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.