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# vikasrawal / orgpaper

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# Introduction

This guide introduces an open-source toolkit for writing research papers and monographs. The main features of this toolkit centered around Emacs and Org-mode are:

• embedded R code in the document that allows for statistical results to be revised and reproduced,
• bibliographic citations from a personal bibliographic database,
• formatting using well defined styles with minimal markup,
• support for production of final output as pdf, odt, docx, html and many other formats.

## Will this guide be useful for you?

This guide will be useful for you if you are writing a research paper, a dissertation or an academic book. It would be useful if your writing involves one or more of the following:

• Citing existing literature in your area
• Presenting results of statistical analyses (in tabular form and/or graphically)
• Using mathematical equations

Following this guide would need some investment of time but benefits far outweigh the investment you make.

## What is our goal?

What are the most interesting features of the writing platform that you will set up using this guide?

• With easy style specifications that you provide, the document will be almost-entirely automatically formatted by the software.
• Complicated LaTeX-style markup is a pain and Openoffice/MS-Word documents require too much manual formatting. Basic Org-mode mark-up is extremely simple, and can be mastered in very little time.
• Org-mode can produce well formatted output in LaTeX, pdf, odt, docx, html and many other formats.
• Instead of including statistical results (tables, graphs, etc), we would embed appropriate R programs in the document, so that when the formatted output is produced, all programs are run to generate the results. Advantages of doing this are:
• Any changes in the data being used can be accommodated just by publishing the document again.
• Any modifications in statistical analysis are easily made by modifying the programs that are embedded in the file itself.
• Anyone who has the org file, can reproduce your results. You can also extract all R programs from the org file and distribute those for reproduction of your results.
• The document will be integrated with a citation manager, so that bibliographic information will be pulled automatically from a central database to create a fully formatted bibliography.
• You will maintain a bibliographic database in BibTeX format, that you can build over time, adding bibliographic information for works that you cite.
• Many websites (including Google Scholar) provide bibliographic information directly in BibTeX format, and we will have integrated tools that will allow us to pull this information directly into our local database.

## Acknowledgements

In my adaptation of Org, I have benefitted immensely from the great community of Orgers. The Org-mode manual, Worg, and archives of the Org-mode mailing list have been the most important resources. In addition, I have greatly benefited from solutions provided by various people to my specific queries on the Org-mode mailing list. What I present in this document is essentially a synthesis of solutions provided by various people. The community has been extremely generous in providing these.

I would particularly like to thank

• Carsten Dominik, the author of Org-mode.
• Bastien Guerry, who has been a great maintainer of Org-mode, after Carsten passed on the baton to him.
• Nicolas Goaziou, who wrote the brilliant new exporter framework. The amount of code Nicolas has contributed to Org over the last two years or so is incredible. Nicolas very kindly responded to several of my queries.
• Eric Schulte, the main author of Babel, which gave Org mode the ability to execute code. I used to use Org-mode as a task manager and for taking notes. I discovered org-babel in the summer of 2010, when I was doing fieldwork in villages in eastern India. This discovery completely changed my work flow, and Org-mode became central to all my academic work.
• In addition to the above, Suvayu Ali, for responses to several of my queries on the mailing list.

# Installing necessary software

This set up will work with any operating system. I have tested it on GNU/Linux and Mac OS-X, but it should work on Windows as well. For this setup, you need to install Emacs (Version 24 along with a few additional Emacs packages), Texlive, R (along with whatever additional R packages you want to use) and Pandoc.

## Emacs

• GNU/Linux

Emacs can be installed using package managers of all GNU/Linux distributions. Latest versions of most common distributions provide version 24. I strongly recommend using the latest version of Emacs.

• Mac OS-X

The built-in Emacs on OS-X is an older version, and it would be a good idea to install the latest version instead.

The best option is to install it via homebrew. I like the version available from railwaycat/emacsmacport tap (https://github.com/railwaycat/emacs-mac-port).

