EU BON Final Meeting 
Meise, Belgium

March 15th-16th, 9:30 - 18:00

Aqua Maps and tools - the R-package "raquamaps"

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• 30 mins overview of AquaMaps species distribution model and most important tools
• 10 mins overview of rAquaMaps
• 30 mins GeoCAT presentation/hands-on
• 20 mins AquaMaps/rAquaMaps hands-on; additional GeoCAT hands-on

• R package created to support workflows in Aqua Maps scenarios, attempts to follow guidelines from professor Hadley Wickham regarding R package development
  • Guidelines for Advanced R: https://adv-r.had.co.nz/
  • Guidelines for R package dvelopment: https://r-pkgs.had.co.nz/
• The sources (under AGLPv3) and a web site informing about installation procedure are available at github
  • https://github.com/raquamaps
  • https://raquamaps.github.io
• A Docker image bundling all dependencies called "mirroreum" is available for local or server eployment. It also includes all other R-packages developed in EUBON.

This is the version is included in "mirroreum" (along with other EUBON packages):

• Vignette - tutorial that outlines common usage / workflows (3 different)
• Bundles a range of various reference data sets in the package
• Developed on Linux - needs more usage on Windows and Mac
• Workflows for marine versus freshwater realms
• Batch calculations

Tutorials with usage instructions - Vignettes - are available in the package and also online here: - https://raquamaps.github.io/raquamaps-intro.html

The development branch includes latest changes:

• Additional documentation, additional reference data sets
• Quarter-degree cell resolutions
• Getting environmental layers from online sources
• Comparisons of calculations made with raquamaps package and results from aquamaps.org
• Shiny web UI with visualizations

• 30 mins overview of AquaMaps species distribution model and most important tools
• 10 mins overview of rAquaMaps
• 30 mins GeoCAT presentation/hands-on
• 20 mins AquaMaps/rAquaMaps hands-on; additional GeoCAT hands-on

• Running raquamaps locally or on a server
• Usage tutorials / Vignettes in raquamaps

The traditional way… set up your laptop with R and RStudio, then install using instructions at http://raquamaps.github.io/ which involves many steps, installing various dependencies.

Or run it using Docker, using three steps:

# pull binary image from remote and run it locally
docker pull raquamaps/mirroreum:v0
docker run -d -p 8787:8787 -v ./src:/home/rstudio raquamaps/mirroreum:v0
firefox http://localhost:8787

Or run it from a server deployment of the above, using one step:

# run "mirroreum" (get login from sysadmin first)
firefox https://nabis.dina-web.net

All data and all code is provided under open source licenses, along with Makefiles enabling local builds, so you can …

# build from source and run locally
cd repos
git clone https://github.com/raquamaps/mirroreum
cd mirroreum
make build-webide
make webide

Make any improvements or changes available under AGPL3 to keep this work open and to make it possible to merge useful modifications into https://github.com/raquamaps/raquamaps!

Walk through of Vignettes to show how to use the raquamaps package for:

• Automating data retrieval from AquaMaps.org
• Running batch calculations