Review request: Petchey, Plebani, Pennekamp

[opetchey]

Dear @ReScience/editors,

I request a review for the reproduction of the following paper:

• Benincà, E., Huisman, J., Heerkloss, R., Jöhnk, K.D., Branco, P., Van Nes, E.H., Scheffer, M. & Ellner, S.P. (2008) Chaos in a long-term experiment with a plankton community. Nature, 451, 822–825.

  I believed the original results have been adequately reproduced as explained in the accompanying article.

  The repository lives at https://github.com/opetchey/ReScience-submission/tree/petchey-plebani-pennekamp-2016

Best wishes
Owen Petchey

---

EDITOR

• Editor acknowledgment (@tpoisot) Feb 23, 2016
• Reviewer 1 (@yoavram) March 3, 2016
• Reviewer 2 (@FedericoV) March 3, 2016
• Review 1 decision [accept] April 5, 2016
• Review 2 decision [accept] April 13, 2016
• Editor decision [accept] April 13, 2016

[opetchey]

@yoavram please can you send me an image of your workspace after all the code is run?
And also what appears in the console if you run type.convert. E.g., I get:

> type.convert
function (x, na.strings = "NA", as.is = FALSE, dec = ".", numerals = c("allow.loss", 
    "warn.loss", "no.loss")) 
.External2(C_typeconvert, x, na.strings, as.is, dec, match.arg(numerals))
<bytecode: 0x7fa355108d40>
<environment: namespace:utils>

[yoavram]

Sure! I get what you get, I think:

> type.convert
function (x, na.strings = "NA", as.is = FALSE, dec = ".", numerals = c("allow.loss", 
    "warn.loss", "no.loss")) 
.External2(C_typeconvert, x, na.strings, as.is, dec, match.arg(numerals))
<bytecode: 0x000000001be04680>
<environment: namespace:utils>

See attached zipped RData file

opetchey.zip

[opetchey]

Yes, I still don't know why we're getting different results. But something to do with treatment of character variables.
In any case, I attempted a further improvement... see commit 860500c

[yoavram]

REVIEWER 1

As far as I'm concerned and following what @tpoisot wrote above (31 Marh 2016) this is a minor issue. I believe the ms can be accepted.

[FedericoV]

I've been very busy but I will be able to handle this tomorrow. Will
update and reproduce all the steps.

On Mon, 4 Apr 2016 at 21:59 Yoav Ram notifications@github.com wrote:

REVIEWER 1

As far as I'm concerned and following what @tpoisot
https://github.com/tpoisot wrote above (31 Marh 2016) this is a minor
issue. I believe the ms can be accepted.

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#15 (comment)

[opetchey]

@FedericoV Thanks. Please be sure to use the latest commit.

[FedericoV]

The last commit reproduces beautifully. The report is also very well done - I don't use R at all, but I could follow almost all the steps/code.

I am satisfied with the paper in its current form. The only minor comments I have is that I would be curious to know how come the results for the Lyapunov coefficients was slightly different, and the exact procedure through which the zeros were removed.

Also - another comment. Is it possible to have within-document links? For example, when you talk about (red line in Fig. S1b) it would be handy to have a link that brought you to the relevant figure immediately.

[tpoisot]

@FedericoV noted -- I think if @opetchey et al. have an idea, it can go in the ms. If not, since the differences are not really big, we can leave with this and move on to the next step.

As for the within-document links: maybe using \autoref in latex would work. But it can be fixed after we made the first decision.

[FedericoV]

Agreed completely.

On Tue, 5 Apr 2016 at 19:54 Timothée Poisot notifications@github.com
wrote:

@FedericoV https://github.com/FedericoV noted -- I think if @opetchey
https://github.com/opetchey et al. have an idea, it can go in the ms.
If not, since the differences are not really big, we can leave with this
and move on to the next step.

As for the within-document links: maybe using \autoref in latex would
work. But it can be fixed after we made the first decision.

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#15 (comment)

[FedericoV]

@tpoisot I edited my first post here suggesting we accept this reproduction. It's very well done, the code is very readable. My suggestions are very minor and the reproduction is more than acceptable in its current form.

[tpoisot]

EDITOR

Accepted, April 13, 2016. Congratulations @opetchey et al. and thanks to @FedericoV and @yoavram

@rougier , what is the next step?

[opetchey]

Excellent! Many thanks!

[rougier]

@tpoisot

Next step is the actual publication but the procedure is not really smooth yet. If you have some time to try it and tell what's not clear (new issue) that woudl be great ! Else I can do it.

The procedure is described at http://rescience.github.io/edit/ (see editing process). But mostly the goal is to freeze the repo (no more commit or only for obvious error), import it in the ReScience Archives (that will be the official repo) and modify the article such as to add editor/reviewers, change code/data repo links, set the volume (2) issue (1)

Once this done, you have to upload the archive to Zenodo (as journal article) and fill the the different fields (don't forget to add the editor field and volume/issue) and the link provided on the page above should make your upload part of the ReScience collection on Zenodo.

Last is to tell the original journal a replication has been published confirming the result, but I can do it.

[opetchey]

@tpoisot @rougier please let me know if I can or should help with any of these next steps.

[rougier]

Nothing is required from you right now. But on the other hand, you can join the board as reviewer if you're interested. Just let me know.

[rougier]

@tpoisot Do you want to handle the actual publication ?

[rougier]

I'll handle it.

[rougier]

@opetchey Can you give me the associated keywords ?

[tpoisot]

Yes, sorry about the delay -- was about to leave for a trip but a snow
storm happened...

Le jeu 21 avr 2016 à 5:31, Nicolas P. Rougier
notifications@github.com a écrit :

@opetchey Can you give me the associated keywords ?

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[rougier]

No problem. Does that mean you can handle the publication ?

[tpoisot]

I'd rather let you do it if you can, I'll be sure to look at what the
different steps are.

Le jeu 21 avr 2016 à 11:29, Nicolas P. Rougier
notifications@github.com a écrit :

No problem. Does that mean you can handle the publication ?

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[opetchey]

@rougier Yes, no problem. Keywords:
Ecology
Forecasting
Prediction
Chaos
Nonlinear dynamics
Plankton community
Species interactions

[rougier]

This submission has been accepted for publication, and has been published and will soon appear at
http://rescience.github.io/read/