After installing homebrew, or if you already have it installed, just do the following from the terminal

$brew tap railwaycat/emacsmacport $ brew install emacs-mac

• Microsoft Windows

## R

In this guide, I assume that you are familiar with R (http://www.r-project.org). I will not cover R programming in this guide.

For GNU/Linux, R can be installed from native package managers (look for r-base in debian and debian-based distributions). For Mac OS-X and Windows, download and see installation instructions at http://www.r-project.org

## Pandoc

Pandoc (http://johnmacfarlane.net/pandoc/) is an extremely powerful converter, which can translate one markup into another. It supports conversion between many file formats, and supports “syntax for footnotes, tables, flexible ordered lists, definition lists, fenced code blocks, superscript, subscript, strikeout, title blocks, automatic tables of contents, embedded LaTeX math, citations, and markdown inside HTML block elements.” That is pretty much everything I use.

We shall use pandoc to convert our file from LaTeX to odt/docx/html formats.

# Emacs basics

GNU Emacs is an extensible platform. Although its primary function is as an editor, it can be extended to do almost anything that you would want your computer to do. Now, that really is not an overstatement. It is a worthwhile aim to slowly shift an increasing number of tasks you do on your computer to emacs-based solutions. For each major task you do on your computer, ask if it can be done using emacs. For almost everything, the answer is yes, and in most cases, emacs does it better than other software you are used to. Many emacs users have learnt emacs by shifting, one-by-one, all major tasks that they do on the computer to emacs.

I am not going to give a detailed guide to use of emacs. A few tasks for which I use Emacs include

• File management (copying files, moving files, creating directories)
• Calender, scheduler, planner
• Calculator
• Statistical work (by hooking Emacs to R)
• And, of course, as an editor (including for writing research papers)

In this guide, I will just provide a minimal set of basic commands in emacs to get you started. This is a minimal but sufficient set to be able to work. I expect that you would learn more commands as you start using emacs.

## Notations

In emacs, a buffer is equivalent to a tab in a web browser. It is normal to have several buffers open at the same time. Each file opens in emacs as a buffer. Buffers could also have processes like R running in them. Emacs displays any messages for you in a separate buffer.

Most commands in emacs are given using the Control (ctrl) or the Meta (often mapped to alt) keys.[fn:3] Control key is usually referred to as C- and the Meta key as M-. So a command C-c means pressing Control and c together. Command M-x means pressing Meta and x together. Everything is case-sensitive. So M-X would mean, pressing Meta, Shift and x together. C-c M-x l would mean pressing C-c, release, then M-x, release, and then l.

## Basic commands

Table essential-emacs-commands gives the commands that are the most important. This is a minimal set, commands that you should aim to learn as soon as possible. There are many more, which you will learn as you start using emacs.

All commands have a verbose version that can be used by pressing M-x and writing the command. For example, M-x find-file to open a file. All major commands are also mapped to a shortcut. For example, instead of typing M-x find-file to open a file, you can say C-x C-f. I remember shortcuts for commands that I use most frequently. For others, I use the verbose versions. Over time, one learns more shortcuts and starts using them instead of the verbose versions.

 M-x followed by Description Verbose command Shortcut *Opening files, saving and closing* Open a file find-file C-x C-f Save the buffer/file save-buffer C-x C-s Save as: prompts for a new filename and saves the buffer into it write-named-file C-x C-w Save all buffers and quit emacs save-buffers-kill-emacs C-x C-c *Copy, Cut and Delete Commands* Delete the rest of the current line kill-line C-k To select text, press this at the beginning of the region and then take the cursor to the end set-mark-command C-spacebar Cut the selected region kill-region C-w Copy the selected region copy-region-as-kill M-w Paste or insert at current cursor location yank C-y *Search Commands* prompts for text string and then searches from the current cursor position forwards in the buffer isearch-forward C-s Find-and-replace: replaces one string with another, one by one, asking for each occurrence of search string query-replace M-% Find-and-replace: replaces all occurrences of one string with another replace-string *Other commands* Divide a long sentence into multiple lines, each smaller than the maximum width specified fill-paragraph M-q *Window and Buffer Commands* Switch to another buffer switch-to-buffer C-x b List all buffers list-buffers C-x C-b Split current window into two windows; each window can show same or different buffers double-window C-x 2 Remove the split zero-window C-x 0 When you have two or more windows, move the cursor to the next window other-window C-x o *Canceling and undoing* Abort the command in progress keyboard-quit C-g Undo undo C-_

