Posts Tagged ‘ graphics ’

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
By
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…

Read more »

Reference Chart for Precision of Wilson Binomial Proportion Confidence Interval

October 16, 2015
By
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 →

Read more »

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

October 9, 2015
By
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) →

Read more »

Delta Method Confidence Bands for Gaussian Density

October 2, 2015
By
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 →

Read more »

Notes on Multivariate Gaussian Quadrature (with R Code)

September 25, 2015
By
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) →

Read more »

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

September 19, 2015
By
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

Read more »

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

September 8, 2015
By
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

Read more »

Mathematical annotations on R plots

September 2, 2015
By
Mathematical annotations on R plots

I’ve always struggled with using plotmath via the expression function in R for adding mathematical notation to axes or legends. For some reason, the most obvious way to write something never seems to work for me and I end up using trial and error in a loop with far too many iterations. So I am […]

Read more »

Visualising the predictive distribution of a log-transformed linear model

August 25, 2015
By
Visualising the predictive distribution of a log-transformed linear model

Last week I presented visualisations of theoretical distributions that predict ice cream sales statistics based on linear and generalised linear models, which I introduced in an earlier post.Theoretical distributionsToday I will take a closer look at t...

Read more »

Visualising theoretical distributions of GLMs

August 18, 2015
By
Visualising theoretical distributions of GLMs

Two weeks ago I discussed various linear and generalised linear models in R using ice cream sales statistics. The data showed not surprisingly that more ice cream was sold at higher temperatures.icecream

Read more »


Subscribe

Email:

  Subscribe