Haynes article typesetting and copyediting

[arcaldwell49]

We need to start working on the copy editing and typesetting for the Courtney Haynes manuscript. I have started a branch entitled "haynes_noise".

Simon, are you able to work on this with me over the next 6 weeks. I would let you lead and assist as needed?

[smnnlt]

Yes, I'll find some time for in in the next weeks.

[smnnlt]

Hi @arcaldwell49

I've started working on the typesetting for the Haynes manuscript (see my recent commits). I used the new CIK Quarto template (arcaldwell49/cik-quarto). It worked quite well in general, but I noted some smaller problems. Those seem to be related to the template, as I can't reproduce them in normal Quarto documents.

• Changing aspect ratio when resizing figures in PDF: Resizing large figures with out.width="100%" works, but changes the aspect ratio (see the PDF). This should be related to the template, as normal Quarto pdf rendering does the resizing automatically while keeping the aspect ratio.
• Cross-referencing in PDF: I tried to do cross-referencing for figures and tables in html and pdf. This requires both html and pdf output to be generated within a single chunk, but that worked for me. I tried to rely on the native Quarto cross-referencing system, which should automatically add something like Figure 1: before the caption. This worked for html, but not for pdf (still the cross-referencing itself did work, just not the automatic caption generation). One could use a workaround, with generating different captions for html (only caption) and pdf ("Figure X:" + caption) with an !expr if (knitr::is_htlm_output()) statement in the chunk options, but as this problem does not occur in normal Quarto pdf rendering, i believe it is better to try to make changes to the template. In the medium term, we could try to get rid of using chunks at all to generate figures with using the default-image-extension YAML option (https://quarto.org/docs/authoring/figures.html#multiformat-figures), assuming that both pdf and html images have the same caption.

Is it possible that you can take a look at both issues and maybe update the Quarto template? I still have some minor work to do with the typesetting, which I would continue once these bigger problems are solved.

[arcaldwell49]

yep, let me open an issue

[arcaldwell49]

Hi Simon,

Issues are fixed in the branch and with the template.

1. Figures should now render to fit width and maintain aspect ratio with PDFs
2. Cross-referencing should work. however, it will not allow you to auto add the "Figure X:" label. In the figure caption you will need to add the notation for what figure number it is.

Let me know if it works on your end!

[smnnlt]

Hi @arcaldwell49

Thank you for fixing the issues. The pdf and html file should now be ready, except for one small problem with the 'less than or equal' sign. I'll open an issue in the cik-quarto repo.

[arcaldwell49]

Is there a less than or equal sign in the text?