Sample size determination in the context of Bayesian analysis

Given my recent involvement with the design of a somewhat complex trial centered around a Bayesian data analysis, I am appreciating more and more that Bayesian approaches are a very real option for clinical trial design. A key element of any study design is sample size. While some would argue that sample size considerations are not critical to the Bayesian design (since Bayesian inference is agnostic to any pre-specified sample size and is not really affected by how frequently you look at the data along the way), it might be a bit of a challenge to submit a grant without telling the potential funders how many subjects you plan on recruiting (since that could have a rather big effect on the level of resources - financial and time - required. [Read More]

Finding answers faster for COVID-19: an application of Bayesian predictive probabilities

As we evaluate therapies for COVID-19 to help improve outcomes during the pandemic, researchers need to be able to make recommendations as quickly as possible. There really is no time to lose. The Data & Safety Monitoring Board (DSMB) of COMPILE, a prospective individual patient data meta-analysis, recognizes this. They are regularly monitoring the data to determine if there is a sufficiently strong signal to indicate effectiveness of convalescent plasma (CP) for hospitalized patients not on ventilation. [Read More]

A Bayesian implementation of a latent threshold model

In the previous post, I described a latent threshold model that might be helpful if we want to dichotomize a continuous predictor but we don’t know the appropriate cut-off point. This was motivated by a need to identify a threshold of antibody levels present in convalescent plasma that is currently being tested as a therapy for hospitalized patients with COVID in a number of RCTs, including those that are particpating in the ongoing COMPILE meta-analysis. [Read More]

Exploring the properties of a Bayesian model using high performance computing

An obvious downside to estimating Bayesian models is that it can take a considerable amount of time merely to fit a model. And if you need to estimate the same model repeatedly, that considerable amount becomes a prohibitive amount. In this post, which is part of a series (last one here) where I’ve been describing various aspects of the Bayesian analyses we plan to conduct for the COMPILE meta-analysis of convalescent plasma RCTs, I’ll present a somewhat elaborate model to illustrate how we have addressed these computing challenges to explore the properties of these models. [Read More]

Diagnosing and dealing with degenerate estimation in a Bayesian meta-analysis

The federal government recently granted emergency approval for the use of antibody rich blood plasma when treating hospitalized COVID-19 patients. This announcement is unfortunate, because we really don’t know if this promising treatment works. The best way to determine this, of course, is to conduct an experiment, though this approval makes this more challenging to do; with the general availability of convalescent plasma (CP), there may be resistance from patients and providers against participating in a randomized trial. [Read More]

A Bayesian model for a simulated meta-analysis

This is essentially an addendum to the previous post where I simulated data from multiple RCTs to explore an analytic method to pool data across different studies. In that post, I used the nlme package to conduct a meta-analysis based on individual level data of 12 studies. Here, I am presenting an alternative hierarchical modeling approach that uses the Bayesian package rstan. Create the data set We’ll use the exact same data generating process as described in some detail in the previous post. [Read More]

Analysing an open cohort stepped-wedge clustered trial with repeated individual binary outcomes

I am currently wrestling with how to analyze data from a stepped-wedge designed cluster randomized trial. A few factors make this analysis particularly interesting. First, we want to allow for the possibility that between-period site-level correlation will decrease (or decay) over time. Second, there is possibly additional clustering at the patient level since individual outcomes will be measured repeatedly over time. And third, given that these outcomes are binary, there are no obvious software tools that can handle generalized linear models with this particular variance structure we want to model. [Read More]