Pandemics

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Check our demo to have a practical example of the formatting possibilities of Pandemics.

Text formatting

You can format text (eg. titles, italics, lists, etc.) using the Markdown syntax. You can find a lot of resources on the web to learn Markdown, like this tutorial. Don’t worry, it will only take you a couple of minutes.

Example

manuscript.md

# A section title
Lorem ipsum.

## A subsection title
- An item in *italic*
- A **bold** item

manuscript.pdf

A section title

Lorem ipsum.


A subsection title

  • An item in italic
  • A bold item

Figures

You can integrate images in your document using the classic Markdown syntax:

![The image legend](relative-path-to/the-image.png)

The path should be given relative to your document.

You can also associate the image with a label. You can then refer to this label, and Pandemics will replace all the references with the correct numbering.

![The image legend](relative-path-to/the-image.png){#fig:my-label}

See figure @fig:my-label.

Some output formats also accept the specification of image attributes, eg.:

![The image legend](relative-path-to/the-image.png){width=60%}

Citations

You can insert references in your markdown document using the markdown citation syntax. By default, Pandemics will look for a bibliography.bib bib file in the source folder to parse the references. You can however override this default by specifying the relative path to you .bib files in the front-matter:

---
bibliography: myReferences.bib
---

You can also provide multiple .bib files if needed:

---
bibliography:
  - myReferences.bib
  - ../shared/references.bib
---

Example

manuscript.md

As demonstrated by @doe2018, ...
# References

bibliography.bib

@article{doe2018,
  author={Doe, John},
  year={2018},
  title={A fantastic paper}
}

manuscript.pdf

As demonstrated by Doe (2018), …


References

Doe, John. 2018. “A Fantastic Paper.”

Equations

You can write equations using the LaTeX syntax. You would just need to enclose your mathematical expression either between $ … $ (inline mode) or $$ … $$ (bloc mode).

As for images, you associate a label to your equation so you can them refer to it and generate an automatic equation numbering:

Example

manuscript.md

$$ \beta = a^2 $${#eq:my-equation}

See equation @eq:my-equation.

manuscript.pdf

See equation 1.

Tables

The best way to include a table is to import it from an external file in .csv format. Of course, you can also enter your table manually using the markdown syntax. Either way, you can add after your table a caption and a label for cross referencing.

Example

manuscript.md

<!-- #csv my-table.csv -->
: A dynamically loaded table {#tbl:dynamic}

See table @tbl:dynamic.

my-table.csv

, Header 1, Header 2
Variable 1, Value A, Value B
Variable 2, Value C, Value D

manuscript.pdf

  Header 1 Header 2
Variable 1 Value A Value B
Variable 2 Value C Value D
Table 1. A dynamically loaded table


See table 1.

Verbatim code

Like for tables, you can either load your code directly from its source file or type it directly in your manuscript between single (' … ', inline) or triple (''' … ''', bloc) fences. With the right recipe, you can have some nice syntax highlighting adapted to the language (automatically detected for dynamically loaded code).

Example

manuscript.md

```js
console.log('Hello World!')
```
<!-- #code some-code.py -->

some-code.py

print("I am Py.")

manuscript.pdf

console.log('Hello World!')



print("I am Py.")

Live results

You can integrate values or elements that have been generated by an external software using Mustache templating templating in your document. This way, you can be sure that you compiled document will always be up-to-date.

To do so, you simply need to specify one or multiple .json or .yaml files which contain the data to be parsed, and Pandemics will automatically take care of it. By default, Pandemics will also look for a results.json file in the same directory as the compiled document and try to mustache it. You can however override this default in the front-matter of your document:

---
mustache: myResults.json
---

or

---
mustache:
  - myResultsA.yaml
  - myResultsB.json
---

Example

manuscript.md

There was an effect ($\beta$ = {{ exp1.beta }}, p = {{ exp1.pvalue }}).

results.json

{
  "exp1": {
    "beta": 2.80,
    "pvalue": 0.036
  }
}

manuscript.pdf

There was an effect of treatment (β = 2.80, p = 0.036).

Multiple files documents

If your working on a large project, you might want to split your manuscript in multiple files (eg. chapters). As for tables and code, you can include those file in your main document in a single line, Pandemics will take care of merging everithing

Example

manuscript.md

<!-- #include chapters/*.md -->

chapters/chapter-1.md

# A title

A paragraph.

chapters/chapter-2.md

# Another title

Another paragraph.

manuscript.pdf

A title

A paragraph.


Another title

Another paragraph.

Comments

You can prevent any part of your manuscript from being displayed in the compiled document by wrapping it in in the special <!-- … --> markup. This allows you eg. to write comments that the authors can read but will not appear in the published version.

Example

manuscript.md

A short sentence, <!-- We need to be more specific here  --> and another one.

manuscript.pdf

A short sentence, and another one.

And more

Pandemics can also interpret other formatting tricks, like footnotes (^[This is a footnote]), links ([inline link](url)), format specific markup (eg. HTML spans and divs with associated class), etc. Checkout the pandocs markdown documentation for an exhaustive list of all the features supported by Pandemics.