box VS workflowr

As for organising code within a project, as mentioned packages really don’t allow this beyond collation order. The best solution in this space is the ‘box’ package which implements a fully-featured module system for R. ‘box’ notably gets used by some folks to implement large-scale Shiny applications; if this is what you’re after, I would recommend the ‘rhino’ framework, which builds upon Siny and ‘box’.

You can write amazing, clean, modular code with the box package.

I would look into box https://github.com/klmr/box if you haven’t heard of it already

Shapeless plug: check out the already mentioned ‘box’, I think it’s strictly superior to ‘import’ (but I’m biased).

By contrast, R code doesn’t need to change the working directory at all! Having to do so hides other flaws in the code. For instance, when trying to load code or data, use the tools provided by R. That is, write packages and use system.file or, when not writing packages, use ‘box’.

‘box’ fixes that.

I think your use-case is best addressed by the ‘targets’ package. But I would also recommend checking out the ‘box’ package for a more general way of structuring R projects in modules which isn’t supported well natively by R (disclaimer: I wrote that package). Writing R code as modules fundamentally side-steps the issue of having to deal with absolute paths. Instead, all code and data are either contained in the module or can be accessed relative to the working directory.

However, using ‘box’, as recommended in another comment, allows you to achieve the same effect with less (and cleaner) code, by declaring your imports locally with the box::use function.

If you're writing you're own code you can use packageName::functionName(), or the box package. Which is definitely useful on larger codebases.

I would start by saying "bioinformatics world" is a very broad term. Most of it does not involve managing multiple models, which is what MLflow seems to be for. Most work is cleaning the data and interpreting the results, which is highly project-specific. Something like workflowr is generally more appropriate, but even that is an overkill for most people.

Targets stores all your data serialised on disk, and only loads them in as needed by the dependencies. For a standardised folder structure, you can take inspiration from workflowr.