From the initial conversation on twitter: https://twitter.com/LoganCorina/status/872833978495115264
@gmbecker: Depending on what you mean, ensuring/enforcing that manuscripts are actually reproducible is really hard in general case. I know about dynamic docs. (subject of my thesis, in fact), but an Rmd/Rnw isn't reproducible by itself, see http://biostats.bepress.com/bioconductor/paper2/ โฆ
Red files don't include data and the exact versions of packages used by original authors, so while u have code, u may not be able to run it.
@chartgerink: well if data are publicly available you can download the data based on a doi so you can ensure provenance and replicate with just rmd.
@lgatto: Yes, if... but the Rmd as such doesn't guarantee it. As it doesn't guarantee that the required software is available. But Rmd + good practice goes a long way to enable reasonable repro in many cases, I think. I am testing submission and handling Rmds with @F1000Research (should submit in a couple of weeks). Will let you know.
@chartgerink: I am amazed with Rmd and the HTMLs it turns out, I can imagine building on that would provide a good way to start. Using Rnotebooks would be even better (show/hide code user). Implement plugins (pubpeer,hypothesis). Easy to include notice of dependencies in manuscript (what I do now already; e.g. last page http://bit.ly/2s8zMlD). absolute direct reproducibility not feasible (nor doable), what we need to know is limits of. With Rmd (example) we can do much. my thoughts on this: automate version testing, determine dependencies upon sharing, look at other versions producing same or diff result. subsequently, we can produce crosstable that actually indicates when results differ from the original. How they differ is something dif.