biostatistics

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Some cool website on study design and biostatistics

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This month (November 2024), I wanted to take a break from writing tutorial and articles. Instead, I wanted update myself on (and share) some very helpful/useful online resources.

A colleague of mine introduced me to website called Datamethods. It’s mainly a discussion forum, but it has some useful resources. This particular post contains references that are very useful for anyone who is interested in study design and biostatistics (link). It is a collection of papers and articles that addresses common myths and practices regarding the application of biostatistics in study designs.

Another great website is Scott Cunningham’s Mixed Taped Sessions. He has a book called Mixed Taped Session about causal inference, and he has regular workshops. I attended his Causal Inference Part 2 workshop, and it was amazing. We learned about the basic difference-in-differences methods (coding in R and Stata), and the innovations surrounding these methods (e.g., Callaway & Sant’Anna’s staggered difference-in-differences approach). Scott also provides the historical perspectives on these methods, which are insightful as they are entertaining. Moreover, he conducts interviews with prominant econometricians, which he posts on his YouTube channel.

Hopefully, these sites are useful for you as they have been for me.

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Linear spline (piecewise) models in Stata

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I wrote a tutorial on how to construct linear spline (also known as piecewise) models using Stata, which has been uploaded to my RPubs site.

Previously, I have developed tutorial on using the linear spline method for interrupted time series analsyis with Stata. However, I did not properly go over the mkspline commands.

In this tutorial, I review the mkspline command and the marginal option to generate coefficients that could be interpreted as the slope within each segment or the change in slope between segments, respectively.

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Staggered difference-in-differences using R

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I was interested in learning how to apply the Callaway & Sant'Anna staggered difference-in-differences framework to my work. After reading several papers and watching the video by Sant'Anna, I wrote a short tutorial on how to apply this framework to a simulated data. The tutorial is located on my RPubs site.

This is a unique method that used the R “did” package, which is based on the paper by Callaway & Sant’Anna.

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Mediation analysis using R

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It’s not uncommon to see covariates in a regression model that should not be there. For example, measurements that occur after the treatment assignment are included into a regression model as baseline covariates. Rather, one should consider a mediation analysis.

I wrote a tutorial on how to perform mediation analysis using R on my RPubs site (link).

I know that I make this mistake at times. This tutorial helped me to carefully consider which covariates to include in a regression model and which ones to consider for mediation analysis.

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Survival Analysis - Immortal Time Bias with Stata

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I wrote a tutorial on how to handle immortal time bias with survival analysis using Stata. In the tutorial, I used a time-varying predictor for the grouping variable and assigned the period before exposure to the control group. This was inspired by the paper Redelmeier and Singh wrote on “Surival in Academy Award-Winner Actors and Actresses.” There was a lot of debate about the rigor of their analyses, and Sylvestre and colleagues re-analyzed the data with immortal time bias in mind. This tutorial uses data from Sylvestre and colleagues to re-create their results.

The tutorial is on my RPubs page. Data used for the tutorial is located on my GitHub page.

To load the data, you can use the Stata import command

import delimited "https://raw.githubusercontent.com/mbounthavong/Survival-analysis-and-immortal-time-bias/main/Data/data1.csv"
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Sample size estimation using the odds ratio in a case-control study

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I wrote a short tutorial on how to use an odds ratio to estimate the sample size needed for a case-control study.

The tutorial is located on my RPubs page (link)

The R Markdown source code is located on my GitHub site (link)

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Sample size estimation and Power analysis in R

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I wrote a tutorial on how to perform sample size estimations and power analysis using R “pwr” package. These are simple examples that will hopefully lead to more complicated estimations. The tutorial is available on RPubs (link). The R Markdown code is available on my Github site (link).

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Logistic regression in R - Part 2 (Goodness of fit tests)

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In a previous tutorial, I discussed how to perform logistic regression using R. I wrote a follow-up tutorial on how to conduct goodness of fit tests for logistic regression models in R and posted it on RPubs. The R Markdown code is available on my Github site.

I’ve learned how to assess model fit using Pearson correlations, deviance, and modified Hosmer-Lemeshow Goodness Of Fit (GOF) tests. I think these are important tools when assessing the fit of a logistic regression model. However, I wanted to focus on the HL GOF tests for this tutorial because there are a lot of nuances that I learned and wanted to share.

Additionally, I added the usefulness of visualizing whether the model over- or under-predicts the actual observed data using the calibration plot in R.

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Logistic regression in R

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I wrote a tutorial on how to construct logistic regression models in R. This tutorial was published on RPubs (link). I go through the use of the glm() command to perform a crude logistic regression model and a multivariable logistic regression model. The data (diabetes.csv) that I used for the motivating example is located here.

The RMarkdown code I used to create the tutorial is located on my GitHub site (link).