# Customising emacs

Emacs is highly customisable. We need several emacs packages and customisations for our workflow.

### Install prelude

While emacs may be customised for individual features, using a kit makes the task easier. Prelude is one such kit.

To install Prelude, download it from here and unzip the files in ~/.emacs.d directory. Better still, clone it using git.


#+NAME: tabularx-yield-out
#+CAPTION: Table formatted using tabularx and siunitx packages
#+ATTR_LATEX: :environment tabularx :width 0.8\textwidth
#+ATTR_LATEX: :align @{}l{S[table-format=3.0]}{S[table-format=5.2]}@{}
#+ATTR_LATEX: :center t :booktabs t :float t
| State          | {{{MCONE(Average yield)}}} | {{{MCONE(Average income)}}} |
|----------------+----------------------------+-----------------------------|
| Haryana        |                        300 |                     2532.30 |
| Punjab         |                        260 |                    35232.45 |

State{{{MCONE(Average yield)}}}{{{MCONE(Average income)}}}
Haryana3002532.30
Punjab26035232.45

### Notes below tables

LaTeX package threeparttable is used for including notes below the table. For using threeparttable you need to call the package. In addition, it is a good idea to include the following special line for better formating of notes below the table

#+LATEX_HEADER: \renewcommand{\TPTminimum}{\linewidth}


The following code produces a table with notes below.

#+NAME: threeparttable-table-yield
#+CAPTION: Table created using tabularx, siunitx and threeparttable
#+ATTR_LATEX: :float t :options [hb] :center t
#+begin_table
#+begin_threeparttable
#+ATTR_LATEX: :environment tabularx :width 0.8\textwidth
#+ATTR_LATEX: :align @{}l{S[table-format=3.0]}{S[table-format=5.2]}@{}
#+ATTR_LATEX: :booktabs t
| State          | {{{MCONE(Average yield)}}} | {{{MCONE(Average income)}}} |
|----------------+----------------------------+-----------------------------|
| Haryana        |                        300 |                     2532.30 |
| Punjab         |                        260 |                    35232.45 |
#+attr_latex: :options [flushleft]
#+begin_tablenotes
#+begin_footnotesize
\item[] \textit{Notes}:
1. This table is very nice. This note is very long. But the long note wraps nicely under the table.
2. This is the second note. But this is not very wide.
\item[] \textit{Source}: http://www.indianstatistics.org}
#+end_footnotesize
#+end_tablenotes
#+end_threeparttable
#+end_table


The notes use just a little bit of direct LaTeX coding. \item[] ensures that Note and Source start from a separate paragraph.

I have used footnotesize to render the notes in a slightly smaller font. Option [flushleft] is used to align the notes to the left.

# Org-mode and R

## Configuration

Following code in research-toolkit.org enables Org to run different types of code. If you have installed research-toolkit.org as specified in #customemacs, these are already enabled.

I have included here the languages that I commonly use. See Org manual, if you would like to add any more.

(org-babel-do-load-languages
'((R . t)
(org . t)
(ditaa . t)
(latex . t)
(dot . t)
(emacs-lisp . t)
(gnuplot . t)
(screen . nil)
(shell . t)
(sql . nil)
(sqlite . t)))

## Special lines for R

Org allows you to run multiple R sessions simultaneously, if you are working on two documents side by side, and would like to keep statistical work for the two separately.

