Welcome to ...                        https://raquamaps.github.io
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Introduction

raquamaps is a set of tools that make it easier to produce Aqua Maps - model-based large-scale predictions of natural occurrences of marine species. The default model uses estimates of environmental preferences with respect to depth, water temperature, salinity, primary productivity, and association with sea ice or coastal areas. These estimates of species preferences, called environmental envelopes, are derived from large sets of occurrence data available from online collection databases.

It's already possible to create Aqua Maps using https://aquamaps.org, but the raquamaps package offers an open source alternative to the earlier MS Access based solution, which simplifies licensing issues and creates a solution which is easier to integrate, maintain and develop further.

This package can be used in an IDE like RStudio (recommended) or from an application like QGIS or the embedded UI can be used directly from a web browser in order to generate predicted distribution maps for marine species.

Installing from github

If you want to install the latest version of the raquamaps package from github, you can do it like so:

# First make sure you have the devtools package
# which simplifies installations from github
# Note: Windows users have to first install Rtools to use devtools

install.packages("devtools") 

# install the raquamaps package from github with this command
# which may require RCurl, if so you can first install RCurl with ...
# install.packages("RCurl")

library("devtools")
#install_github('raquamaps/raquamaps', build_vignettes=TRUE) 
install_git("https://github.com/raquamaps/raquamaps.git", build_vignettes=TRUE)
# ... or if you have RCurl:
install_github("raquamaps/raquamaps")  

Quick start

Load the package in your R environment:

library("raquamaps")

To see some quick usage examples to get you started, open the Vignette.

Click to see Vignette

Building this package - for developers

Open the raquamaps directory's .Rproj file in RStudio and use the Build tab to build a source tarball (it will use the version number in the DESCRIPTION file).

You may need to install a few libraries for the build to go through. R libraries can be installed from within RStudio. Or you could do it at the R prompt using commands like:

install.packages("RCurl")  

On some linux distros you may need system libraries, which can be installed like so:

sudo apt-get install libgdal1-dev libproj-dev libcurl4-openssl-dev

Don't forget to put the .tar.gz source tarball into the archive-tarball directory before pushing changes to gitorious/github.

Credits

raquamaps would have not been possible without many amazing R libraries, such as

• dplyr, tidyr, stringr etc from Hadley Wickham
• rgbif etc from ROpenSci

References

• Kaschner, K., R. Watson, A.W. Trites and D. Pauly. 2006. Mapping worldwide distributions of marine mammals using a Relative Environmental Suitability (RES) model. Mar. Ecol. Prog. Ser. 316:285-310.

• Ready, J., K. Kaschner, A.B. South, P.D. Eastwood, T. Rees, J. Rius, E. Agbayani, S. Kullander, and R. Froese. 2010. Predicting the distributions of marine organisms at the global scale. Ecol. Model. 221: 467-478, doi:10.1016/j.ecolmodel.2009.10.025

• Kesner-Reyes, K., K. Kaschner, S. Kullander, C. Garilao, J. Barile, and R. Froese. 2012. AquaMaps: algorithm and data sources for aquatic organisms. In: Froese, R. and D. Pauly. Editors. 2012. FishBase. World Wide Web electronic publication. www.fishbase.org, version (04/2012).

• Östergren J, Kullander S O, Prud'homme O, Reyes K K, Kaschner K and Froese R (in preparation) Predicting freshwater-dependent species distributions in Europe

Meta

• Please report any issues or bugs.
• License: AGPL