PhD, […]

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My problem with the Lindley paradox

March 12, 2013
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From a couple years ago but still relevant, I think: To me, the Lindley paradox falls apart because of its noninformative prior distribution on the parameter of interest. If you really think there’s a high probability the parameter is nearly exactly zero, I don’t see the point of the model saying that you have no [...]

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Examen intra, régression logistique et de Poisson

March 12, 2013
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Examen intra, régression logistique et de Poisson

L’examen intra du cours ACT2040 aura lieu mercredi matin, de 9:00 à 12:00. Aucun document autorisé, sauf les calculatrices (modèle standard, cf plan de cours), et les téléphones seront formellement interdits. Il y aura 34 questions portant sur la première partie du cours (jusqu’à la fin des modèles de comptage, sections 1 à 5 des transparents). 15 questions porteront sur la base décrite dans un précédant billet, sur le nombre…

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Simulating Random Multivariate Correlated Data (Categorical Variables)

March 12, 2013
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Simulating Random Multivariate Correlated Data (Categorical Variables)

This is a repost of the second part of an example that I posted last year but at the time I only had the PDF document (written in ). This is the second example to generate multivariate random associated data. This example shows how to generate ordinal, categorical, data. It is a little more complex than generating continuous [...]

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Attention Radar: How Political Trends Develop over Time

March 11, 2013
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Attention Radar: How Political Trends Develop over Time

Attention Radar [minddesign.info], designed by Mind Design, is a web app, specifically designed to be viewed on the iPad, that visualizes the changes in political agendas of the Netherlands over time. The interactive, stacked area chart contrasts dif...

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Simulating Random Multivariate Correlated Data (Continuous Variables)

March 11, 2013
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Simulating Random Multivariate Correlated Data (Continuous Variables)

This is a repost of an example that I posted last year but at the time I only had the PDF document (written in ).  I’m reposting it directly into WordPress and I’m including the graphs. From time-to-time a researcher needs to develop a script or an application to collect and analyze data. They may also need [...]

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Simulating Random Multivariate Correlated Data (Continuous Variables)

March 11, 2013
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Simulating Random Multivariate Correlated Data (Continuous Variables)

This is a repost of an example that I posted last year but at the time I only had the PDF document (written in ).  I’m reposting it directly into WordPress and I’m including the graphs. From time-to-time a researcher needs to develop a script or an application to collect and analyze data. They may also need [...]

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Yes, the decision to try (or not) to have a child can be made rationally

March 11, 2013
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Yes, the decision to try (or not) to have a child can be made rationally

Philosopher L. A. Paul and sociologist Kieran Healy write: Choosing to have a child involves a leap of faith, not a carefully calibrated rational choice. When surprising results surface about the dissatisfaction many parents experience, telling yourself that you knew it wouldn’t be that way for you is simply a rationalization. The same is true [...]

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Hexadecimal literals in GNU R

March 11, 2013
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Recently I have used hexadecimal numbers in GNU R. The way they are parsed surprised me and is inconsistent with Java. As R Language Definition pdf only briefly mentions hexadecimal numbers here is what I have found.First I have checked the following c...

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Construct normal data from summary statistics

March 11, 2013
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Construct normal data from summary statistics

Last week there was an interesting question posted to the "Stat-Math Statistics" group on LinkedIn. The original question was a little confusing, so I'll state it in a more general form: A population is normally distributed with a known mean and standard deviation. A sample of size N is drawn [...]

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Visualization Makes Things Real

March 11, 2013
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Visualization Makes Things Real

Vision is the sense we most identify with: it tells us where we are, who we are talking to, what we are doing. It defines our world like no other sense. What we can see is real, for better or worse. Reproductive Cloning In 2003, Nigel Holmes was working on an information graphic on stem cells for Stanford Magazine. This was the result of extensive discussions with the scientists, in…

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