I’ve also found that concepts that some people take for granted get turned into jargon that makes communicating this to non-users challenging. The focus can sometimes be on why Word, Endnote, and SPSS are bad, not why Markdown, and R are better options than Word, and SPSS. As I pointed out earlier, when confronted by open science advocates, many of us feel like the kid who got caught by the dentist not flossing between his incisors, and is subsequently chided. So getting people comfortable with any sort of command line operation or mark-up coding will require a significant shift in a field not known for its shifting.Īnother challenge is in the way that tools like R, Markdown, and the open science movement are proselytized*.
How to use endnote to cite rmarkdown manual#
Among the 15-20 manuscripts I’m asked to review by journals and colleagues each year, I’d say that half have errors in the literature cited that reveal such a manual strategy. i still know folks who manage citations in their manuscripts by manually typing them in. 2013”), but it’s workable.īut what we agreed was the biggest hurdle is the cultural shift required, particularly among field ecologists. It’s not as slick as the Endnote/Word interface in my view (especially when dealing with two papers that could be cited as “Smith et al. Markdown doesn’t handle citations natively, but integrating with the program pandoc can take advantage of the LaTeX reference format, and programs like JabRef can be used to facilitate inline citations. Here is an example of git diff –color-words /TpmOWY0smi
I haven’t played around with it, but Andrew sent an example: There’s a command in the program git that will compare two markdown files, and highlight changed words in different colours.
In my original response, I highlighted three issues that would be required for me to break out of the Word paradigm that dominates ornithology like wetness dominates the ocean: But if anyone figures that out, let me know). Instead of separating the stats/modeling, plotting, and writing, one could do them all in one self-updating document (well, except the writing. Consider, too, a manuscript with a complex analysis that keeps getting tweaked. Just enter the data, “knit” the file, and you’re off to the races. In a more ecological application, consider an annual report where similar elements are required each year (e.g., temperature and precipitation plots, or a running graph of a bird population’s reproductive success). Whereas I would have entered the data, generated new figures, and pasted them into the document manually before, the combination of Markdown and R/knitr is fantastic. Andrew showed me an example of the departmental coffee co-op he runs where after entering each month’s consumption, the document automatically produces the most recent stats, graphs, and customer balances. Let me say that Markdown (and integrating it with R using the R package knitr) is REALLY NEAT. May you often have conversations that improve & change your thinking on a topic, like the one I just had with - Andrew MacDonald August 27, 2013
How to use endnote to cite rmarkdown update#
Will digest some thoughts & post an update tomorrow In typical Canadian fashion, we both really enjoyed our chat, and learned something from each other in the processĪbsolutely fantastic chat with on Markdown, open science, & writing tools. Earlier this week, as promised, I had a chat with Andrew MacDonald about the recent back and forth and back again about the use of writing tools in ecology.
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