Hello Folks, As some of my old code broke when an updated package changed its interface, I started thinking about reproduction of analyses. It's not good enough to save our code - we have to save the package versions those analyses used as well as the R-core. I saw a couple references to "reproduction archives" around, but nothing specific. Is there any good way to package up code along with the relevant packages and R version in order to guarantee that we can reproduce our results in the future? I suppose that one could make note of all package versions, etc, but automating the process would mean that it would be followed more often. (also, tracking down those packages and installing them all just to reproduce a result could be an undertaking). Thanks, Allie
On Sun, Jun 05, 2011 at 03:07:44PM -0500, Alexander Shenkin wrote:> Hello Folks, > > As some of my old code broke when an updated package changed its > interface, I started thinking about reproduction of analyses. It's not > good enough to save our code - we have to save the package versions > those analyses used as well as the R-core. I saw a couple references to > "reproduction archives" around, but nothing specific. Is there any good > way to package up code along with the relevant packages and R version in > order to guarantee that we can reproduce our results in the future? I > suppose that one could make note of all package versions, etc, but > automating the process would mean that it would be followed more often. > (also, tracking down those packages and installing them all just to > reproduce a result could be an undertaking).Hello Allie: Reproducibility of the results is an important question. Personally, i do not believe much to automated solutions, although i may be wrong. When i store a result of a simulation for future reference as an ".rda" file, then the script includes into it an object "identification", which contains seeds, a critical function used in the simulation and also a package and R version. The last two things may be obtained for example as R.version.string library(help=mvtnorm)[[3]][[1]][3] Up to now, i did not really needed these things, so i also do not know, whether they are sufficient. Petr Savicky.
On 11-06-05 4:07 PM, Alexander Shenkin wrote:> Hello Folks, > > As some of my old code broke when an updated package changed its > interface, I started thinking about reproduction of analyses. It's not > good enough to save our code - we have to save the package versions > those analyses used as well as the R-core. I saw a couple references to > "reproduction archives" around, but nothing specific. Is there any good > way to package up code along with the relevant packages and R version in > order to guarantee that we can reproduce our results in the future? I > suppose that one could make note of all package versions, etc, but > automating the process would mean that it would be followed more often. > (also, tracking down those packages and installing them all just to > reproduce a result could be an undertaking).If you get your packages from CRAN, you should be able to retrieve old versions indefinitely. The important thing is to know what version to ask for. But when you wrote up your report, you cited R (including its version) and each package with version, right? Duncan Murdoch> > Thanks, > Allie > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
On 5 June 2011 21:07, Alexander Shenkin <ashenkin at ufl.edu> wrote:> Hello Folks, > > As some of my old code broke when an updated package changed its > interface, I started thinking about reproduction of analyses. ?It's not > good enough to save our code - we have to save the package versions > those analyses used as well as the R-core. ?I saw a couple references to > "reproduction archives" around, but nothing specific. ?Is there any good > way to package up code along with the relevant packages and R version in > order to guarantee that we can reproduce our results in the future? ?I > suppose that one could make note of all package versions, etc, butsessionInfo() is your friend here. And when included in a Sweave report, toLatex(sessionInfo()) will itemize the output. Hope this helps, Laurent> automating the process would mean that it would be followed more often. > (also, tracking down those packages and installing them all just to > reproduce a result could be an undertaking). > > Thanks, > Allie > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >