Are there examples of R packages changing dramatically between version such that the results of a statistical function were significantly different?

Im trying to understand how people use R packages and was wondering if there are documented cases where R packages have produced different answers.

Clarification: The motivation behind this question comes from an effort I’m involved in where the goal to understand the importance of provenance in the analytical methods and how it facilitates reproducible research. While R is big in the science community at present, and R packages are versioned in CRAN, without detailed information [especially version numbers], someone trying to reproduce a body of work in the future might come to a different conclusion that the original work (even with the original data).

Example: Paper by John Doe says “we used R 2.3.1 and package glmulti to fit our models”. 10 years from now, someone might use a new version of glmulti (no one knows what version was used in the original) which might produce a much different conclusion. My question: Are there examples of such a thing happening already? Version 2 or R package produces a much different result that version 1.

Answer

I’ve had issues with package glmnet over versions. If I remember well, it was going from version 1.5 to 1.6, but I may be off a little.

The package creators/maintainers changed the order of the classes of their objects (so it became c("lognet", "glmnet") instead of c("glmnet", "lognet") – or it may have been the other way around). Of course, they also changed all their S3 functions to properly handle this (e.g. predict.lognet).

The problem with this was: an object you had created with an old version of glmnet was not compatible with the new functions (since dispatching worked the other way around). Most people wouldn’t be in that spot (who saves a glmnet object for later use?), but I was.

Mind you: this is a very powerful package, developed by extremely intelligent people, so it could happen to anyone 🙂

Attribution
Source : Link , Question Author : Maiasaura , Answer Author : Nick Sabbe

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