This is done by naming the R session which a particular Org file is linked to. All R code in this file would be run in the specified R session. You could have, at the same time, another R session, with a different name, being called by another Org buffer.

We can give a name to the R session (let us say, my-r-session) that our Org buffer should be linked to by adding the following line at the top (in the preamble, that is).

#+property: session my-r-session


## Embedding R code in an Org document

Org uses ESS (emacs-speaks-statistics) to provide a fully functional, syntax-aware, development environment to write R code. R code is embedded into Org as a source block. The basic syntax is

#+NAME: name_of_code_block

#+END_SRC


This is how source blocks are created.

• First write the lines starting with #+NAME, #+BEGIN_SRC and #+END_SRC.
• Then with your cursor in between the BEGIN_SRC and the END_SRC lines, give the command C-c ’ (that is, press Ctrl-C, release, and press ‘).
• This would open a new buffer using ESS mode. If you type your code in this buffer, you will see that ESS is syntax-aware and nicely highlights R code.
• ESS also allows you to run (evaluate) the code that you write, to test what your code is doing. Use C-j for evaluating a single line of code, C-b for evaluating the whole ess buffer, or C-r for a marked region within the ess buffer.
• Once you have finished writing a code block and tested it, press C-c ’ again to come back to your Org buffer.
• In your Org buffer, with your cursor in a source-block, press C-c C-c to evaluate the whole code block and have the results included in your document.
• You can always edit your source code by opening a temporary ESS buffer using C-c’

## Code blocks that read data and load functions for later use in the document without any immediate output

I normally have one or two code blocks that read the data I am going to use, call the libraries that I use, and define a few functions of my own that I plan to use. I want this code block to be evaluated, so that these data, libraries and functions become available in my R environment. But no output from such code blocks is expected to be included into the document.[fn:4]

Code block readdata-code is an example of such a code block. Note :results value silent switch used in the #+begin_src line.

#+NAME: readdata-code
#+BEGIN_SRC R :results value silent

#+END_SRC


## Code blocks that produce results in the form of a table

Most of code blocks in my papers fall in this category. The code block may use data and functions made available by previous code blocks, read some new data and may load some new functions. The code block does some statistical processing. The last command of the code block produces an object (for example, a data.frame) that is included in the document as a Table.

For example, the code block r-code-table below uses mydata1 read in the previous code block, reads a new dataset, and processes them to create a table that shows average BMI by country.

#+NAME: bmi-table-code
#+BEGIN_SRC R :results value :colnames yes :hline yes
aggregate(height~Country,data=mydata1,mean)->a1
aggregate(weight~Country,data=mydata2,mean)->a2
merge(a1,a2,by="Country")->a1
a1$weight/a1$height->a1\$BMI
subset(a1,select=c("Country","BMI"))
#+END_SRC


You can evaluate this code using C-c C-c. When you do that, it produces the output, and places it immediately below the code block. The results display the output of the code under a line that looks like below

#+RESULTS: bmi-table-code


Note that the results are tied to the code block using the name of the code block. Every time you go to the source code block and press C-c C-c, the code will be evaluated again and the results will be updated.

On top of the line starting with #+RESULTS:, we shall add two more lines, to give the table a title and a name. Note that both the code block and the result of the code block have separate names.

#+NAME: bmi-table-output
#+CAPTION: Average BMI, by country
#+RESULTS: bmi-table-code


Like any Org table, you can cross-refer to this table using [[bmi-table-output]].

## Code blocks that produce a graph to be included in the document

These code blocks can have a series of commands. The last command produces a graph that we would like to be included in the document.

The following code shows an example of a code block that produces a graph.

#+NAME: mygraph-code
#+BEGIN_SRC R :results output graphics :file bmi2.png :width 825 :height 1050 :fonts serif

#+END_SRC


As before, for creating your graph, you first write the #+NAME, BEGIN_SRC and the END_SRC lines, and then go into a temporary ESS buffer by using C-c ‘.

