This template uses recent versions of pandoc and pandoc-crossref to faciltate the referencing of equations, figures, and tables within the text. For example, the following equation

$$J'(p) = \frac{1}{\text{log}(S)}\times\left(-\sum p \times \text{log}(p)\right)\qquad(1)$$

is produced using

$$J'(p) = \frac{1}{\text{log}(S)}\times\left(-\sum p \times \text{log}(p)\right)$$ {#eq:eq1}

and can be referenced using @eq:eq1, which will result in eq. 1.

All documents will be deployed to gh-pages only on push events from the master All of the artifacts will be built when doing pull requests, so you can check that merging a branch is not going to cause the compilation of the documents to fail.

Using references

The references are managed by the citeproc filter for pandoc. Note that we do not use pandoc-citeproc, which was an external moduler for older pandoc versions. References have to be stored in a references.bib file. We use Zotero for references management, and for the lab’s manuscripts, we work from folders in a shared library (with a folder for every manuscript).

We use the Better BibTeX plugin for citation key generations, and auto-export of the shared library to the references.bib file. We use a citation key format meant to convey information on the author, date, year, and title. It must be set in the Better BibTeX preferences as

[auth:fold][year][title:fold:nopunctordash:skipwords:lower:select=1,1:substring=1,3:capitalize][title:fold:nopunctordash:skipwords:lower:select=2,2:substring=1,3:capitalize]

The citations are done using normal markdown, where @Elton1927AniEco produces Elton (1927), and [@Camerano1880EquViv] produces (Camerano 1880).

Tables

Tables are supported in their normal markdown way:

Figures

Figures can have a legend – all figures must be in the figures/ folder of the project:

![This is the legend of the figure](figures/biomes.png){#fig:biomes}

We can now use @fig:biomes to refer to fig. 1.

References