I would like to use org-mode for organizing information about research papers. Each paper has its own .org file. There is also one main .org file where the papers are organized in categories.
So, suppose that I have an .org file for a paper as follows:
- Goldenberg2011CDH
- Goldenberg et al., "The Compressed Differential Heuristic", AAAI 2011
In the main .org file, I might have:
* AAAI
** 2011
- Goldenberg2011CDH
Is there a way I can have org-mode show the title (i.e. Goldenberg et el., "The Compressed Differential Heuristic", AAAI) instead of the key (i.e. Goldenberg2011CDH) in such a way that, if the title changes in the paper's .org file, then it would be shown updated automatically in the main .org file? That is, I am looking for a hyperlink that works sort of like a speadsheet formula -- when the linked cells change, the answer in the formula cell is updated automatically.
Related
My desired output is both an (1) MSWord and (2) PDF document, both with (a) in-text citations, (b) citations in some footnotes/endnotes, (c) chapter bibliographies, and (d) cumulative bibliography, (a)-(d) according to the .csl file, Springer - Humanities (author-date).
My tools are: .Rmd files, bookdown, LibreOffice, Zotero.
My problem:
IF(MSWord output) {NO chapter bibliographies}
IF(PDF output AND chapter bibliographies) {citation_package: natbib OR citation_package: biblatex}
IF(PDF output AND .csl file) {citation_package: none}
I hope to avoid breaking the book into separate bookdown projects for each chapter---this is annoying manual work and some chapters build R objects that are used in subsequent chapters (so it would be required rewriting code and caching things, etc.).
Attempted solutions:
I have successfully implemented both the biblatex and the natbib solutions to "bookdown + chapter bibliographies + PDF" here, but that solves one part of my problem: Is there a way to add chapter bibliographies using bookdown?
I have successfully implemented the solution to "bookdown + .csl file + PDF" here, but that solves one part of my problem: use csl-file for pdf-output in bookdown
Notes
The PDF output will be considered a reference document, thus solving the MSWord document problem is the priority (which may involve manually copying and pasting from the PDF output).
Technically, I'm also using the documentclass: svmono (where author/svmono.cls is here: Springer LaTeX2e macro packages for monographs and no "Humanities" .bst file is offered)
I use '.md' to generate '(index).html' and '(refman*).rtf' documentation with doxygen 1.8.14.
The mathematical equation in '*.md' gives a correct equation in html output but not in the file 'refman.rtf'. The other theoretical parts like paragraph and other stuff work well between *.md and rtf output.
I guess *.rtf is not recognizing the equation part of the *.md document.
Does the RTF generation through doxygen read the *.md files?
Do I need to change any tag to make *.md work with rtf output?
Not only for markdown but also for "normal" doxygen input formulas do not work.
From the documentation:
Doxygen allows you to put LATEX formulas in the output (this works
only for the HTML and LATEX output, not for the RTF nor for the man
page output).
A workaround workflow, at the moment for non inline formulas, is to do something like:
Create an image with the formula e.g in a dummy doxygen run where one does not use MATHJAX, this will result in an image with a name like: 'form_0.png'.
In the code one has to place an if construct like:
\if rtf_run
\image rtf form_0.png
\else
\f... with the formula
\endif
One now has to run doxygen twice:
once for the output without rtf, i.e. without setting rtf_run in ENABLED_SECTIONS
once for rtf output by setting rtf_run in ENABLED_SECTIONS
EDIT June 5, 2018: I've just pushed a proposed patch to github pull request 756. Here the formulas are rendered as png images and included in the RTF documentation.
EDIT: 2018/06/10: The push request has been integrated in the master version on github.
To distinguish this question from Doxygen: Adding a custom link under the "Related Pages" section which has an accepted answer that is not a real answer to the question, I specifically add prewritten to the question.
What I want:
Write one document tex file (without preamble, since this file will be \input-ed into a full document)
Import the document into Doxygen's HTML output.
Using Doxygen to produce tex file will probably not work, since it does too much layout work [This holds for its HTML output too like empty table rows 2015]. If Doxygen takes some other input that can easily be transformed into LaTeX, that will do.
You can easily add an already existing Latex file to your doxygen documentation using \latexonly\input{yourfile}\endlatexonly.
I would assume you put it e.g. under a doxygen \page.
I am playing with Tal's intro to producing word tables with as little overhead as possible in real world situations. (Please see for reproducible examples there - Thanks, Tal!) In real application, tables are to wide to print them on a portrait-oriented page, but you might not want to split them.
Sorry if I have overlooked this in the pandoc or pander documentation, but how do I control page orientation (portrait/landscape) when writing from R to a Word .docx file?
I maybe should add tat I started using knitr+markdown, and I am not yet familiar with LaTex syntax. But I'm trying to pick up as much as possible while getting my stuff done.
