Joss-reviews: [PRE REVIEW]: fgivenx: a python package for functional posterior plotting

[whedon]

Submitting author: @williamjameshandley (Will Handley)
Repository: https://github.com/williamjameshandley/fgivenx
Version: v2.1.0
Editor: @arfon
Reviewers: @FaustinCarter, @zhampel

Author instructions

Thanks for submitting your paper to JOSS @williamjameshandley. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@williamjameshandley if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

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[whedon]

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[arfon]

:wave: @williamjameshandley - could you please take a look at this list of potential reviewers and identify some potential candidates to review your submission? https://bit.ly/joss-reviewers

[williamjameshandley]

pragyansmita
nilesh-patil
ygrange
mattpitkin
zingale
adam-m-jcbs
ziotom78
wtgee
benjaminrose
Cadair
zhampel
nespinoza
FaustinCarter

[arfon]

:wave: @zhampel @FaustinCarter - would you be willing to review this submission for JOSS?

[FaustinCarter]

Sure. I can do that. Give me a week or so to look over the code. After skimming the paper quickly I think it could benefit from a rewrite. Some specific comments by paragraph:

1:
-Why does this end in a colon? Are you about to present an example?
-Your tense is off. I think you mean "probability distributions" rather than "a probability distribution" (which would imply a single distribution for all unknown parameters in the universe!)

2:
-I'm not sure what the point of this paragraph is. The age of the universe and the idea that space expands don't seem to be relevant at any further point in the paper.

3:
-Plots like what? Are you suggesting that the idea in the above paragraph could be parameterized into two variables that have a joint probability distribution? What are those variables? Can you include the plot of those variables made from your software?

4:
-scipy, getdist, and corner all have instructions on how to cite them in an academic publication. It would be good to include those citations in addition to links to their webpages. A reference to a MCMC paper would also be good to make it easy for readers to look that up.
-I'll also put in a shameless plug here for the pygtc package (10.21105/joss.00046) which is an alternative to corner and probably belongs in that list, although that's up to you.
-After a more careful reading I think you are implying that corner plots are nice, but there is more to the story (i.e. looking at the actual model described by all the MCMC realizations?) and that's where your software comes in? Might be good to make this more explicit.

5:
-Mixed voice. You switch between third person (one does, one could) and first person plural (we do, we could, our ability). It would be good to unify the voice over the whole paper.
-Is the phrase "plotted thus" supposed to be a reference to Fig. 1? If so, say something like: "in Fig. 1 panel (a) we plot the parameter covariances between m and c for X realizations. In panel (b) we plot the function y=mx+c for X realizations. In panel (c) we plot something called DxL which is never mentioned in the paper and should be. In panel (d) we plot the probability of measuring y for a given x, which is essential a contour version of panel (b)."
-Why is there a red distribution and a blue distribution? Is that two separate sets of fake data that are being fit to the same model?

6:
-A couple references seem broken?

7:
-The first line of this is the first mention you make of what your package actually does in words. I think this should come earlier and there should be a little more description of what fgivenx is designed to do right from the start.

That's enough for now. Let me dig into the code an run it and I'll have more comments. Oh, and is there a link to hosted documentation somewhere (I didn't see one on the github page)? Preferably documentation that includes installation instructions and a description of options (see the docs for corner as a great example)?

[arfon]

Thanks for agreeing to work on this @FaustinCarter. I'd like to find a couple of reviewers for this submission. Once I've identified a second reviewer, I'll go ahead and set up the main review issue which will provide a checklist for you to work through.

[zhampel]

Hey @arfon, yes I'd be willing to review, however, I will realistically be able to take a close look in a week. If that's too long of a delay, then feel free to request another reviewer.

[arfon]

@whedon add @FaustinCarter as reviewer

[whedon]

OK, @FaustinCarter is now a reviewer

[arfon]

@whedon add @zhampel as reviewer

[whedon]

OK, @zhampel is now a reviewer

[arfon]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/849. Feel free to close this issue now!

[arfon]

@FaustinCarter & @zhampel, many thanks for agreeing to review this submission. Please head over to #849 to carry out your review.