New writing workflow

I wrote Functional programming in R using Ulysses and have used Ulysses to write the first part of Object oriented programming in R as well. It is a very nice editor and I am definitely using it in the future for other writing projects, but for the workflow with these books it doesn’t really work for me anymore.

The way I write the books is this: I write in R Markdown that I then need to run through ‘knitr’ to get the R code executed, this generates Markdown files that I then process using ‘pandoc’.

To get the full set of features in Ulysses, I have to use their internal file format, which means I have to export files ever time I need to compile the text. It is not a major hassle, but it is a little annoying.

It is especially annoying with Object-oriented programming in R where the second chapter has some performance measurement code that takes a while to run. I don’t want to run that every time I compile the book, so having a make file that makes sure I only compile and run the R code when necessary is the way to go, but either I have to be careful to export chapters in separate files (and remember to do that every time I change the text), or I have to just edit the raw Markdown files and not bother with the internal file format.

I have decided on the latter. I can’t use the more advanced features then, so I will edit with iA Writer instead, I think, just to give that a good try for comparison with Ulysses. I already use iA Writer for most Markdown editing, but I haven’t tried using it for a book yet. I will miss Ulysses’ sheets — they make it easy to move sections about — but I am sure I can manage without them.

With iA writer I can’t use the more advanced features like embedded files and such outside of iCloud, as far as I can see, but that wouldn’t really work well with the book compilation framework anyway. Embedding figures, for example, doesn’t really work for me because I need different figures when compiling to PDF and when making EPub. So I have to have the figures external to the text in any case.

You can see my current setup at github. I just have a Makefile for processing the files. First I send the R Markdown through a pre-processor — this is how I can have different code run depending on whether I’m making a PDF or an ebook — and after that through knitr and finally through pandoc.