additional documentation about graphsim HOT 11 CLOSED

Version 1.0.1 has been pushed to CRAN so I think we can close this one.

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I think this is a good idea if CRAN will allow it. The TGF-Beta/Smad pathway was selected for the manuscript because should be a manageable to size to run examples (although the runtime will be longer than the test examples).

Would a vignette using the biological networks be helpful? I have tried pre-generating figures for vignettes in HTML but CRAN has a limit on package size of 5MB which makes this difficult.

I'll review the examples in the documentation and see if it can pass CRAN checks.

from graphsim.

It would make a lot of sense to use these examples in a vignette, especially if there's no room to use them in the examples.

By the way, the existing vignettes rely on the animation package (among others), though the package itself does not; so it would be helpful to mention, with the installation instructions, that these packages must be installed in order to build the vignettes when installing graphsim:

remotes::install_github("TomKellyGenetics/graphsim", build_vignettes = TRUE)

from graphsim.

Thanks I'll come back to the examples once the vignettes are update as per #11 and #13.

By the way, the existing vignettes rely on the animation package (among others), though the package itself does not; so it would be helpful to mention, with the installation instructions, that these packages must be installed in order to build the vignettes when installing graphsim

I'll bear this in mind. I may consider removing additional dependencies for the vignettes that aren't strictly needed. I think gplots for "heatmap.2" may fall into this category (looking into it this should really be under Suggests: in this case).

from graphsim.

Dependency on the animation package has been removed. Examples with empirical data are given in the vignettes. I'll relevant examples like this to the documentation #' @usage section if CRAN allows larger computations.

from graphsim.

The documentation is much improved in the current version! Again i have a couple of suggestions, but these need not be met for me to recommend acceptance of the paper.

• While several objects (including functions) include links to related objects in their descriptions, others (for example, the make_distance_*() functions) don't include links to other documentation. Two roxygen2 fields that help cross-reference related objects are @seealso and @family.
• The package itself does not have a documentation page that can be accessed by help(graphsim-package) or just help(graphsim). This isn't strictly necessary, but i find it very helpful. For an example, see the package documentation for igraph—which is unusually long (in my experience) but showcases the kinds of elements that often make up such a page.

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Thanks, I had some trouble with links recently actually (see 5bf900f). There has been some updates to CRAN checks (as discussed here: r-lib/roxygen2#707). Co-incidentally, this was caused by linking to the help(igraph-package) because you now have to link to the file name: aaa-igraph-package.

I hadn't considered doing a "help" page for the overall package but I agree this may be helpful to describe the different functions. I'm planning to release a minor update to CRAN soon anyway so I look into including these suggestions (#6) or (#11) for that. This would also update citation information if the paper is accepted.

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This is a work-in-progress (on dev branch). I'll try to have a help(graphsim-package) page ready for the next release but I may not have time to go into details, yet. I'm in conferences most of this week and taking the following week off (#14 needs to be addressed by then).

from graphsim.

These are good suggestions though, thanks @corybrunson. Since it is not clear how the functions relate to each other I think the help(graphsim-package) (and vignettes) are helpful for users.

from graphsim.

I think this is addressed by graphsim-package.R for a help(graphsim-package) call. I will try to get the vignettes compatible with CRAN checks and bundle this into a minor release in a few days.

from graphsim.

Fine by me! Kudos.

from graphsim.