Translate dwc_checklist.R to Rmd, standardize its structure, add website

[peterdesmet]

This pull request contains a bunch of stuff, that I unfortunately couldn't neatly split. 😬 I'm first going to resolve the conflicts and then describe the changes.

[peterdesmet]

This PR contains a HTML website, which explains why so many files were added. Important changes are:

• README: updated cf alien-fishes-checklist
• description.csv: updated DOI format
• distribution.csv: updated DOI format
• speciesprofile.csv: exactly the same data, but no longer sorted on taxonID (cf. distribution and taxon). @LienReyserhove Maybe we should always sort on taxonID for every file (cf. description)
• Move SQL out of src to be close to raw data
• CARTO map has moved from index.html to map.html
• _site.yml: defines website
• dwc_checklist.Rmd: most important update. This file replaces dwc_checklist.R (and dwc_checklist.md). It is restructured exactly like alien-fishes-checklist: https://github.com/trias-project/alien-fishes-checklist/pull/20
• dwc_occurrence.md: had to save as UTF-8 to be able to render. Should be removed once we create a dwc_occurrence.Rmd instead of a dwc_occurrence.R.

I started this branch without internet and unfortunately without the speciesProfile changes (#40), but I have added back.

The dwc_occurrence.R should still be translated to a dwc_occurrence.Rmd, but can best be done in another PR.

[peterdesmet]

Oh, forgot to mention: I moved the join between raw_data and sources to the top (just after generation of taxonID). Currently it was implemented twice (once for distribution and once for description), which is agains DRY (don't repeat yourself) principles. 😄

[peterdesmet]

Regarding the .gitignore:

1) do you have files generated by knit that are not in docs (because that should not happen) 2) normally only html files should be updated... if not, please update all packages first

[LienReyserhove]

Thanks for the changes! I will close this PR when I update the installation guide.

[LienReyserhove]

I updated the installation guide. As promised, I will merge this PR :tada: