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Clone or download this repository to your working computer. Then, locate the folder corresponding to the journal you wish to submit to. Use the following table to find your journal. Can't find your journal? Request it here.
| Folder name | Journal(s) | Link to style guide |
|---|---|---|
amstat |
JASA, TAS, JBES, JCGS, SBP, Technometrics | amstat |
biometrical-journal |
Biometrical Journal | biometrical-journal |
biometrics |
Biometrics | biometrics |
biometrika |
Biometrika | biometrika |
biostatistics |
Biostatistics | biostatistics |
ims |
AOAS, AOP, AAP, AOS, SSY | ims |
jss |
Journal of Statistical Software | jss |
stats-in-med |
Statistics in Medicine | statmed |
Copy the entire contents of the appropriate folder to your paper's working directory. If you are working on a paper called mypaper and it is located in ~/Papers/October/ and you want to submit to Biostatistics, then copy the contents of the biostatistics folder to ~/Papers/October/. The folders contain everything necessary to compile a markdown document into the correct Latex format.
Each folder comes with an example Rmarkdown file called example.Rmd and its associated bib file example.bib. The important metadata must be supplied in the yaml front-matter of the markdown document, which are key: value pairs enclosed between --- and ... at the top of the document. For example, the author, title, bibliography, and abstract are defined there:
---
title: Pandoc templates for common statistics journals
author:
- first: Michael
last: Sachs
affilnum: a,b
email: [email protected]
ekey: e1
- first: Homer
last: Simpson
affilnum: b
email: [email protected]
ekey: e2
affiliation:
- name: National Cancer Institute
key: a
- name: Moe's Tavern
key: b
date: October 2014
year: 2014
abstract: 'Lorem ipsum dolor sit amet, consectetur adipiscing elit.'
keywords: In hac; habitasse; platea; dictumst
bibliography: example
...Each journal has their own requirements for front-matter. For details, see the Wikis at the sidebar, or look at the example headers.
When you are ready to compile, it is simple from the command line:
make example.pdfIf you have an Rmd file with R code embedded in it, it will automatically be processed by knitr. If you have just an .md file, no problem, it will be processed directly. To save the intermediate tex file
make example.pdf example.texYou may need to edit the tex by hand, but these templates will get you 99% of the way to submission.
The templates all use natbib to create the citations and reference list, except for AMSTAT, which requires the reference list be contained in the .tex file. In either case, references should be contained in a single bibtex file.
To create in-text citations, use the following guide. Pandoc automatically converts to the natbib style. The following is quoted from the Pandoc README
"Citations go inside square brackets and are separated by semicolons.
Each citation must have a key, composed of '@' + the citation
identifier from the database, and may optionally have a prefix,
a locator, and a suffix. The citation key must begin with a letter
or _, and may contain alphanumerics, _, and internal punctuation
characters (:.#$%&-+?<>~/). Here are some examples:
Blah blah [see @doe99, pp. 33-35; also @smith04, ch. 1].
Blah blah [@doe99, pp. 33-35, 38-39 and *passim*].
Blah blah [@smith04; @doe99].
A minus sign (-) before the @ will suppress mention of
the author in the citation. This can be useful when the
author is already mentioned in the text:
Smith says blah [-@smith04].
You can also write an in-text citation, as follows:
@smith04 says blah.
@smith04 [p. 33] says blah.
If the style calls for a list of works cited, it will be placed at the end of the document. Normally, you will want to end your document with an appropriate header:
last paragraph...
# References
The bibliography will be inserted after this header. Note that
the unnumbered class will be added to this header, so that the
section will not be numbered."
The md document needs to have a YAML header which contains metadata that will be rendered into the final document. This includes the title, abstract, author names, addresses, and so on. Each journal uses these items in unique ways in their Latex templates. Therefore, the headers differ slightly. The common entries are listed in the table below.
| field | description |
|---|---|
title |
Every journal uses the title field. If your title contains a colon (:), enclose it in double-quotes (") |
abstract |
Every journal uses the abstract field. If your title contains a colon (:), enclose it in double-quotes ("). Be sure to check the word limits. |
bibliography |
Path to the .bib file. With the exception of AMSTAT, omit the .bib extension from the filename. |
Details on the possible fields and options for each journal are listed in their own Wikis (see the sidebar). Some entries are allowed to be lists, which follow the following syntax. The list name is at the top. Each element of the list starts with - followed by the first named entry. Every element must contain the same named entries in the key: value syntax.
authors:
- name: Michael C. Sachs
affiliation: National Cancer Institute, Bethesda, MD 20892
email: [email protected]
- name: Homer J. Simpson
affiliation: Moe's Tavern, Springfield, USA
email: [email protected]Raw tex can be inserted directly into the markdown document for things like, equation arrays, sidewaystables, subfloats, and so on. The Journal of Statistical Software encourages the use of the \proglang{} to indicate programming languages, \pkg{} to indicate packages, and \code{}. You can use these in the markdown document just as you would in Latex.
For figures generated in R, I recommend either using the pdf device, or better yet the tikzDevice. For the pdf device, use the chunk option dev='pdf'. For the tikzDevice, insert this chunk at the start of your document.
library(knitr)
knit_hooks$set(plot = function(x, options) {
if ('tikz' %in% options$dev) {
hook_plot_tex(x, options)
} else hook_plot_md(x, options)
})Then use the chunk option dev='tikz'. The main advantage of tikz is that the fonts in the figures will match the document fonts. See the knitr Graphics Manual for more details and examples.