What is the make file/rule you talked about towards the end of video? Do you already have a separate video showing how we can incorporate into our data analysis pipeline?
Pat, Very interesting how you write your RMarkdown file in a simple text file and then format it. I recognize a bunch of pure LaTeX commands in your code. The one difference I do see is that RMarkdown is a bit more tolerant than LaTeX. In LaTeX all instructions about the overall look of the manuscript are in the Preamble of the document (sort of like the YAML header). I am coming from LaTeX to RMarkdown so the latter seems quite easy to me. But I think that if you are familiar with RMarkdown (or just plain Markdown) that the transition to LaTeX woul not be all that hard. LaTeX has gotten a lot of more user-friendly these last years due to some of IDEs that have been built for it (sort of like what RStudio did for R). As a Mac user I use TeXShop which I think is terrific (all kinds of fill-down menus and built-in macros and templates). Windows users also have a lot of good choices. Beginners like TeXMaker which also works on Macs. Most journals will have a LaTeX template so all we have to do is just plug in our text. Similarly most top universities (I am sure Michigan has one) have thesis and dissertation templates on hand taking the pain out of the formatting (I recall turning in my dissertation to an inspector who used a ruler on margins etc - I wrote mine in an early version of MS Word).
One thing is not clear to me: Animals, for example, asked me to send the document using their template (latex or word). So I can't use the default rmarkdown style? What is usually done in these cases?
Thank you for your video! Do you know a reliable way to check grammar in real time when writing on rmarkdown? I also find that when I knit to tex or word, the formatting turns out weird.
I often write rmarkdown using vscode and vscode has plugins that will do grammar checking for you. For knit'ing to word, you will need a reference file that has the formatting built into it already. It's pretty painful. I usually do everything with PDFs and if I need a word version, I take what it generates and reformat the final draft to look right
@@Riffomonas Thank you for the suggestion, I was able to use vscode with LTex, I was also able to use a Zotero extension (Zotex) to manage my citations and bibliography. Thank you once again!
Yes, but getting your co-workers or supervisor to even consider switching from Word or using Git is too often a fool's errand which will take you several steps down the path to ostracization and ridicule. Manually verify every single number for every single draft only to have Word crash before saving because you scrolled over the figures section too fast(???)? Some just don't want to wake up from that nightmare.
This is why I love being the boss. I make people rewrite it if it’s in word. 😂 you can always render to word give everyone a docx file and then reinsert the corrections yourself
I use both and in some instances prefer LaTeX. Lately I have use a LaTeX package called tcolorbox to imbed copied R code directly into LaTeX. It looks pretty nice actually. I have also used TikZ/PGFPLOTS to plot natively inside LaTeX but it can be pretty slow especially if you have large data files but it looks great if you can do. The figure just blends right into the LaTeX document (the fonts are consistent etc). I like RMarkdown but find it cumbersome when the documents get long. The knitting seems to hang up too often at that point at least for me.
Rmarkdown, a life changing package for reproducible research and elegant reports. Always enjoy learn something new from you! Thank you very much.
Agreed! Thanks for watching 🤓
I just discovered your channel and it's such a treasure trove! Thanks for sharing all your knowledge :)
Glad you enjoy it!
I am writing my Literature Review and current progress report for my PhD 9 month review, your videos are exactly what I need, thanks for all the help!
That's awesome to hear - good going!
What is the make file/rule you talked about towards the end of video? Do you already have a separate video showing how we can incorporate into our data analysis pipeline?
Pat,
Very interesting how you write your RMarkdown file in a simple text file and then format it. I recognize a bunch of pure LaTeX commands in your code. The one difference I do see is that RMarkdown is a bit more tolerant than LaTeX. In LaTeX all instructions about the overall look of the manuscript are in the Preamble of the document (sort of like the YAML header).
I am coming from LaTeX to RMarkdown so the latter seems quite easy to me. But I think that if you are familiar with RMarkdown (or just plain Markdown) that the transition to LaTeX woul not be all that hard. LaTeX has gotten a lot of more user-friendly these last years due to some of IDEs that have been built for it (sort of like what RStudio did for R). As a Mac user I use TeXShop which I think is terrific (all kinds of fill-down menus and built-in macros and templates). Windows users also have a lot of good choices. Beginners like TeXMaker which also works on Macs.
Most journals will have a LaTeX template so all we have to do is just plug in our text. Similarly most top universities (I am sure Michigan has one) have thesis and dissertation templates on hand taking the pain out of the formatting (I recall turning in my dissertation to an inspector who used a ruler on margins etc - I wrote mine in an early version of MS Word).
Thanks! I keep wanting to learn more latex. Admittedly a lot of it is google - copy - paste at this point
One thing is not clear to me: Animals, for example, asked me to send the document using their template (latex or word). So I can't use the default rmarkdown style? What is usually done in these cases?
I'm sure there's a way to use the latex template, but that's past my latex skills! I'd probably get the docx and copy and paste into the template
Thank you for your video! Do you know a reliable way to check grammar in real time when writing on rmarkdown? I also find that when I knit to tex or word, the formatting turns out weird.
I often write rmarkdown using vscode and vscode has plugins that will do grammar checking for you. For knit'ing to word, you will need a reference file that has the formatting built into it already. It's pretty painful. I usually do everything with PDFs and if I need a word version, I take what it generates and reformat the final draft to look right
@Riffomonas Thank you for your suggestion. I'll try using vscode.
@@Riffomonas Thank you for the suggestion, I was able to use vscode with LTex, I was also able to use a Zotero extension (Zotex) to manage my citations and bibliography.
Thank you once again!
Yes, but getting your co-workers or supervisor to even consider switching from Word or using Git is too often a fool's errand which will take you several steps down the path to ostracization and ridicule.
Manually verify every single number for every single draft only to have Word crash before saving because you scrolled over the figures section too fast(???)? Some just don't want to wake up from that nightmare.
This is why I love being the boss. I make people rewrite it if it’s in word. 😂 you can always render to word give everyone a docx file and then reinsert the corrections yourself
@@Riffomonas you're one of the good ones. 👨🎓👌
RMarkdown reminds of LaTeX...
Definitely. I think if you know latex you can really get a lot out of r markdown
I use both and in some instances prefer LaTeX.
Lately I have use a LaTeX package called tcolorbox to imbed copied R code directly into LaTeX. It looks pretty nice actually. I have also used TikZ/PGFPLOTS to plot natively inside LaTeX but it can be pretty slow especially if you have large data files but it looks great if you can do. The figure just blends right into the LaTeX document (the fonts are consistent etc). I like RMarkdown but find it cumbersome when the documents get long. The knitting seems to hang up too often at that point at least for me.
Arial rules!
Hah! Thanks for watching 🤓