Most of the time between starting manuscript and having it accepted after peer-review is spent writing, re-writing and re-arranging content. In Word, keeping track of figure numbers is a big pain, even more so when figures are moved between the main manuscript and the supplement. Moving my Word manuscript to knitr, I first had to decide between RMarkdown and LaTeX. Adding citations and figure references in RMarkdown seems still a bit experimental, and I decided to go with LaTeX.
For my template, I implemented two main features. First, thanks to a tip by Iddo Friedberg, supplemental figures are automatically numbered "S1", "S2", etc. Second, I added a bit of LaTeX magic to interleave parts of the main manuscript and the supplement: If I want to move a paragraph or figure to the supplement, I just wrap it with a "\supplement{ }" command. That is, in the source code, the main and supplemental text are right next to each other, and only in the generated PDF are they separated into two parts of the document.
Of course, fulfilling journal requirements once the manuscript is accepted might still take some time, but compared to the time saved in the previous stages this is quite acceptable.
Here is the template, and here an example PDF generated from the template. (For a complete manuscript, see here.)
