Our vertebral orientation paper is up as a preprint
September 30, 2019
Regular readers will remember that we followed up our 1VPC talk about what it means for a vertebra to be horizontal by writing it up as a paper, and doing it in the open. That manuscripts is now complete, and published as a preprint (Taylor and Wedel 2019).
Taylor and Wedel (2018: Figure 5). Haplocanthosaurus sp. MWC 8028, caudal vertebra ?3, in cross section, showing medial aspect of left side, cranial to the right, in three orientations. A. In “articular surfaces vertical” orientation (method 2 of this paper). The green line joins the dorsal and ventral margins of the caudal articular surface, and is oriented vertically; the red line joins the dorsal and ventral margins of the cranial articular surface, and is nearly but not exactly vertical, instead inclining slightly forwards. B. In “neural canal horizontal” orientation (method 3 of this paper). The green line joins the cranial and caudal margins of the floor of the neural canal, and is oriented horizontally; the red line joins the cranial and caudal margins of the roof of the neural canal, and is close to horizontal but inclined upwards. C. In “similarity in articulation” orientation (method 4 of this paper). Two copies of the same vertebra, held in the same orientation, are articulated optimally, then the group is rotated until the two are level. The green line connects the uppermost point of the prezygapophyseal rami of the two copies, and is horizontal; but a horizontal line could join the two copies of any point. It happens that for this vertebra methods 3 and 4 (parts B and C of this illustration) give very similar results, but this is accidental.
The preprint has all the illustrations and their captions at the back of the PDF. If you prefer to have them inline in the text, where they’re referenced — and who wouldn’t? — you can download a better version of the manuscript from the GitHub archive.
By the way, you may have noticed that what started our written in Markdown has mutated into an MS-Word document. Why? Well, because journals won’t accept submissions in Markdown. It eas a tedious and error-prone job to convert the Markdown into MS-Word, and not one I am keen to repeat. For this reason, I think I am unlikely to use Markdown again for papers.
References
- Taylor, Michael P., and Mathew J. Wedel. 2019. What do we mean by the directions “cranial” and “caudal” on a vertebra? PeerJ PrePrints 7:e27437v2. doi:10.7287/peerj.preprints.27437v2
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Sauropod Vertebra Picture of the Week 
October 1, 2019 at 5:50 pm
You know about pandoc?
https://www.mscharhag.com/software-development/pandoc-markdown-to-pdf
It knows a lot of formats. You can add LaTeX styles inline, in the markdown, too.
On September 30, 2019 3:41:30 PM Sauropod Vertebra Picture of the Week
October 1, 2019 at 7:22 pm
Yep, I know of Pandoc: it’s what I used to convert the Markdown document into Open Document format, as you can see at https://github.com/MikeTaylor/palaeo-vo/blob/master/Makefile
From there it was a matter of opening the generated document in LibreOffice and exporting it as MS-Word.
But it still involved a lot of manual work, such as resizing the images appropriately. It was enough work that I can’t continue to consider the Markdown copy as the master, and re-export as necessary. That’s why the MS-Word version is now the master.
October 3, 2022 at 8:43 am
[…] made available as a preprint, which led to us writing the paper in the open, which led to another preprint (of the paper this time, not the […]