• Once in this temporary ESS buffer, you can write the R commands for making your graph.
• As you write, you can evaluate the commands using C-j, C-r and C-b and see what your output looks like.
• The output is displayed on your screen using the default graphic device used by R (X11, quartz or windows graphic device depending upon your operating system).
• Once you have finalised your graph, you press C-c ’ and come back to the Org buffer.

Note that creation of the image file is left to appropriate switches in the #+BEGIN_SRC line. Org automatically chooses appropriate graphic device to produce the file. When you evaluate this code using C-c C-c, the results are displayed below the code block as follows.

#+RESULTS: mygraph-code
[[bmi2.png]]


Note that, taking the file name from our #+BEGIN_SRC line, a file called bmi2.png was automatically created and linked, so that the graph would be inserted in the document when you produce the formatted output.[fn:5] Every time you evaluate the code using C-c C-c, the underlying image file containing the graph is overwritten by a new file.

As with the tables, we shall add a caption and a name to it as follows

#+NAME: my-bmi-graph
#+CAPTION: Average BMI, by Country
#+RESULTS: mygraph-code
[[gini.png]]


You can now refer to this graph in the text using [[my-bmi-graph]].

# Citations and Bibliographies using Org-mode

We shall use a master bibliographic database to contain bibliographic records for the literature that we cite. The database, in Biber or BibTex format, is stored in a text file with .bib extension.

In a BibTex/Biber database, each bibliographic record is given a unique key, which is used to cite it. Each record is classified as one among various categories of publications (journal article, book, etc.), and for the given publication type, the record specifies values for various fields (author, title, volume, publisher, etc). Biber recognises a wider variety of publication types and fields than BibTex, and is a better choice to use. Since it is compatible with BibTex, you can also add a BibTex record as it is as a Biber record.

To start with, it may be a good idea to use applications like JabRef (cross-platform, http://jabref.sourceforge.net/) or BibDesk (OS-X only, http://bibdesk.sourceforge.net/) to build your database. Eventually, you should use bibretrieve and RefTeX (http://www.gnu.org/software/auctex/reftex.html) from within Emacs to add entries to your database. org-ref.el provided by John Kitchin (https://github.com/jkitchin/jmax) has some useful functions.

Bibliographic information in BibTex/Biber format is available from many online sources, including Google Scholar. JabRef/BibDesk allow you to directly import BibTex citations from online databases rather than having to enter everything yourself. Of course, where the bibliographic information in BibTex/Biber format is not available from any existing database, you may have to enter the information yourself.

As a sample, my own bibliographic database is available from https://github.com/indianstatistics/bibliobase/blob/master/bibliobase.bib.

## Using biblatex with Org

### Setup

Using biblatex with Org requires some customisation of variables. This is already done for you if you have installed research-toolkit.org.

The operative part in research-toolkit.org is the following:

(setq org-latex-to-pdf-process
'("pdflatex %f" "biber %b" "pdflatex %f" "pdflatex %f"))


Once this is done, every time you export the document to pdf via latex, it runs pdflatex, then runs Biber and then runs pdflatex twice again. This is necessary to get the citations in the pdf file.

In research-toolkit.org, the package biblatex is loaded with following options:

("citestyle=authoryear-icomp,bibstyle=authoryear,hyperref=true,backref=true,
maxcitenames=3,url=true,backend=biber,natbib=true" "biblatex" t)


You may want to modify this if you want to change the citation and bibliography styles. If you want to do it differently in each document, you can remove this line from research-toolkit.org, and add the following special line in your document.

#+LATEX_HEADER: \usepackage["citestyle=authoryear-icomp,bibstyle=authoryear, \
hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true"] {biblatex}


### Adding citations and bibliography in Latex/PDF export

The following special line, to be placed among other special lines at the top of the file, specifies the BibTex/Biber database that has the bibliographic records.