I am pretty sure the docx writer has no section breaks implemented, also as far as I understand --reference-docx allows for customizing styles and not the page layout (but I might also be wrong here), this is from pandocs guide on --reference-docx:
--reference-docx=FILE
Use the specified file as a style reference in producing a docx file.
For best results, the reference docx should be a modified version of a
docx file produced using pandoc. The contents of the reference docx
are ignored, but its stylesheets are used in the new docx. If no
reference docx is specified on the command line, pandoc will look for
a file reference.docx in the user data directory (see --data-dir). If
this is not found either, sensible defaults will be used. The
following styles are used by pandoc: [paragraph] Normal, Title,
Authors, Date, Heading 1, Heading 2, Heading 3, Heading 4, Heading 5,
Block Quote, Definition Term, Definition, Body Text, Table Caption,
Image Caption; [character] Default Paragraph Font, Body Text Char,
Verbatim Char, Footnote Ref, Link.
Which are styles that are saved in the /word/styles.xml component of the docx document.
The page layout on the other hand is saved in the /word/document.xml component in the <w:sectPr> tag, but pandoc's docx writer ignores this part as far as I can tell.
The docx writer builds by default a continuous document, with elements such as headers, paragraphs, simple tables and so on ... much like a html output.
Option #1 (doesn't solve the page orientation problem):
The only page layout option that you can define through styles is the pageBreakBefore which will add a page break before a certain style
Option #2 (seems elegant but hasn't been tested):
Recently the custom writer has been added that allows for a custom lua script, where you should be able to define how certain Pandoc blocks will be written into the output file ... meaning you could potentially define section breaks and page layout for a specific block inserting the sectPr tag into the document. I haven't tried this out but it would be worth investigating. On pandoc github you can check out a sample lua script file for custom html output.
However, this means, you have to have lua installed, learn the language, and it is up to you if you think its worth the time investment.
Optin #3 (a couple of clicks in Word might just do):
As you will probably spend quite some time setting up how to insert sections and what would be the right size, margins, and figuring how to fit the table to such a layout ... I recommend that you use pandoc to put write your document.docx, that you open in Word, and do the layout by hand:
select the table you want on the landscape page
go to Layout > Margins
> select Apply to: Selected text
> choose Page Setup > select Landscape
Now a new section with a landscape orientation should surround your table.
What you would anyway also probably want to do is styling the table and table caption a little (font-size,...), to achieve the best result (all text styling can be already applied with pandoc where --reference-docx comes handy).
Option #4 (in situation when you can just use pdf instead of docx):
As far as I could figure out is that with pandoc does a good job with tables in md -> docx (alignment, style, ... ), in tex -> docx it had some trouble sometimes. However if your option allows for a pdf output latex will be your greatest friend. For example your problem is solved as easily as just using
\usepackage{pdflscape}
and adding this around your table
\begin{landscape}
...
\end{landscape}
This are the options that I could think of so far.
I would always recommend using the pdf format for reports, as you can style it to your liking with latex and the layout will stay the way you want it to be.
However, I also know that for various reasons word documents are still the main way of reviewing manuscripts in many fields ... so i would most likely just go with my suggested option 3, mostly cause it is a lazy and quick solution and because I usually don't have many documents with tons of giant tables with awkward placement and styling.
Good luck ;-)
Based on Taleb's answer here and some officer package functions, I created a little gist that one can use like this:
---
title: "Example"
author: "Dan Chaltiel"
output:
word_document:
pandoc_args:
'--lua-filter=page-break.lua'
---
I'm in portrait
\endLandscape
I'm in landscape
\endPortrait
I'm in portrait again
With page-breaks.lua being the file hosted here: https://gist.github.com/DanChaltiel/e7505e62341093cfdc489265963b6c8f
This is far from perfect (for instance it won't work without the last portrait section), but it is quite useful sometimes.
Background
With SyncTeX you can get forward and backward search between a source document and the typeset material. More specifically:
Forward search is to jump from a particular place in the source document, e.g. a LaTeX file, to the corresponding place in the typeset material, e.g. a PDF file.
Backward search is to jump from a particular place in the typeset material, e.g. a PDF file, to the corresponding place in the source document, e.g. a LaTeX file.
With Org-mode you can export as LaTeX and process it to PDF.
Question
It would be useful to be able to do forward and backward search between an Org-mode file and the PDF it produces on LaTeX export. Is this possible?
As mentioned, SyncTeX already implements forward and backward search between a LaTeX file and its resulting file. So the missing link seems to be the jump between the Org-mode file and the LaTeX file it is exported as.
I found a similar question on the mailing list: [Orgmode] synctex!! ...syncorg? It got no answer involving a solution.
There is a recent (April 2013) thread on the org-mode mailing list which has some preliminary patches. However, reading the emails, it seems like it's a tricky problem.
There is a more recent (depending on your frame of reference) post from October 2013 which has a solution. However, I have not been successful with that code, and re-raised the issue in this thread.