Proofing PDF

[asmeurer]

PeerJ has a PDF for proofing. They want it back within one business day, so if you want to look at it, please do so by tomorrow.

Here is the PDF: peerj-cs-103-proof.pdf. Do not circulate this proofing PDF as it will change before publication.

Here are their instructions:

Please do:

1. Clearly mark-up all changes on the proofing PDF downloaded below.
2. Read your article carefully and annotate it using Adobe Reader, Preview, or an alternative application that supports PDF annotation. If necessary, submit comments in a text or Word document, referencing line numbers and any relevant query numbers.
3. Collect all changes in a single file, whether in the PDF, or a text document.

Please do not:

1. Change any of the content: text, figures, tables, or data.
2. Edit the original text of the PDF file.
3. All changes must be clearly marked-up on the proofing PDF downloaded below. Please do not change any of the text or data, and do not edit the original PDF's content.

Check the following

• Are there any numbered queries in the margins (e.g. Q1, Q2)? If so, please address them.
• Is the information on page 1 correct? This is where most errors often occur.
• Are the figures sharp and clear? If not, please upload identical hi-res figures (minimum 900px x 900px).
• Are all the figure and table legend texts complete and accurate?
• Is the Additional Information and Declarations section (at the end) correct, and does it read smoothly?

[asmeurer]

Please leave any comments about it here and I will include mark them up in the PDF.

[certik]

I read through it, and I didn't find any issues. I think it looks great.

[asmeurer]

There are a few questions at the end that we need to address.

[asmeurer]

I have found and left comments on the following so far:

• The examples have been rendered with curly quotes. They should use straight ASCII quotes.
• The mpmath.mpf example (and likely others) have two single opening quotes and one double closing quote. It should be mpmath.mpf("0.1").
• The Unicode pprint example is rendered too small compared to the surrounding examples.

I'll upload the final annotated PDF here before I submit it so that people can review the comments.

[asmeurer]

I also never got @aktech to confirm the spelling of his name.

[asmeurer]

Comments on questions at the end of the PDF:

Please check the author affiliations to confirm they are accurate.

Yes, these appear to be correct (from what I can tell, they are identical to the ones in our pdf, except US state names have been abbreviated).

Tables 1-3/Figure 1: Please confirm whether the text provided is a title or the legend body.

These all look correct.

References Adams & Loustaunnau (1994), Biggs et al. (1976), Ciurana (2009), Fetter & Walecka (2003), Kane & Levinson (1985), Lang (1966), Lutz (2013), Nielsen & Chuang (2011), Peeters (2007), Rose (1999), Rosen (2005), Rocklin & Terrel (2012), Shaw & Garlan (1996) Sakurai & Napolitano (2010), Sussman & Wisdom (2013), Tai (1997), Zare (1991) and Zienkiewicz et al. (2013) are incomplete. Please provide any of the relevant missing information: author list with initials, title, publication year, volume, page range, website, location of publisher, publisher name.

(TODO)

Reference Turk et al. (2011) appears with one page number instead of a page range. If this is not a single page reference, please provide the page range. If this is an abstract, please confirm that it is a single page abstract and we will insert "[Abstract]" in the reference.

I do not know here. Perhaps @matthewturk can answer this. The automatically generated citation at http://iopscience.iop.org/article/10.1088/0067-0049/192/1/9/meta (the URL from the DOI) gives a single page number as we have used.

[asmeurer]

Another comment: supplement links have been changed from "supplement section 3" to "section S3" throughout. Should we modify and update the supplement to number sections with the "S" prefix? This may not be worth the hassle.

Also, interesting note: it appears that cross document links will work (they link to the DOI).

[asmeurer]

The supplement still has line numbers so we may want to try to submit an updated version anyway.

[asmeurer]

Another note, I don't know if it was intentional, but all the internal cross-section links have been changed to plain text (like in footnote 9, "as noted in section 5.1" was changed to "as noted in Section, 'The core'" with no linking).

[asmeurer]

I don't know if I should bother about it, but I also noticed that the document table of contents metadata is missing from the PDF, making it harder to navigate in a PDF viewer that supports that.

[aktech]

I also never got @aktech to confirm the spelling of his name.

@asmeurer Sorry about the delay, the following spelling works for my name as it is:
"Amit Kumar"

[asmeurer]

@aktech thank you. Can you please correct the spelling on the PeerJ site.

[asmeurer]

Did not hear from @matthewturk, so I will just say that I do not know about the Turk, et. al. reference. As far as I tell, the reference is correct. It is what is given as the citation at the DOI.

[matthewturk]

I think that's right, yes.

…

On Fri, Dec 9, 2016 at 3:06 PM, Aaron Meurer ***@***.***> wrote: Did not hear from @matthewturk <https://github.com/MatthewTurk>, so I will just say that I do not know about the Turk, et. al. reference. As far as I tell, the reference is correct. It is what is given as the citation at the DOI <http://iopscience.iop.org/article/10.1088/0067-0049/192/1/9/meta> . — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#220 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAFbu2hOJTFbB0m8XX87EJ2_uk12sXg0ks5rGcK_gaJpZM4LISVG> .

[asmeurer]

Here is the final proof with annotations. Please review the annotations
peerj-cs-103-proof-annotated.pdf

[asmeurer]

I also plan to leave the following in the "notes for staff" field when I upload it:

We would like to resubmit our supplement, which has the following changes:

1. Line numbers removed
2. Section numbers changed to use "S" prefix to match references in paper (S1, S2, ...)
3. Citations updated, as per Q3.

[aktech]

@aktech thank you. Can you please correct the spelling on the PeerJ site.

Done.

[certik]

I went over the pdf document and I think the annotations looks good.