Peer-reviewed R packages?

November 22, 2012
By

(This article was first published on Rmazing, and kindly contributed to R-bloggers)

Dear R-Users,

a question: I am the author of the ‘qpcR’ package. Within this, there is a function ‘propagate’ that does error propagation based on Monte Carlo Simulation, permutation-based confidence intervals and Taylor expansion. For the latter I recently implemented a second-order Taylor expansion term that can correct for nonlinearity. The formulas are quite complex and I had quite a hard time to transform the second-order term that has covariance included into a matrix form. The first order expansion can be represented by GRAD * SIGMA * t(GRAD) with GRAD being the gradient matrix and SIGMA the covariance matrix. The second order term is 0.5 * trace(HESS * SIGMA * HESS * SIGMA) with HESS being the Hessian matrix of partial second derivatives.
So here the problem: Being a molecular biologist, my statistical skills have limitations. I am pretty sure my implementation is right (I checked the examples in GUM “Guide to the evaluation of uncertainties in experiments” and got the same results). BUT: Being sure says nothing. It could well be that I’m on the wrong track and people use a function that gives essentially wrong (maybe slightly wrong which may still be fatal…) results because they rely on me doing things right.
Now let’s suppose I’m not the only one with a queer feeling when submitting packages to CRAN in the hope that everything I did is right.
Which brings me to the question: What are the merits of a peer-review system for R packages? I would suppose (if the paradigm is right that peer-reviewing DOES increase quality…) that if packages were independently peer-reviewed in a way that a handful of other people inspect the code and check for detrimental bugs that are enigmatic to the packages author, then this would significantly increase the credibility of the packages functions.
Now I know that there is the “R Journal” or the “Journal of Statistical Software” that regularly publish papers where new R packages are explained in detail. However, they are restricted to the statistical background of the implementations and I’m not sure if the lines of code are actually checked.
An idea would be that such a review system is voluntary, but if a package has been reviewed and declared as “passed”, then this would be some sort of quality criterion. For scientists like me that need to write grant applications, this would give more impact on the work one has dedicated into developing a “good” package that could maybe be cited as being “peer-reviewed”.

Pros:
* increase of quality
* maybe citable
* beneficial for grant applications or C.V.

Cons:
* reviewers must meticulously inspect the code
* longer time to CRAN submission
* no platform yet to publish the reviews which can be cited like a journal

Comments welcome!

Cheers,
Andrej


Filed under: General Tagged: packages, peer-review

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