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My Poster at Rocky 2015: Estimating parameters of the Hodgkin-Huxley cardiac cell model by integrating raw data from multiple types of voltage-clamp experiments

December 18, 2015
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My Poster at Rocky 2015: Estimating parameters of the Hodgkin-Huxley cardiac cell model by integrating raw data from multiple types of voltage-clamp experiments

I'm recently returned from the 2015 Rocky Mountain Bioinformatics Conference, where I presented the above poster. This is work with a colleague, Rick Gray, at the FDA. He and I collaborate on our NIH award "Optimal Design of Challenge-Response Experiments in Cardiac Electrophysiology" (HL118392) The (original) poster abstract is below, but the poster content is … Continue reading My Poster at Rocky 2015: Estimating parameters of the Hodgkin-Huxley cardiac cell…

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‘The Libertarian Republic’ author refers to Obamacare ‘spike’ in medical adminstrators before it even became law.

December 3, 2015
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‘The Libertarian Republic’ author refers to Obamacare ‘spike’ in medical adminstrators before it even became law.

I don't usually read 'The Libertarian Republic', but this article was shared by a friend on my Facebook feed. The author writes that the 'armies of bureaucrats' (i.e., medical administrators), necessitated by government regulation, are responsible for the rise in medical costs. The evidence presented is a figure that shows the growth of physicians and … Continue reading 'The Libertarian Republic' author refers to Obamacare 'spike' in medical adminstrators before…

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Reference Chart for Precision of Wilson Binomial Proportion Confidence Interval

October 16, 2015
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Reference Chart for Precision of Wilson Binomial Proportion Confidence Interval

I am often asked about the number of subjects needed to study a binary outcome, which usually leads to a discussion of confidence intervals for binary proportions, and the associated precision. Sometimes the precision is quantified as the width or half-width of a 95% confidence interval. For proportions, I like the Wilson score interval because … Continue reading Reference Chart for Precision of Wilson Binomial Proportion Confidence Interval →

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Delta Method Confidence Bands for Gaussian Mixture Density (Can Behave Badly)

October 9, 2015
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Delta Method Confidence Bands for Gaussian Mixture Density (Can Behave Badly)

This post follows from a previous post (2798), in which the delta method was used to create an approximate pointwise 95% confidence band for a Gaussian density estimate. Note that the quality of this estimate was not assessed (e.g., whether the band has the correct pointwise coverage). Here we extend that approach to the Gaussian … Continue reading Delta Method Confidence Bands for Gaussian Mixture Density (Can Behave Badly) →

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Delta Method Confidence Bands for Gaussian Density

October 2, 2015
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Delta Method Confidence Bands for Gaussian Density

During one of our Department's weekly biostatistics "clinics", a visitor was interested in creating confidence bands for a Gaussian density estimate (or a Gaussian mixture density estimate). The mean, variance, and two "nuisance" parameters, were simultaneously estimated using least-squares. Thus, the approximate sampling variance-covariance matrix (4x4) was readily available. The two nuisance parameters do not … Continue reading Delta Method Confidence Bands for Gaussian Density →

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Arbitrage with the In-laws!

September 30, 2015
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I've just discovered the Predictit.org website, which is a "Prediction Market" where participants can place bets on the occurrence of future events, such as the outcome of political elections. Predictit.org is similar in function to the defunct website Intrade.com (Wikipedia). But, unlike Intrade.com, they seem to have done their homework with U.S. regulatory bodies beforehand. … Continue reading Arbitrage with the In-laws! →

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Notes on Multivariate Gaussian Quadrature (with R Code)

September 25, 2015
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Notes on Multivariate Gaussian Quadrature (with R Code)

Statisticians often need to integrate some function with respect to the multivariate normal (Gaussian) distribution, for example, to compute the standard error of a statistic, or the likelihood function in of a mixed effects model. In many (most?) useful cases, these integrals are intractable, and must be approximated using computational methods. Monte-Carlo integration is one … Continue reading Notes on Multivariate Gaussian Quadrature (with R Code) →

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Recipe for Computing and Sampling Multivariate Kernel Density Estimates (and Plotting Contours for 2D KDEs).

September 19, 2015
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Recipe for Computing and Sampling Multivariate Kernel Density Estimates (and Plotting Contours for 2D KDEs).

The code snippet below creates the above graphic: ## radially symmetric kernel (Gussian kernel) RadSym

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Recipe for Centered Horizontal Stacked Barplots (Useful for Likert scale responses)

September 8, 2015
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Recipe for Centered Horizontal Stacked Barplots (Useful for Likert scale responses)

There is a nice package and paper about this here: http://www.jstatsoft.org/v57/i05/paper. However, the associated code is complex and uses lattice. Here's a brief recipe using base graphics that implements the above figure: set.seed(40) x

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Nested vs. Non-nested (crossed) Random Effects in R

June 13, 2015
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Nested vs. Non-nested (crossed) Random Effects in R

The R script below illustrates the nested versus non-nested (crossed) random effects functionality in the R packages lme4 and nlme. Note that crossed random effects are difficult to specify in the nlme framework. Thus, I've included a back-of-the-envelope (literally a scanned image of my scribble) interpretation of the 'trick' to specifying crossed random effects for … Continue reading Nested vs. Non-nested (crossed) Random Effects in R →

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