RStudio ioslides, mathjax, what the heck? - latex

So typically I use beamer for presentations, but I thought what the heck just for fun I would do a ioslides presentation so I could embed a shiny app into the presentation. For the most part making the slides has been pretty smooth, but I cannot seem to get any of the math latex setting to work. Here is a toy example where I simply want the KM estimator to display
---
title: "test"
author: "tes"
date: "1/1/16"
output:
ioslides_presentation:
widescreen: true
mathjax: "http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
runtime: shiny
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```
## Test
$$
\hat{S}(t)=\prod_{y_{(i)}\leq t}\hat{p}_{t}=\prod_{y_{(i)}\leq t}\dfrac{n_{i}-d_{i}}{n_{i}}=\prod_{i=1}^{k}\dfrac{n_{i}-d_{i}}{n_{i}} & \quad\textrm{where }y_{k}\leq t<y_{k+1}
$$
All I get is a slide with a simple wireframe box around the latex call (e.g the \hat{S}(t)=\prod_{y_{(I)}... I should note that I have also tried just simply wrapping with single $ to no avail.
What am I missing? - I looked all over the R markdown documentation but I cannot see to figure it out.
Simple latex calls work jut fine, for example
$x^{2}$
renders exactly as I would expect.
I assume this is something silly, but it is besting me.
Thanks!

Your equation is actually not valid. It contains an ampersand (&) that is not within an alignment, so MathJax rejects it. If you remove the ampersand, I suspect it will work for you.
If there is a way to configure MathJax from within your slides, you could disabled the noErrors extension so that the actual error messages will be displayed rather than the boxed source.

Related

Mathjax does not render colorbox correctly

I try to render \colorbox{yellow}{\sigma} and configurate the mathjax following http://docs.mathjax.org/en/latest/tex.html), but it just does not work.
Result:
Configuration I find from http://docs.mathjax.org/en/latest/tex.html (I tried with and without autoload-all.js, both don't work):
It looks like the same issue here on https://tex.stackexchange.com/
The problem here is that \colorbox reverts its argument back to text mode
Then you should write:
\colorbox{yellow}{$\sigma$}
Convenient sites to test your syntax:
http://quicklatex.com/
(add \usepackage{color} in the Custom LaTeX Document Preamble option to test colors)
and
here for Tex supported by mathjax.
Note: as \colorbox is displayed in red perhaps the command is not recognized, which means that your configuration contains errors. You can test with the macro require and write
\require{color}\colorbox{yellow}{$\sigma$}

NBConvert PDF/Latex page formatting IPython

Got some good advice on suppressing code and other items on NBConvert output,, Here Suppress code in NBConvert? IPython
BUT: now It seems I need to change top and bottom margins And I can see that it seems that it may be set in the sphnix template, (if I even know where it is), which I don't want to mess with but I cannot figure out how to edit the Latex output to get at the margins I attempted to place this in the import headers
\usepackage[margin=0.5in]{geometry}
But nothing happened.. I know squat about latex I am using the TexStudio package to modify the Latex output of NB convert, but at this point I don't see something to modify for margins...
I'm trying to touch up some page flow issues involving placement of output graphs that are just too big so I end up with big ugly blank spots,, pretty sure that if I can get at the margins I can...
To change the margins using your proposed code, you have to put this line after the other inputs, e.g. about line 71. If you put it at the top, it will be overridden by another call. With my notebook this works fine.
I'm pretty sure you know you can specify different margins using
\usepackage[left=0.5in, right=0.5in, top=0.5in, bottom=0.5in]{geometry}
see e.g. wikibooks.
Btw. be aware that the sphinx based templates are removed in current master. The new templates are much more customizable and remove some issues due to the mdframed packages (GitHub Issue)

How to display plain text from markdown [duplicate]

I'm currently using BlueCloth to process Markdown in Ruby and show it as HTML, but in one location I need it as plain text (without some of the Markdown). Is there a way to achieve that?
Is there a markdown-to-plain-text method? Is there an html-to-plain-text method that I could feel the result of BlueCloth?
RedCarpet gem has a Redcarpet::Render::StripDown renderer which "turns Markdown into plaintext".
Copy and modify it to suit your needs.
Or use it like this:
Redcarpet::Markdown.new(Redcarpet::Render::StripDown).render(markdown)
Converting HTML to plain text with Ruby is not a problem, but of course you'll lose all markup. If you only want to get rid of some of the Markdown syntax, it probably won't yield the result you're looking for.
The bottom line is that unrendered Markdown is intended to be used as plain text, therefore converting it to plain text doesn't really make sense. All Ruby implementations that I have seen follow the same interface, which does not offer a way to strip syntax (only including to_html, and text, which returns the original Markdown text).
It's not ruby, but one of the formats Pandoc now writes is 'plain'. Here's some arbitrary markdown:
# My Great Work
## First Section
Here we discuss my difficulties with [Markdown](http://wikipedia.org/Markdown)
## Second Section
We begin with a quote:
> We hold these truths to be self-evident ...
then some code:
#! /usr/bin/bash
That's *all*.
(Not sure how to turn off the syntax highlighting!) Here's the associated 'plain':
My Great Work
=============
First Section
-------------
Here we discuss my difficulties with Markdown
Second Section
--------------
We begin with a quote:
We hold these truths to be self-evident ...
then some code:
#! /usr/bin/bash
That's all.
You can get an idea what it does with the different elements it parses out of documents from the definition of plainify in pandoc/blob/master/src/Text/Pandoc/Writers/Markdown.hs in the Github repository; there is also a tutorial that shows how easy it is to modify the behavior.

