Software paper: Summary

[ms609]

re. openjournals/joss-reviews/issues/6722

• [x] The summary paragraph at present feels overly general. The opening paragraphs on the role of simulations in interrogating evolution and methods are effective – though I wonder whether it might be justified to draw a tighter focus, and assume that the reader already has some concept that simulations may in general be useful?

simulations can create a known phylogenetic tree alongside associated character data, and therefore play a powerful role in assessing the adequacy of approaches for inferring trees from character data

• [x] This sentence sounds like it is just one more thing that simulations in general can do, rather than one of the distinctive features of TrevoSim.

• [x] It's not immediately obvious what "individual-based" means in the context of line 25. Something akin to "Trevosim simulates reproducing individuals in order to create a known phylogenetic tree alongside character data, which can be a useful tool when..." might combine these two points to give a reader a clearer immediate picture of the motivation of TREvoSim.

• [x] The final sentence of the Summary paragraph is a little hard to decipher; I think it means "whereas previously TREvosim could only be used to study phylo methods, now it can also help study processes"; it's not clear whether the new features also help to better test phylogenetic methods.

• [x] It would be useful if the summary could summarize what features are introduced in this release - tricky, I appreciate, as there are a fair number and few words available. But I can imagine a future researcher using v7 of the software wanting to see which release introduced feature X – it would be helpful if the abstract gave some indication as to the specifics of the new additions.

[RussellGarwood]

With the above commits I have rewriten the abstract/summary with these changes in mind. I did find it quite challenging but I hope I have addressed these points without expanding the summary too much by doing the following:

• I have reduced the amount of general information regarding simulations in the abstract, and more specifically tied one of the examples highlighted to TREvoSim, reordering the sentences to achieve this
• I incorporated a brief description of what an individual based model is in the abstract, however, I also elected to keep individual-based in, and added agent-based as well, given that these are specific terms used in ecology / digital evolution communities that might appreciate this software
• I've provided, I hope, clarity on the nature of the new additions and how they might be helpful, whilst keeping additional words to a minimum.

[ms609]

Looks great – you accomplish a lot with few words!

I had to read one sentence twice to understand that the "inference methods used" are not used by TREvoSim; perhaps removing 'the' from 'allowing assessment of the inference methods used' would clarify this?

[RussellGarwood]

Thanks - tried to clarify with above push!