#+LATEX_HEADER: \addbibresource{filename.bib}


There are various commands that you can use for citations. These use different styles for citation. The general syntax of citation commands is:

\command[<prenote>][<postnote>]{<Key>}

Where [<prenote>] refers to any text you want before citation (for example “for more details, see”) and [<postnote>] refers to any text you want after citation (for example, “Chapter 2”).

The two most useful citation commands are \parencite (or \citep) and \citet. Their usage is illustrated in Table citation-commands.

Citation commandOutput
\parencite{jon90}(Jones et al., 1990)
\parencite[chap. 2]{jon90}(Jones et al., 1990, chap. 2)
\parencite[see][]{jon90}(see Jones et al., 1990)
\parencite[see][chap. 2]{jon90}(see Jones et al., 1990, chap. 2)
\parencite*{jon90}(Jones, Baker, and Williams, 1990)
\citet{jon90}Jones et al. (1990)
\citet[chap. 2]{jon90}Jones et al. (1990, chap. 2)
\citet*{jon90}Jones, Baker, and Williams (1990)

To insert the bibliography, add the following line where you want to insert the bibliography (usually, at the end of your paper, but before the Footnotes)

\printbibliography


# Producing a formatted LaTeX, pdf, odt, docx or html file

From Org, we can get a well-formatted document as a LaTeX, PDF, odt, docx or html file. To produce a formatted output, we shall use the built-in exporters provided with Org, and for some file types, use Pandoc for further conversion.

Built-in exporters can be called in Org using C-c C-e or M-x org-export-dispatch.

## Creating LaTeX and/or PDF files

The file default_packages.org lists a set of LaTeX packages that I normally use. Please modify this as you please, save it in a convenient location, and call it using a line of the following kind.

~#+INCLUDE: “path/to/default_packages.org”~

For producing LaTeX and/or PDF files, use C-c C-e to call the Org export dispatcher.

• Press l to select LaTeX, and then chose one of the following options.
• Press l again, if you just want to create a LaTeX file
• Press p, if you want to create a pdf file. This will first create a latex file, then use pdflatex and Biber to create a pdf file.
• Press o, if you want to create pdf and have it opened in the default pdf viewing application.

## Creating odt or docx files

There is a built-in odt exporter in Org. While it works well for most situations, there are two components of the setup proposed here that it does not support. It does not support biblatex and it does not support LaTeX-specific solution we have for Notes under Tables and Images.[fn:6]

Fortunately, Pandoc provides an excellent solution for converting LaTeX output to odt or docx documents. Pandoc supports all the LaTeX syntax that Org produces from our files, and you can get a very well formatted output.

Use C-c C-e l l to create a LaTeX file. Then, from the terminal, use Pandoc as follows to create an odt or a docx file.

pandoc --bibliography=biblidatabase.bib --filter pandoc-citeproc \
latexfile.tex -o outputfile.odt

pandoc --bibliography=biblidatabase.bib --filter pandoc-citeproc \
latexfile.tex -o outputfile.docx


If you want, you can use –template to specify an ott or a .dotx template file, so that the fonts and other formatting attributes are to your liking.

## HTML

For html as well, there is a built-in exporter in Org. The built-in exporter is very good, and the way to go if you are planning to maintain a website using Org (as I do for http://www.indianstatistics.org).

The built-in exporter can support BibTex citations using ox-BibTex.el, which is including in Org, and will be loaded if you have installed research-toolkit.org. You may need to install BibTex2html separately to make it work.

However, ox-BibTex.el uses BibTex2html for converting citations and bibliography to html. BibTex2html provides limited support for citation and bibliography styles.

If you want full support for bibliography and citation styles, as well as for other LaTeX components like Table notes explained in this document, you can use Pandoc for converting LaTeX to html.

This section points some additional solutions that you may like to use. Some of these may come handy when you start using Org for documenting your research.

