Model diagrams and equations, straight from the code

Watch on YouTube Many pharmacometric reports have the same two items near the top of the methods section: a compartment diagram of the final model and the equations that define it. They are also two of the easiest things to get wrong. The diagram is usually drawn by hand in PowerPoint or Visio early in the analysis. The equations are typed into Word or LaTeX from the control stream. Then the model changes – a transit compartment is added, the effect goes from stimulation to inhibition, a covariate moves – and the code is updated but the figure and the math are not.

Adaptive dosing in rxode2

Watch on YouTube In the past, every rxode2 simulation started the same way: you coded down the doses first, and then you solved. The event table is fixed before the solver takes its first step. That is fine for a fixed schedule. It is not fine clinical adaptive dosing. Real protocols have clinical endpoints decide: hold this cycle, cut the dose one level, start the rescue infusion, draw an extra sample.

nlmixr2 7.0’s covariance step, all grown up

Watch on YouTube In the 7.0 post, I talked mostly about parallel solving in focei. This time I want to talk about a feature that has been requested frequently: a full covariance step, and other refinements to the covariance steps. Two things changed there, and they are related: Nearly any covariance method can now be requested from nearly any estimation method, and you can switch a finished fit to a different one without refitting.

nlmixr2 7.0

Watch on YouTube nlmixr2 7.0 This is the release where focei finally solves in parallel on all OpenMP-enabled platforms. Along with that, a few defaults changed, which means that by default focei will not give you the same numbers it gave you in nlmixr2 6. This is a deliberate change and we will talk about the motivation in this post (and how to get the old behavior back if you need it).

Fitting PK/PD models to published data with admixr2

Usually, pharmacometric modelling starts with a dataset with individual patient data: one row per observation, in a software-ready format. To model these data, you would first need to get access to the data, which means data-sharing agreements, trial access, or in-house studies. This process is often slow or even not possible due to privacy or competition. However, researchers do publish their model and sometimes summary metrics. The published reports do contain useful information.