Materials and methods in thesis

Question

[Amr]

What should be written in materials and methods in thesis ?

If I am performing analysis of samples on R, what should I write in materials and methods? for example, should I write what R packages I used ? or no ? should I only mention R software without mentioning what packages and libraries I used or I should mention the packages names?

Thanks

[Pierre Lindenbaum]

you should put everything that is needed to reproduce the analysis: R, packages, versions, etc... A minimum would be to put your code on gihtub/gitlab/zenodo.

[Amr]

Excuse me, I don't understand well, you mean for example if I use filter command from dplyr package, should I mention filter(bla bla bla ) or to mention that I used dplyr package only?

Second question : I should not mention any results or outcomes in materials and methods part, right?

Thanks

[Pierre Lindenbaum]

if I use filter command from dplyr package, should I mention filter(bla bla bla )

... data where filtered with R( version) using the dplyr (version) package. All scripts are available on github (url / release).

[Amr]

Thanks a lot

[Trivas]

For a thesis, talk to your advisor about including your code as an appendix. But Pierre is absolutely correct and what I'd minimally expect to see in a methods section of a paper.

Answer 1

[Mensur Dlakic]

I don't think it matters much what most of us think, because we are not on your committee, and most likely at your institution either. It is not surprising that people are taking time to offer their advice, but you will not defend in front of any of us. The very first advice you got - everything that is needed to reproduce the analysis - is probably universally applicable to any piece of academic writing.

Your thesis advisor and committee members presumable have some thoughts on how to handle this chapter. Also, I assume others at your institution have written on a similar subject, and their theses or dissertations are usually publicly available.