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Review Request: T. Poisot #39

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tpoisot commented Oct 18, 2017

AUTHOR

Dear @ReScience/editors,

I request a review for the following replication:

Original article

Title: On the coexistence of specialists and generalists
Author(s): David Sloan Wilson and Jin Yoshimura
Journal (or Conference): The American Naturalist
Year: 1994
DOI: 10.1086/285702
PDF: http://www.journals.uchicago.edu/doi/abs/10.1086/285702

Replication

Author(s): Timothée Poisot
Repository: https://github.com/PoisotLab/ReScience-submission
PDF: https://github.com/PoisotLab/ReScience-submission/blob/poisot-2017/article/Poisot-2017.pdf
Keywords: community ecology, specialist, generalist, coexistence, discrete time model
Language: Julia v0.6
Domain: Ecology

Results

  • Article has been fully replicated
  • Article has been partially replicated
  • Article has not been replicated

Potential reviewers


EDITOR

  • Editor acknowledgment
  • Reviewer 1 (@pboesu, assigned on 2017/10/27)
  • Reviewer 2 (@ElOceanografo , assigned on 2018/03/13)
  • Review 1 decision [accept/reject]
  • Review 2 decision [accept/reject]
  • Editor decision [accept/reject]

@tpoisot tpoisot requested a review from karthik Oct 18, 2017

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rougier Oct 18, 2017

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

🎉 First submission in Julia

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rougier commented Oct 18, 2017

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

🎉 First submission in Julia

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rougier Oct 20, 2017

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@karthik Can you edit this submission ?

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rougier commented Oct 20, 2017

@karthik Can you edit this submission ?

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karthik Oct 24, 2017

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

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karthik commented Oct 24, 2017

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

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karthik Oct 26, 2017

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

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karthik commented Oct 26, 2017

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

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pboesu Oct 27, 2017

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Looking forward to reviewing this submission!

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pboesu commented Oct 27, 2017

Looking forward to reviewing this submission!

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rougier Nov 2, 2017

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@karthik Any progress on 2nd reviewer ?

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rougier commented Nov 2, 2017

@karthik Any progress on 2nd reviewer ?

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karthik Nov 2, 2017

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

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karthik commented Nov 2, 2017

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

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pboesu Nov 2, 2017

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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 .

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pboesu commented Nov 2, 2017

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 .

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tpoisot Apr 9, 2018

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.

tpoisot commented Apr 9, 2018

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.

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rougier Apr 23, 2018

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

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rougier commented Apr 23, 2018

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

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rougier May 2, 2018

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@karthik @tpoisot Any update?

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rougier commented May 2, 2018

@karthik @tpoisot Any update?

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karthik May 3, 2018

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@rougier Still waiting to hear from Tim.

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karthik commented May 3, 2018

@rougier Still waiting to hear from Tim.

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tpoisot May 4, 2018

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

tpoisot commented May 4, 2018

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

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tpoisot May 8, 2018

🎉 finally managed to update the PDF

tpoisot commented May 8, 2018

🎉 finally managed to update the PDF

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rougier Jun 9, 2018

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

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rougier commented Jun 9, 2018

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

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pboesu Jun 11, 2018

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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.

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pboesu commented Jun 11, 2018

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.

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ElOceanografo Jun 11, 2018

I am also happy with the changes and recommend acceptance.

ElOceanografo commented Jun 11, 2018

I am also happy with the changes and recommend acceptance.

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rougier commented Jun 19, 2018

@karthik ping!

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rougier Jul 6, 2018

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@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.

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rougier commented Jul 6, 2018

@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.

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khinsen Jul 6, 2018

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

khinsen commented Jul 6, 2018

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

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karthik Jul 6, 2018

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

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karthik commented Jul 6, 2018

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

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karthik Jul 7, 2018

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@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?

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karthik commented Jul 7, 2018

@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?

@ReScience ReScience locked as resolved and limited conversation to collaborators Jul 7, 2018

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tpoisot Jul 9, 2018

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

tpoisot commented Jul 9, 2018

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

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rougier Jul 31, 2018

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Just a gentle reminder for @karthik.

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rougier commented Jul 31, 2018

Just a gentle reminder for @karthik.

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karthik Aug 10, 2018

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

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karthik commented Aug 10, 2018

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

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karthik Aug 14, 2018

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

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karthik commented Aug 14, 2018

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

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rougier Aug 20, 2018

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@karthik Done (I've invited you)

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rougier commented Aug 20, 2018

@karthik Done (I've invited you)

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karthik Aug 22, 2018

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

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karthik commented Aug 22, 2018

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

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karthik Aug 23, 2018

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@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.

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karthik commented Aug 23, 2018

@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.

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karthik Aug 23, 2018

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Congrats @tpoisot! Your paper has been published.

DOI

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karthik commented Aug 23, 2018

Congrats @tpoisot! Your paper has been published.

DOI

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