Posts Tagged ‘ Tutorials ’

Video Tutorial: Allelic Frequencies Remain Constant From Generation to Generation Under the Hardy-Weinberg Equilibrium

The Hardy-Weinberg law is a fundamental principle in statistical genetics.  If its 7 assumptions are fulfilled, then it predicts that the allelic frequency of a genetic trait will remain constant from generation to generation.  In this new video tutorial in my Youtube channel, I explain the math behind the Hardy-Weinberg theorem.  In particular, I clarify […]

Automatic bias correction doesn’t fix omitted variable bias

July 8, 2014
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Page 94 of Gelman, Carlin, Stern, Dunson, Vehtari, Rubin “Bayesian Data Analysis” 3rd Edition (which we will call BDA3) provides a great example of what happens when common broad frequentist bias criticisms are over-applied to predictions from ordinary linear regression: the predictions appear to fall apart. BDA3 goes on to exhibit what might be considered […] Related posts: Frequentist inference only seems easy Six Fundamental Methods to Generate a Random…

Video Tutorial – Calculating Expected Counts in Contingency Tables Using Marginal Proportions and Marginal Totals

A common task in statistics and biostatistics is performing hypothesis tests of independence between 2 categorical random variables.  The data for such tests are best organized in contingency tables, which allow expected counts to be calculated easily.  In this video tutorial in my Youtube channel, I demonstrate how to calculate expected counts using marginal proportions […]

Introduction to R for Life Scientists: Course Materials

July 7, 2014
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Last week I taught a three-hour introduction to R workshop for life scientists at UVA's Health Sciences Library.I broke the workshop into three sections:In the first half hour or so I presented slides giving an overview of R and why R is so awesome. Du...

Frequentist inference only seems easy

July 1, 2014
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Two of the most common methods of statistical inference are frequentism and Bayesianism (see Bayesian and Frequentist Approaches: Ask the Right Question for some good discussion). In both cases we are attempting to perform reliable inference of unknown quantities from related observations. And in both cases inference is made possible by introducing and reasoning over […] Related posts: Bayesian and Frequentist Approaches: Ask the Right Question Automatic bias correction doesn’t…

Bedtools tutorial from 2013 CSHL course

June 24, 2014
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A couple of months ago I posted about how to visualize exome coverage with bedtools and R. But if you're looking to get a basic handle on genome arithmetic, take a look at Aaron Quinlan's bedtools tutorials from the 2013 CSHL course. The tutorial uses ...

R minitip: don’t use data.matrix when you mean model.matrix

June 10, 2014
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A quick R mini-tip: don’t use data.matrix when you mean model.matrix. If you do so you may lose (without noticing) a lot of your model’s explanatory power (due to poor encoding). For some modeling tasks you end up having to prepare a special expanded data matrix before calling a given machine learning algorithm. For example […] Related posts: Level fit summaries can be tricky in R What does a generalized…

R style tip: prefer functions that return data frames

June 6, 2014
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While following up on Nina Zumel’s excellent Trimming the Fat from glm() Models in R I got to thinking about code style in R. And I realized: you can make your code much prettier by designing more of your functions to return data.frames. That may seem needlessly heavy-weight, but it has a lot of down-stream […] Related posts: Prefer = for assignment in R Your Data is Never the Right…

Determining chemical concentration with standard addition: An application of linear regression in JMP – A Guest Blog Post for the JMP Blog

$Determining chemical concentration with standard addition: An application of linear regression in JMP – A Guest Blog Post for the JMP Blog$

I am very excited to announce that I have been invited by JMP to be a guest blogger for its official blog!  My thanks to Arati Mejdal, Global Social Media Manager for the JMP Division of SAS, for welcoming me into the JMP blogging community with so much support and encouragement, and I am pleased to […]

Video Tutorial – Useful Relationships Between Any Pair of h(t), f(t) and S(t)

$Video Tutorial – Useful Relationships Between Any Pair of h(t), f(t) and S(t)$

I first started my video tutorial series on survival analysis by defining the hazard function.  I then explained how this definition leads to the elegant relationship of . In my new video, I derive 6 useful mathematical relationships that exist between any 2 of the 3 quantities in the above equation.  Each relationship allows one quantity […]