@tpoisot Thanks for your submission. An editor will soon be assigned.
@karthik Can you edit this sumbission ?

🎉 First submission in Julia

@karthik Can you edit this submission ?

@rougier Yes, I'm happy to edit this.

👋 I've contacted both reviewers. Will update thread when I have a response and when the reviews begin.

Looking forward to reviewing this submission!

@karthik Any progress on 2nd reviewer ?

@rougier Just sent a second reminder yesterday. Will start lining up others

Hi @tpoisot and @karthik

This is a very nice and compact replication of the original article by Wilson and Yoshimura. The paper is clear, concise, and well written. The accompanying code is clear and well annotated. Most of the results from the original work are fully replicated (@tpoisot chose not to reproduce specific stochastic model runs presented by the original authors, which is fine as far as I'm concerned).

I only have some relatively minor suggestions, none of which are critical to the substance of the reproduction. Otherwise this is an accept pending minor revisions from my side.

1. Random seeds: I'd love to get input on this from the author and editor(s), but I was wondering whether in the pursuit of full reproducibility it would be preferable to always use explicit RNG seeds for the stochastic simulations?
   As is, the code will reproduce almost, but not quite identical figures every time the manuscript is reproduced from scratch.

2. Figure captions: The author clearly explains plotting symbols in the text, but the figure captions themselves are rather too terse. I'm a big fan of "stand-alone" figure captions, and would prefer if the plotting symbols were explained in the figure captions.

3. Figure 3 axis labels: I personally find the format of the axis tick labels (fractional powers of 10) in Figure 3 unintuitive, and would prefer the use of integers as in Fig. 4 of the original study.

4. Figure 4 z axis label: The z axis in Figure 4 is missing a label.

5. Figure and Table cross references: Possibly an issue with templates in the markdown to PDF toolchain for ReScience, but figure and table cross references lack a label. E.g. https://github.com/PoisotLab/ReScience-submission/blame/poisot-2017/article/Poisot-2017.md#L151 prints as 'All default parameter values are given in 1.' rather than 'All default parameter values are given in Table 1.'

6. I believe the reference for Pielou's evenness index J' is incorrect. The cited paper discusses the uses and misuses of the Shannon-Weaver diversity index, and makes no mention of evenness. The earliest derivation of J' I could find (in an non-exhaustive search) is in Pielou 1966 J Theor Biol 10:370-383 https://doi.org/10.1016/0022-5193(66)90133-0 .

I have modified the text to answer @ElOceanografo comments. I have been unable to build the PDF on my laptop, but I can give it a try when I regain access to my desktop.

Sorry for the delay. Any progress with the manuscript build, do you need some help?

@karthik @tpoisot Any update?

@rougier Still waiting to hear from Tim.

@karthik @rougier will try to update this week, but I'm away teaching

🎉 finally managed to update the PDF

@karthik @pboesu @dmcglinn @ElOceanografo Can we make a decision about this submission?

Apologies for not being more explicit about this following my initial review. @tpoisot addressed all my comments in 4989845 / #39 (comment) so I am more than happy to recommend acceptance.

I am also happy with the changes and recommend acceptance.

@karthik ping!

@khinsen Could you handle the end of the edition process. The paper has been accepted by both reviewers and only need the publication. If not, I could do it but I've another one to do.

Sorry, I cannot do it before July 26, when I will be back from vacation.

Apologies again @rougier Back in town now and happy to proceed with acceptance.

@tpoisot I'm happy to finally accept your paper after all these delays. There are several steps (mostly at my end) to complete this. First, can you please provide some keywords for publication?

Sure! Do you want more than the ones in the first message (community ecology, specialist, generalist, coexistence, discrete time model) ?

Just a gentle reminder for @karthik.

Hi @tpoisot No worries, the ones you have are sufficient. Bear with me as I work through the remaining steps.

@rougier Can you please give me access to Rescience Archives?

@karthik Done (I've invited you)

Hi @tpoisot Once you ok this PR (ReScience-Archives/Poisot-2018#1) I will be able to proceed with next steps. 🙏

@tpoisot Thank you! Here is the article pdf with all the metadata. I'm about to archive in Zenodo and post to the journal shortly.

Congrats @tpoisot! Your paper has been published.