http://statacumen.com/teaching/ada1/
UNM Stat 427/527: Advanced Data Analysis I (ADA1)
Prof Erik Erhardt

Converting from Markdown to LaTeX for poster.

This video illustrates the process below:
  https://www.youtube.com/watch?v=9ttx1FNcOwk&list=PLpN_zjlfJSrATZin6LCWpq9ihsoXpHaqS&index=57

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Step 0:
- Install LaTeX
  - On Windows, open MikTeX options, install Packages Always on-the-fly.
- Place ADA1_PosterTemplate_Portrait.Rnw file in the same folder as your ALL Rmd file.
- Open in RStudio and Compile PDF and verify you see a pdf poster.
- Make sure your ALL Rmd file knits completely.


Step 1:
Export the source code from your Rmd (Markdown) file so it can be read into
your Rnw (LaTeX) file.

  R Console: Output R code from your homework (see top of my HW.Rmd file)
    setwd("C:/Dropbox/UNM/teach/ADA_Redesign_2015/ADA1_Content/homework")
    knitr::purl("ADA1_HW_ALL_NESARC_Project.Rmd")         # write .R file

  LaTeX
  %% Add your HW file's *.R file (from perl()) here
  <<source, cache = TRUE, comment = NA, echo = FALSE, message = FALSE, warning=FALSE, results='hide', include=FALSE>>=
  setwd("C:/Dropbox/UNM/teach/ADA_Redesign_2015/ADA1_Content/homework")
  source("ADA1_HW_ALL_NESARC_Project.R")    # run code into environment, cache results
  @


Step 2:
Copy blocks of text/code from your Rmd file to Rnw, fix up into LaTeX, and
compile.  Do one small part at a time and make sure each change you make
continues to work. If it stops working, it was the last thing you did.  Read
any compile error message and try to fix it.


Step 3:
Figure sizes. Adjust fig.width and fig.height for the size the figure is
created, then adjust out.width for the size the figure is displayed on the
page. For example, if fig.* were both really big (around 20, inches is the
unit), but out.width='1\\textwidth', then the text would look very small (since
a big image was squeezed into a small area). This is one strategy for
controlling the text size of the figure.


Bibliography:
For the bibliography to show, it needs to be compiled from auxilary files that are created when the poster is first compiled.
Then, the poster needs to be compiled again to incorporate the bibliography information.
Whenever citations are added or removed, the bibliography should be recompiled.

To compile (bibtex) the bibliography:
- Set WD: Session / Set Working Directory / Choose Directory ...
- Get terminal in WD: Tools / Terminal / New Terminal
- Verify you're in the folder/directory with your poster files:
  - dir [Enter]   (if Windows)
  - ls  [Enter]   (if Mac or Linux)

    Example output:
      C:\Users\erik\Desktop>ls
      ADA1_PosterTemplate_Portrait.nav   ADA1_PosterTemplate_Portrait.toc   UNM_logo.pdf
      ADA1_PosterTemplate_Portrait.Rnw   ADA1_PosterTemplate_Portrait.out   ADA1_PosterTemplate_Portrait.vrb
      ADA1_PosterTemplate_Portrait.aux   ADA1_PosterTemplate_Portrait.pdf   beamerthemeUNM.sty
      ADA1_PosterTemplate_Portrait.bbl   ADA1_PosterTemplate_Portrait.snm   bib_example.bib
      ADA1_PosterTemplate_Portrait.log   ADA1_PosterTemplate_Portrait.tex   figure
      NESARC.RData                       AddHealth.RData                    addhealth_public4.RData

- bibtex [poster file name, no period or extention]
  - bibtex ADA1_PosterTemplate_Portrait

    Example output:
      C:\Users\erik\Desktop>bibtex ADA1_PosterTemplate_Portrait
      This is BibTeX, Version 0.99d (MiKTeX 2.9.7140 64-bit)
      The top-level auxiliary file: ADA1_PosterTemplate_Portrait.aux
      The style file: plain.bst
      Database file #1: bib_example.bib



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A Helpful reference for translations between Markdown and LaTeX

Code chunks
  Markdown
    ```{R, options}
    code
    ```
  LaTeX
    <<unique_name, options>>=
    code
    @

Citations
  Markdown
    [@ref1;@ref2]
  LaTeX
    \cite{ref1,ref2}

List
  Markdown
    * a1
    * a2
  LaTeX
    \begin{itemize}
    \item a1
    \item a2
    \end{itemize}

Bibliography
  Markdown
    bibliography: bibfile.bib
  LaTeX
    \bibliography{bibfile}

Values in text
  Markdown
    `r nrow(NESARC)`
  LaTeX
    \Sexpr{nrow(NESARC)}

Variable names in text
  Markdown
    `VarName`
  LaTeX
    \verb|VarName|

Quotes
  Markdown
    "begin and end"
  LaTeX
    ``begin and end''

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