Miscellaneous improvements to the R package

[pcarbo]

@eweine I'm going to use this issue to suggest a few miscellaneous improvements to the package. Please update the issue when you have made the suggested changes by checking off the item and/or posting a reply. I will also update this list periodically.

• Update the description in DESCRIPTION to reflect our descriptions in the paper (e.g., I suggest introducing the terminology of "Poisson NMF with the shifted log link function").

• We discussed this, but I think you should remove the version numbers for the dependencies except when we have good reason not to include them, e.g., for Rcpp, I think.

• This seems like a strange default: fit_poisson_log1p_nmf_control_default()$threads = 7. I tend to think that a default of 1 is better. (Or set it automatically somehow using an environment variable or by detecting the number of available processors.)

[eweine]

@pcarbo regarding your third point, my default is:

threads = max(parallel::detectCores() - 1, 1)

So, presumably you are seeing 7 cores because you have 8 cores available.

[pcarbo]

I see… somehow that seems weird or unexpected to me, but let's leave it for now.

[eweine]

Sorry @pcarbo I think the current description does mention the shifted log-link?

Implements (approximate) maximum likelihood estimation of Poisson
    non-negative matrix factorization models with a shifted log link function.

[pcarbo]

Okay, good!