Reviews of another manuscript

After last night’s premature excitement about reviews being ready for my review of high-resolution reconstructions, today I received reviews of a different manuscript. It includes this:

4. The authors applied high-end modern statistics and gave full reference. However, their analyses may only be re-produced by using the same scripts in R. A re-calculation with a different statistics software package is not possible, either the respective analyses were not included or derivate variables were used. A focusing on simpler and wider distributed multivariate statistics would be appropriate.

I need to confess: most the analyses were done with a terribly obscure R package known as vegan. The manuscript uses the avant-garde methods redundancy analysis and canonical correspondence analysis which, I admit, are almost impossible to fit outside vegan unless one uses CANOCO, XLSTAT, or half a dozen other statistical programs or R packages.

It’s not much of a stretch to realise that few of the potential readers of the manuscript will have heard of Procrustes analysis, which we use next to compare our ordinations, but reflect on this, our code can be translated to a DOS program. PROTEST if you want, but don’t get into a twist.

Finally we use a co-correspondence analysis from the cocorresp  package to compare community patterns in two species groups. This is a less commonly used method, but downloading R and the package won’t bankrupt anybody (those not afraid of being bankrupted can run the analysis in MATLAB).

Had the reviewer complained that the co-correspondence analysis was redundant, I would not have objected. Had the reviewer explained that our analyses were inappropriate or sub-optimal, I would have paid attention. But this claim that our analyses can only be reproduced with R is both wrong (as shown above) and irrelevant as these packages can be freely downloaded, and the vague suggestion we use simpler methods is unhelpful.

UPDATE: CANOCO version 5 will run all the analyses used in the manuscript.




About richard telford

Ecologist with interests in quantitative methods and palaeoenvironments
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2 Responses to Reviews of another manuscript

  1. Words fail me, Richard. This ranks as one of the dumbest responses from a reviewer I have ever seen.

    Regarding cocorresp; I know the R code is reproducible and comparable with Andre Schaffers Matlab code because I ported the latter to R. I didn’t have easy access to Matlab so I used Octave to evaluate the Matlab scripts for most of the code and compare them with R and the outputs in the paper in Ecology. The results are repeatable to many decimal places between the two software packages. Now, there may be bugs or errors in the math, but if so those bugs are in both packages & reproducibly so!

    (You are free to quote me on this in your rebuttal, of course! And FYI CoCA is now in Canoco so one other option, also not free but not bankruptcy-level costs, for reproducing your results.)

  2. How truly bizarre! ‘Only reproduced …’ using a common, free, cross-platform, and high-end programming language? What a utterly and completely bonkers reviewer comment

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