## Evaluating code during export

By default, Org evaluates source code at the time of exporting. If your code involves a lot of computation, this can slow down exporting.

You can block evaluation of a source code block at the time of export by using :eval never-export in the header arguments of the block. Such code blocks will have to be evaluated manually using C-c C-c. To prevent all blocks from being evaluated, set it buffer-wide using:

#+PROPERTY: header-args :eval never-export~


If your buffer has this line, the source code is not evaluated at the time of export, and whatever already exists in #+RESULTS block is exported.

## Fonts

I like to use the Garamond font. If you do too, add this special line at the top:

#+LaTeX_CLASS_OPTIONS: [garamond]


## Margins

In LaTeX, package Geometry allows you to modify page margins. The following line in research-toolkit.org sets the margins. You can tweak this to define the margins as you like.

("innermargin=1.5in,outermargin=1.25in,vmargin=1.25in" "geometry" t)


If you would like to do it for each document separately, remove the above line, and add the following special line at the top in your documents.

#+LaTeX_HEADER: \usepackage[innermargin=1.5in,outermargin=1.25in,vmargin=3cm]{geometry}


## Line spacing

Use the following line at the top. Modify the number to whatever suits you.

#+LATEX_HEADER: \linespread{1.3}


## Acknowledgements in footnote

When writing a research paper, it is common to put acknowledgements in a special footnote to names of authors. It is conventional to use * as the symbol for this footnote, and to keep this footnote out of the list of numbered footnotes that the paper may have.

This is achieved as follows.

• As illustrated in the example below, add acknowledgements in the special line that specifies authors of the paper.
#+AUTHOR: Vikas Rawal\footnote{Write your acknowledgements here...}

{% begin group
\renewcommand{\thefootnote}{\fnsymbol{footnote}}% set smybols
\setcounter{footnote}{0}% set footnote counter back to 0
}% end group


## Restricting location of tables and images in LaTeX export

LaTeX has a very sophisticated algorithm for determining the location of Tables and Images in a document. If, however, you want to add a restriction that the Tables and Images should not cross section boundaries, or a particular boundary, this can be done using command \FloatBarier provided by placeins package in LaTeX.

You can put any number of \FloatBarrier commands, each in a line by itself, in the document. Tables and Images before such a barrier will be placed before the barrier.

You can use the following special line at the top to restrict all Tables and Images within their own sections.

#+LATEX_HEADER: \usepackage[section]{placeins}


An extension to placeins package, extraplaceins can be used if you want to restrict the Tables and Images within subsections.[fn:7]

## Customising Biblatex style

I like to use authoryear bibliography style. However, I need some customisations. The file vikas-bibstyle.org contains all my customisations.

#+INCLUDE: /path-to-the-file/vikas-bibstyle.org

# Footnotes

[fn:1] These are available at http://mirrors.ctan.org/macros/latex/required/tools/tabularx.pdf and http://mirrors.ctan.org/macros/latex/contrib/siunitx/siunitx.pdf.

[fn:3] Depending on the keyboard and the default configuration of the flavour of emacs you have installed, Meta may instead be mapped to a different key (for example, Windows key, or Option or Command key in Apple computers.

[fn:4] For libraries and functions that you need to call, it is even better to include them in a .Rprofile file in your working directory. These libraries and functions would then be called when R is started, and not each time you evaluate code blocks in your document.

[fn:5] Of various image formats, I find that png files are most versatile. png files support transparency, and are rendered well both on the web and in print. You can also specify jpeg or pdf files. pdf files for images work very well if you are only going to produce a pdf document.

[fn:6] Author of the odt exporter has chosen to develop the exporter outside Org-mode. He has developed a JabRef exporter to integrate citations into odt exports, but that is not a part of Org-mode and needs to be installed separately. In any case, since our toolkit primarily uses LaTeX, using Pandoc to create odt or docx files from LaTeX export works better.

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