As a researcher at a non-academic institute I cannot use Code Ocean to run the code. Instead, I created a project in Rstudio using the Posit workbench and downloaded everything needed using git.

I am not familiar with Code Ocean, but very familiar with R.

Nothing else needed to install.

Rstudio

A project file needed to be created in the /code folder otherwise the 'here' statements did not work. After that most of the code worked except for this part:

{r render_appendix, include=FALSE} render_appendix("supplementary_information.Rmd") the Papaya::render_appendix is no longer supported. Quite a few changes needed to be made to get everything running smoothly again;

At the top of the .Rmd file the output statement has to change to:

output : pdf_document

The render_apendix statement was adjusted as follows:

References

\newpage

Appendix A

```{r appendix : "supplementary_information.Rmd"}

```

However, even though this produces all information needed, nicely in one paper, the original paper has the appendix in a separate document.

Figures and the main text of the paper were produced without problems and look the same as the original paper.

Try to make the project reproducible also without Code Ocean, perhaps also provide a Docker container.

Nicely documented, perhaps include a line in the Readme file that if you download the project, you need to put the project file in the /code folder instead of the main folder.

I have not read in detail but it looks alright

all code is there publicly available, as well as the data and the paper

Provide a Docker container as well or try to improve the project in such a way that you can also download it and reproduce it in R/Rstudio.

Thanks, it was a nice learning experience for me :)