Thank you. This was very helpful. Please keep up the good work with the video's: they're demystifying the plain-text toolchain approach to scholarly publishing.
This video was good at the time but is now showing its age. A number of commands and options have changed, and it's up to the individual users to find out the current versions. At times like this mass-production software like MS Word is in a good position because many people have used it, and it might be easier to find answers to one's questions.
Based on this video I downloaded a trail version of iThoughts HD and it was a revelation, particularly its capacity to play nice with Markdown. I've been happily using Visual Understanding Environment (VUE) from Tufts Uni for many years; however, I've been looking at a pathway for concept-mapping that is less dependent on a specific format or platform. Markdown-to-outline-to-map looks promising.
you know multimarkdown can do citations, even citep/citet for latex, footnotes etc. I also feel that OmniOutliner in combination with Marked and Textmate(or any other texteditor) works better than scrivener. edit: textexpander is ridiculously great with markdown/latex
Thanks for the info, Felix. You are right, TextExpander is a must-have for this kind of writing. I'd love you hear more about how you do your writing in OmniOutliner. Let me know!
I basically throw all my research into outliner (as external links e.g. papers, devonthink files, markdown,...) and add additional notes. Then I move it all around until it has a nice flow and finish writing all the parts in multimarkdown (still linked in outliner so I can change the order at any time). In the end I compile all the files into one latex document (just to remain in full control of the pdf output).
I tried to export ithought HD file into Marked2 file. However, the figure inside the ithought doesn't appear properly. Are there any solutions? Many thanks!
Great collection of videos but I'm having problems with the Marked 2 one. I have the same problem that B Zhang had a year ago. When the data is entered in the args box, you get the message he shows. It's easy enough to get rid of the, apparently redundant, --normalize, but the new +smart extension either throws an error message, or has no effect. From what I can make out from the documentation, it isn't intended to work with html anyway. Any thoughts?
Hi Nicholas, thanks for another great video! BTW, your students are extremely lucky to have you helping them through all this. Question for you on this video and your use of iThoughts and DevonThink. I see that you are linking to your notes in DevonThink and I understand that bit I think. I notice that within DevonThink you appear to be using the RichText note type so that you can do your linking between notes (as if I understand correctly, the text version of notes in DevonThink does not support that linking). But then it appears that you are writing your notes in markdown. Is that right? And last question: why do you have ## Tags as a section in your notes versus using the DevonThink tagging feature? Is that so you can some day move them out of DevonThink easily? Thanks again, Nathan
Hi again, Nathan. All my notes in DEVONthink are plain text. The linking you see is an option in DEVONthink. Go to Preferences > Editing, and then click on "WikiLinks". When this is selected, every time you type the name of a file, it turns into a link to that file. So you can write in plain text but still move easily between files. Best of both worlds! For tagging, you are right. I start with my tags in DEVONthink and then I manually copy-paste them into the body of the document. As you say, I do that in case I move my files to another system someday. Happy writing!
In a word, yes. My suggestion would be to watch my Pandoc video to get started: th-cam.com/video/N31E_NZYQQY/w-d-xo.html. First, for citations, you decide the format --- MLA, Chicago, APA, whatever. That will be determined by what's called a CSL file. Second, in terms of the formatting of the document, you can create a template. There's more information about this on the Pandoc website: pandoc.org/MANUAL.html. Search the page for "reference.docx," and you will find more info. Good luck with your writing!
Thanks for the video, but I got this message after I followed all the steps --smart/-S has been removed. Use +smart or -smart extension instead. For example: pandoc -f markdown+smart -t markdown-smart. --normalize has been removed. Normalization is now automatic. Try pandoc --help for more information. what should I do?
It's true. The update to Pandoc means that the command has changed a little bit. So instead of: -f markdown -t html5 --bibliography=filepath/testlibrary.bib --smart --normalize -s Try: -f markdown+smart -t html5 --filter pandoc-citeproc --bibliography filepath.bib You should join our group! launchpass.com/researchhacking
I also watched your video "Using Better Bib(La)Tex", but I don't have the option "force citation key to ASCII", could this be the reason for the problem? what should I do?
Pandoc was updated so the commands have changed. Try this out and let me know if it works (works for me): -f markdown+smart -t html5 -s --filter=/usr/local/bin/pandoc-citeproc --bibliography=PATHTOBIBLIOGRAPHY.bib --csl=PATHTOCSL.csl
Thank you. This was very helpful.
Please keep up the good work with the video's: they're demystifying the plain-text toolchain approach to scholarly publishing.
Couldn't ask for a higher complement, Chris. Thank you!
Oh, but this doesnt work with Marked 2 from App Store. It has to be from their site to allow using pandoc..
This video was good at the time but is now showing its age. A number of commands and options have changed, and it's up to the individual users to find out the current versions. At times like this mass-production software like MS Word is in a good position because many people have used it, and it might be easier to find answers to one's questions.
