# What I look for in 'Software Papers'

## pet peeves and faux pas

Update Thanks to the rich discussion in the comments and beyond, I’ve revised my thoughts on this somewhat, as I discuss in this more recent post.

I am more and more frequently reviewing ‘software papers:’ which I define as publications whose primary purpose is to publicize a piece of scientific software and provide a traditional research product with hopes that it will receive citations and recognition from other researchers in grant and job reviews. To me this feels very much like hacking the publication recognition system rather than the ideal way to recognize and track the role of software in research communities, but a very practical one in the current climate. I have written two myself, so I have been on both ends of this issue. In this post, I share what I look for in such papers and what omissions I see most frequently.

## Reviewing software

If we are going to employ this hack of the publication system for software, we should at least use it to maximal advantage. As a reviewer, I feel that means reviewing not just the submitted manuscript but the software itself. If we can agree on nothing else, we as a community should at least be able to say:

my review of a software paper is a review of the software

I assume most other authors, reviewers and editors on this content share this implicit assumption, but I’d love to hear first hand from anyone else. For instance: as an editor, what would you do if your reviewers only commented on the paper directly and not on the software distributed?

We are not really taught to review software, any more than we are taught to write it in the first place. Most journals offer little guidance on this (though see the Journal of Open Research Software guidelines for peer review of software, all though they are still rather minimal.) In the absence of a culture on software reviewing, I thought I would lay out my own perspective with the hope of hearing feedback and push back from others. Perhaps through such dialogs we can develop clearer expectations for this rapidly expanding genre.

## Reviewing the software paper

I don’t include “to document” the software as a purpose, since none do so very comprehensively, and besides, documentation belongs in the software, not in a journal. “Publicize” usually includes some motivating examples that could convince many readers that the software does something useful for them without too much effort. As such, I expect the paper to:

• provide the journal’s audience with a clear motivation for why the package is useful, * and have at least one functioning “wow” example that I can run (by copy-paste) and understand without difficulty (e.g. without referring to code comments or the package manual to understand the function calls and their arguments).

This is an intentionally low bar that I hope helps promote these kinds of contributions. Despite this, papers frequently fail the copy-paste test or the plain text explanations of the function calls. Come on people. Meanwhile, I try to focus the rest of my review on the software itself.

## My partial list of criteria

As I am almost always reviewing R packages, the software already meets some very basic standards required by submission to CRAN: dependencies and license stated, built-in documentation, passing some minimal automatic checks, etc. (See the CRAN Policies and the Writing R Extensions Manual for details). This is great, as it clears the first few hurdles of installation, etc. without much fuss, but still provides a bar that is by itself unacceptably low for published scientific software. Here is a list of the things I see that most often frustrate me. This isn’t intended as a style-guide or a comprehensive list of best practices, just my own pet peeves. I have somewhat tongue-in-cheek labeled them by severity of the review I might give; which like any other use of these terms is more of a measure of how annoyed I am then anything else. Critiques and suggestions welcome.

### Edit:

The comments from other reviewers, authors, and editors have been fantastic, thank you all. I particularly appreciate the opportunity to have reviewing styles critiqued, something that does not happen in normal peer review.

Just a note on my headings here. I do not see any of these things as “gatekeeping requirements” and have intentionally omitted the option of “Reject”. I would reject such a paper for methodological flaws, etc., but not for any of the reasons on my list below. The list is intended only to improve, not prevent, software publication.

I believe any of the decisions below typically result in a revision to the same journal, that authors judiciously choose how to respond to reviewer comments guided by the editor’s own feedback, and that it is ultimately the editor’s decision whether any of this is relevant. </edit>

## “Reject and resubmit”

### Automatic tests

A scientific R package must must must have some automated tests that are run by R CMD check. Even if further development of the package doesn’t break anything (most likely only if further development doesn’t happen), changes to the package dependencies could still break things, and so it is crucial to have a mechanism in place to detect these problems when they arise. For code that runs quickly, the simplest way to do this is through the examples in the documentation. I don’t expect all scientific software to have a complete test suite with 100% coverage covering all the weird things that can happen if a user passes in a matrix when the function expects a data frame or has some unanticipated missing values, etc. Just some tests to make sure the basic examples execute and I’ll be happy. Longer running functions or those that need calls to external web resources shouldn’t be run in the examples (too much of a burden for CRAN’s automatic testing) so they should be marked dontrun and put in a separate test suite or vignette as it says in the manual.

### Passing optional arguments

I see authors write functions like this all the time:

f <- myfunction(f, p){
#  stuff
o <- optim(f, p)
#  stuff
}

calling an existing library function like optim that has a whole host of very useful optional arguments that have a significant impact on how the algorithm functions. Whenever you a rich function like optim, please have the courtesy to make it’s arguments available to future users and developers through your function call. Yes, most users will just want the default arguments, (or your default arguments, if different), and that can be handled just fine by providing default values as optional arguments. R has a fantastic mechanism for this exact issue: the ... argument. The above code could be fixed simply by using:

f <- myfunction(f, p, ...){
#  stuff
o <- optim(f, p, ...)
#  stuff
}

which works just they way you think it would. If you have more than one such function (ask yourself if you can write shorter functions first and then) pass optional arguments as lists,

f <- myfunction(f, p, optim_options, fn2_options){
# stuff
o <- do.call(optim, as.list(c(f, p, optim_options)))
# stuff
b <- do.call(fn2, fn2_options)
# stuff
}

arguments can also be extracted with list(...)\$arg1 etc.

A converse of this issue is not providing default arguments where it might be natural to do so. This does not bother me so much, as it is probably useful to force the user to think how many iterations n are appropriate for their problem rather than just assuming that 100 is good because it is the default. The only time this case is annoying is when the argument will not be changing – such as a user’s authentication token to access a web resource. Don’t make me manually pass the token to every function in the library please.

### Development site and bug tracker

I would really like to see a link to the software development page, such as r-forge or Github. The primary asset in this context is pointing reviewers to an address with a bug tracking system where issues can be assigned ticket numbers and readers can transparently see if a package is being actively maintained. A reader who comes across the paper years later who has only an email address that may or may not work has little way to determine what the latest version of the code is, whether it is actively maintained, or whether earlier versions that may have been in used in previous publications suffered from any significant bugs.

We write software papers with the sometimes vain hope that they will be cited by users, so authors of such papers should at least follow these best practices themselves. R includes a native mechanism for providing citations to packages, citation(packagename), including the information for any software paper published along with it. Be sure to add your own software papers to the CITATION file. More information can be found in my post on Citing R packages.

## “Major Revisions”

These are other things that commonly frustrate me, but fall on a bit more of a continuum of style rather than gross oversights. As such I’m not sure that any one of these things would justify rejection.

### Functionalize the code

Style guides will tell you to keep functions short, not more than a screen or 20 lines. Breaking large functions into a series of smaller functions and documenting those smaller functions – even if they are only used internally – is a great help to a reviewer trying to understand what a function is supposed to do and also test that it does what it says. Anyone building the code base later (most often yourself) will appreciate the reusable modules.

### Stable, clean, and complete return objects

An extension of providing optional arguments to functions is to also provide access to all of their return information. To extend the example from wrapping optim, this would involve returning the convergence information. Using object classes and helper functions for return objects helps keep code stable and lets users leverage existing code for similar objects, such as fitting or plotting routines. More discussion on this topic based on my own experiences in the post, we need more object oriented design in comparative methods