I’ve heard something frightening from practicing statisticians who frequently use mixed effects models. Sometimes when I ask them whether they produced a [semi]variogram to check the correlation structure they reply “what’s that?” –Frank Harrell When it comes to statistical modeling, semivariograms help us visualize and assess correlation in residuals. We can use them for two […]
Getting Started with Gamma Regression
In this article we plan to get you up and running with gamma regression. But before we dive into that, let’s review the familiar Normal distribution. This will provide some scaffolding to help us transition to the gamma distribution. As you probably know, a Normal distribution is described by its mean and standard deviation. These […]
Understanding Deviance Residuals
If you have ever performed binary logistic regression in R using the glm() function, you may have noticed a summary of “Deviance Residuals” at the top of the summary output. In this article we talk about how these residuals are calculated and what we can use them for. We also talk about other types of […]
Logistic Regression Four Ways with Python
What is Logistic Regression? Logistic regression is a predictive analysis that estimates/models the probability of an event occurring based on a given dataset. This dataset contains both independent variables, or predictors, and their corresponding dependent variable, or response. To model the probability of a particular response variable, logistic regression assumes that the log-odds for the […]
Getting Started with Bootstrap Model Validation
Let’s say we fit a logistic regression model for the purposes of predicting the probability of low infant birth weight, which is an infant weighing less than 2.5 kg. Below we fit such a model using the “birthwt” data set that comes with the MASS package in R. (This is an example model and not […]
Mathematical Annotation in R
In this article we demonstrate how to include mathematical symbols and formulas in plots created with R. This can mean adding a formula in the title of the plot, adding symbols to axis labels, annotating a plot with some math, and so on. R provides a \(\LaTeX\)-like language for defining mathematical expressions. It is documented […]
Comparing Mixed-Effect Models in R and SPSS
Occasionally we are asked to help students or faculty implement a mixed-effect model in SPSS. Our training and expertise is primarily in R, so it can be challenging to transfer and apply our knowledge to SPSS. In this article we document for posterity how to fit some basic mixed-effect models in R using the lme4 […]
Comparing the accuracy of two binary diagnostic tests in a paired study design
There are many medical tests for detecting the presence of a disease or condition. Some examples include tests for lesions, cancer, pregnancy, or COVID-19. While these tests are usually accurate, they’re not perfect. In addition, some tests are designed to detect the same condition, but use a different method. A recent example are PCR and […]
Correlation of Fixed Effects in lme4
If you have ever used the R package lme4 to perform mixed-effect modeling you may have noticed the “Correlation of Fixed Effects” section at the bottom of the summary output. This article intends to shed some light on what this section means and how you might interpret it. To begin, let’s simulate some data. Below […]
List Comprehensions in Python
List comprehensions are a topic a lot of new Python users struggle with. This article seeks to explain the benefits of list comprehensions and how list comprehensions work in a digestible manner. Single for loop list comprehension The following code uses a traditional for loop to change each string in a for loop from upper […]