Based on this video I downloaded a trail version of iThoughts HD and it was a revelation, particularly its capacity to play nice with Markdown. I've been happily using Visual Understanding Environment (VUE) from Tufts Uni for many years; however, I've been looking at a pathway for concept-mapping that is less dependent on a specific format or platform. Markdown-to-outline-to-map looks promising.
you know multimarkdown can do citations, even citep/citet for latex, footnotes etc. I also feel that OmniOutliner in combination with Marked and Textmate(or any other texteditor) works better than scrivener.
edit: textexpander is ridiculously great with markdown/latex
Thanks for the info, Felix. You are right, TextExpander is a must-have for this kind of writing. I'd love you hear more about how you do your writing in OmniOutliner. Let me know!
I basically throw all my research into outliner (as external links e.g. papers, devonthink files, markdown,...) and add additional notes. Then I move it all around until it has a nice flow and finish writing all the parts in multimarkdown (still linked in outliner so I can change the order at any time). In the end I compile all the files into one latex document (just to remain in full control of the pdf output).
Sounds excellent. You should make a video and share it!
I wish I had the time to do that ;-p
Felix Grabowski I know the feeling!
I tried to export ithought HD file into Marked2 file. However, the figure inside the ithought doesn't appear properly. Are there any solutions? Many thanks!
Great collection of videos but I'm having problems with the Marked 2 one. I have the same problem that B Zhang had a year ago. When the data is entered in the args box, you get the message he shows.
It's easy enough to get rid of the, apparently redundant, --normalize, but the new +smart extension either throws an error message, or has no effect. From what I can make out from the documentation, it isn't intended to work with html anyway.
Any thoughts?
Hi Nicholas, thanks for another great video! BTW, your students are extremely lucky to have you helping them through all this.
Question for you on this video and your use of iThoughts and DevonThink. I see that you are linking to your notes in DevonThink and I understand that bit I think. I notice that within DevonThink you appear to be using the RichText note type so that you can do your linking between notes (as if I understand correctly, the text version of notes in DevonThink does not support that linking).
But then it appears that you are writing your notes in markdown. Is that right? And last question: why do you have ## Tags as a section in your notes versus using the DevonThink tagging feature? Is that so you can some day move them out of DevonThink easily? Thanks again, Nathan
Hi again, Nathan. All my notes in DEVONthink are plain text. The linking you see is an option in DEVONthink. Go to Preferences > Editing, and then click on "WikiLinks". When this is selected, every time you type the name of a file, it turns into a link to that file. So you can write in plain text but still move easily between files. Best of both worlds!
For tagging, you are right. I start with my tags in DEVONthink and then I manually copy-paste them into the body of the document. As you say, I do that in case I move my files to another system someday.
Happy writing!
Hope they soonish will fix image display with iThoughts files in Marked2. Have been waiting for some months.
Scrivener 3 tutorial, please!
Is there a Marked style for academic papers (ie. double-spaced, etc.)? Even better, for Chicago, MLA, etc.?
In a word, yes. My suggestion would be to watch my Pandoc video to get started: th-cam.com/video/N31E_NZYQQY/w-d-xo.html.
First, for citations, you decide the format --- MLA, Chicago, APA, whatever. That will be determined by what's called a CSL file. Second, in terms of the formatting of the document, you can create a template. There's more information about this on the Pandoc website: pandoc.org/MANUAL.html. Search the page for "reference.docx," and you will find more info.
Good luck with your writing!
Thanks for the video, but I got this message after I followed all the steps
--smart/-S has been removed. Use +smart or -smart extension instead.
For example: pandoc -f markdown+smart -t markdown-smart.
--normalize has been removed. Normalization is now automatic.
Try pandoc --help for more information.
what should I do?
It's true. The update to Pandoc means that the command has changed a little bit.
So instead of: -f markdown -t html5 --bibliography=filepath/testlibrary.bib --smart --normalize -s
Try: -f markdown+smart -t html5 --filter pandoc-citeproc --bibliography filepath.bib
You should join our group! launchpass.com/researchhacking
Thanks but still does not work. I got this..."Unknown option --/Users/beibeizhang/Desktop/testlibrary.bib.
Try pandoc --help for more information."
I also watched your video "Using Better Bib(La)Tex", but I don't have the option "force citation key to ASCII", could this be the reason for the problem? what should I do?
@@beibeizhang6964 it should be --bibliography /Users/beibeizhang/Desktop/testlibrary.bib. it's always --option or --option file
The panda command no longer works, do you have a updated version I could use?
pandoc*
Pandoc was updated so the commands have changed. Try this out and let me know if it works (works for me):
-f markdown+smart -t html5 -s --filter=/usr/local/bin/pandoc-citeproc --bibliography=PATHTOBIBLIOGRAPHY.bib --csl=PATHTOCSL.csl
works for me. Thank you so much
@@manuelangelmacia9098 Thank you! Now it's updated to just --citeproc instead of (-filter=/usr/local/bin/pandoc-citeproc)
Is anyone else storing their .bib file in Dropbox? I can't seem to get Pandoc to use it unless I drag it to the desktop.
Hi, Nathan. Thanks for your comment!
Did you give Pandoc use the complete filepath for Dropbox?
Nicholas Cifuentes-Goodbody I did... with and without quotes. (Sorry for delay, I’ve been in doctoral seminars this week.)
Why don't you share the code in the Slack group. Let's see if the hive-mind can help. :)