Evaluating ecological uniqueness over broad spatial extents using species distribution modelling

Manuscript from my M.Sc work on identifying hotspots of unique biodiversity across increasing spatial scales.

Deals with beta diversity, eBird, species distribution modelling, spatial scales, and more!

Manuscript versions

• 📘 website
• 📄 draft
• 📰 preprint
• 🎉 EcoEvoRxiv preprint

Teaser

See the code repo for more!

About the manuscript building

• Edit manuscript.md to make changes to the text.
• The website, draft, and preprint versions are updated after each commit on main.
• Previews are also generated for commits on pull-requests, but they need to be downloaded as artifacts. The two options to access them are:
  1. Go the Actions tab, select the action related to your recent commit, and download the manuscript zip file in the Artifacts section at the bottom of the page.
  2. Go the Checks tab of your PR (or of one of its commits), select one of the jobs on the left, click on Artifacts on the right of the page, and download the manuscript file.

About the references

• We use Zotero for references management
• We use the Better BibTeX plugin for citation key generations
• The citation key format we use is meant to convey information on the author, date, year, and title. It must be set in the Better BibTeX preferences (Preferences > Better BibTeX > Citation keys) 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]
  

• We also use the same package to automatically export the manuscript references to references.bib. To do so, right-click on a collection, select Export Collection, select the Better BibTeX format, and check Keep updated.
• It is a good idea to remove a lot of fields that are not strictly speaking required for references (Preferences > Better BibTeX > Export > Fields). The list of fields we usually ignore is:

  abstract, copyright, annotation, file, pmid, month, shorttitle, keywords
  

About Markdown formatting

• This is a citation: @HampAnde15. We can also have citations in brackets: [@HampAnde15].
• This is an equation, which we can cite with @eq:eq1: $$J'(p) = \frac{1}{\text{log}(S)}\times\left(-\sum p \text{log}(p)\right)$$ {#eq:eq1}
• Inline eq. look like this $\mathbf{U}\cdot\mathbf{\Sigma}\cdot\mathbf{V}^T$
• This is a figure, which we can cite a figure with @fig:biomes: ![This is the legend of the figure](figures/conceptual.png){#fig:conceptual}

More details in the template repo's manuscript.md.