May 25, 2020
This post presents the workflow of interacting with R in org mode. I am mainly seeking three functions in this workflow: automatic output; persistent R session across multiple source blocks; ability to present both codes and outputs.
Preparation org-babel for executing and tangling source blocks ESS for interacting directly with R in emacs through the inferior R process Instruction set up proper sub-tree/buffer header arguments, for this blog post I used sub-tree header arguments: :header-args:R: :session *R* :exports both :eval no-export run org-bable-execute-src-block (or on sub-tree/buffer level) to produce outputs in the text area Example Plot output For the following code block, I used the source block header arguments #+begin_src R :results output graphics file :file test.
Sep 9, 2020
Get references Search engine like Google scholar, or databases like Scopus Social network like email, journal club, researcher gate, rss of keywords or journals Remember to take note of search keywords and the thinking process Why am I interested in this article? What leads me here (keyword, or citation from another article, or interested authors) Save new references with proper tags as best as you can in Inbox collection for further processing Review Inbox Clean the citation format, see Citation format checking workflow Use Zotfile to rename attached pdf files and move the attachment to customized location, see Notes about Zotero plugins Add appropriate tag/notes For articles that need deeper processing, add “todo” tag and read the article according to My Academic Reading Workflow Move the articles out of Inbox to appropriate collection (cmd + drag) once reviewed Citation format checking workflow Check whether the item type is correct (book chapter, conference paper, journal article, etc.
Sep 8, 2020
Tools Skim notes are saved in a separate .skim file, cannot be extracted in Zotero resolution not as sharp as acrobat only one highlight color no type machine function small and fast, good for note taking Adobe Acrobat highlights color coding:
light green: key word ! light yellow: key statement ! light pink: method, operationalisation, key results !
Sep 8, 2020
Citavi my team is already using this software proprietary, mostly used by German institutions Prossss in-app pdf viewer, pretty fast compared to Acrobat, similar with Preview save pdf annotation directly in app embedded todo management powerful note taking system (Quotation) able to preview search result Con proprietary, not many users outside Germany (forum discussion mostly in German) only supports windows the transfer and sharing of references between projects is more effortful (import, export) unable to change interface font size, unable to change layout to column and row Zotero the reference management tool that I have used the longest and most often Pros free, light weight, open source, cross platform active community for Q&A and add-on development able to organize all references in library or in specific “Collection” better bibtex support Cons note taking ability is very limited and simplistic Current pick 2020-08-26 still using zotero for my personal library, but use Citavi for a cloud project shared with my team (share articles with each other for journal club and journal briefing) importing Zotero bibtex to Citavi issues: no collection, tag, related (article) info
Sep 8, 2020
cite a paper: [locator][#citationkey] (locator is optional) cite multiple paper: [locator1][#citationkey1][locator2][citationkey2]… inline citation: [#citationkey; locator] ## Pandoc
citation: Citations go inside square brackets and are separated by semicolons cite a paper: [@citekey, locator] cite multiple paper [@citekey, locator; @citekey, locator…] inline citation: @citekey [locator] ## bibtex BibTeX cheat sheet and entry templates ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ by email@example.com at Wed Jul 29 15:42:08 CEST 2009
Based on information form http://en.