How do I disable colors in LaTeX output generated from sphinx?

When I build the LaTeX file generated from sphinx, the TOC entries, and section headers are blue. Is there an easy way to disable coloring these items? If not, is there an easy way to make them black instead? My goal is to print the document on a non-color printer, and the TOC and headings do not look as dark as the rest of the text when I do so.
I would like to make one change that applies to the whole document if possible.
Note: I am using the howto document class.
Update
Thanks to ddbeck's input, I took a closer look at sphinx.sty which defines the colors that I needed to change. I set (created) the latex_elements dictionary in conf.py as follows:
mypreamble ='''
\\pagenumbering{arabic}
\\definecolor{TitleColor}{rgb}{0,0,0}
\\definecolor{InnerLinkColor}{rgb}{0,0,0}
'''
latex_elements = {
'papersize':'letterpaper',
'pointsize':'11pt',
'preamble':mypreamble
}
This worked out exactly as I wanted it. Thanks ddbeck!
You can add LaTeX by using the latex_elements['preamble'] configuration option. If you change the value of that key, you can override Sphinx's normal LaTeX. The docs on this option aren't particularly illuminating, however. You may find this thread from sphinx-dev a bit more helpful; it has more detail on how that might be used, as well as some good links for learning about LaTex (if that's something you need to get black and white output). Finally, it might help to take a look at the default .cls and .sty files.

Adding MS-Word-like comments in LaTeX

I need a way to add text comments in "Word style" to a Latex document. I don't mean to comment the source code of the document. What I want is a way to add corrections, suggestions, etc. to the document, so that they don't interrupt the text flow, but that would still make it easy for everyone to know, which part of the sentence they are related to. They should also "disappear" when compiling the document for printing.
At first, I thought about writing a new command, that would just forward the input to \marginpar{}, and when compiling for printing would just make the definition empty. The problem is you have no guarantee where the comments will appear and you will not be able to distinguish them from the other marginpars.
Any idea?
todonotes is another package that makes nice looking callouts. You can see a number of examples in the documentation.
Since LaTeX is a text format, if you want to show someone the differences in a way that they can use them (and cherry pick from them) use the standard diff tool (e.g., diff -u orig.tex new.tex > docdiffs). This is the best way to annotate something like LaTeX documents, and can be easily used by anyone involved in the production of a document from LaTeX sources. You can then use standard LaTeX comments in your patch to explain the changes, and they can be very easily integrated. If the document lives in a version control system of some sort, just use the VCS to generate a patch file that can be reviewed.
I have used changes.sty, which gives basic change colouring:
\added{new text}
\deleted{old text}
\replaced{new text}{old text}
All of these take an optional parameter with the initials of the author who did this change. This results in different colours used, and these initials are displayed superscripted after the changed text.
\replaced[MI]{new text}{old text}
You can hide the change marks by giving the option final to the changes package.
This is very basic, and comments are not supported, but it might help.
My little home-rolled "fixme" tool uses \marginpar where possible and goes inline in places (like captions) where that is hard to arrange. This works out because I don't often use margin paragraphs for other things. This does mean you can't finalize the layout until everything is fixed, but I don't feel much pain from that...
Other than that I heartily agree with Michael about using standard tools and version control.
See also:
Tips for collaboratively editing a LaTeX document (which addresses you main question...)
https://stackoverflow.com/questions/193298/best-practices-in-latex
and a self-plug:
How do I get Emacs to fill sentences, but not paragraphs?
You could also try the trackchanges package.
You can use the changebar package to highlight areas of text that have been affected.
If you don't want to do the markup manually (which can be tedious and interrupt the flow of editing) the neat latexdiff utility will take a diff of your document and produce a version of it with markup added to visually display the changes between the two versions in the typeset output.
This would be my preferred solution, although I haven't tested it out on large, multi-file documents.
The best package I know is Easy Review that provides the commenting functionality into LaTeX environment. For example, you can use the following simple commands such as \add{NEW TEXT}, \remove{OLD TEXT}, \replace{OLD TEXT}{NEW TEXT}, \comment{TEXT}{COMMENT}, \highlight{TEXT}, and \alert{TEXT}.
Some examples can be found here.
The todonotes package looks great, but if that proves too cumbersome to use, a simple solution is just to use footnotes (e.g. in red to separate them from regular footnotes).
Package trackchanges.sty works exactly the way changes.sty. See #Svante's reply.
It has easy to remember commands and you can change how edits will appear after compiling the document. You can also hide the edits for printing.

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