Hi everyone,

I am working on my Master's thesis and need some advice on the statistical workflow for validating scoring methods (Visual assessment) for pathogens. I’ve designed an augmented RCBD (Randomized Complete Block Design) with standards to account for environmental effects and included a control to observe the pathogen effect on inoculated plants.

Each week, I visually assessed all plants (both control and inoculated) and assigned scores. Now I want to analyze the data using R, but I’m not sure about the best sequence of steps for data correction and analysis.

Two possible approaches I’ve considered are:

I’m leaning towards calculating the AUDPC first and then applying corrections using the standards, but I’m unsure if this is the most appropriate method.

What do you think? Which approach would make more sense? Or is there an alternative workflow I haven’t considered?

Any guidance or references would be greatly appreciated!

Thank you in advance!