Species Distribution Modelling

An extensible framework for developing species distribution models using individual and community-based approaches, generate ensembles of models, evaluate the models, and predict species potential distributions in space and time. For more information, please check the following paper: Naimi, B., Araujo, M.B. (2016) .


sdm is an object-oriented, reproducible and extensible R platform for species distribution modelling. The sdm package is designed to create a comprehensive modelling and simulation framework that: 1) provides a standardised and unified structure for handling species distributions data and modelling techniques (e.g. a unified interface is used to fit different models offered by different packages); 2) is able to support markedly different modelling approaches; 3) enables scientists to modify the existing methods, extend the framework by developing new methods or procedures, and share them to be reproduced by the other scientists; 4) handles spatial as well as temporal data for single or multiple species; 5) employs high performance computing solutions to speed up modelling and simulations, and finally; 6) uses flexible and easy-to-use GUI interface. For more information, check the published paper by Naimi and Araujo (2016) in the journal of Ecography.

Installing sdm and all the required packages

sdm is also on CRAN, therefore, it can simply be installed using the standard install.packages function as:

install.packages('sdm')

The GitHub version of sdm may be newer than CRAN version, and can be installed using the install_github function from the devtools package:

devtools::install_github("babaknaimi/sdm")

Depending on the methods are selected through the modelling and using the package, several packages may be needed, and therefore, should be installed on your machine. A quick way to install all the required packages (to guarantee having full functionaliy of sdm), is to simply use the function installAll offered by the sdm package. You can simply call it without any argument:

installAll()

sdm website:

The official website of the package is currently can be accessed at http://biogeoinformatics.org

There is a Google group/forum for the users of the package where the questions can be posted and discussed:

https://groups.google.com/d/forum/rsdm

The authors of the package (Miguel Araujo & Babak Naimi) organise a summer school (usually for PhDs and Postdocs) every year, where both the conceptual theories and practices of species distribution modelling are well discussed. If you are interested, you can find more information on the next course at http://www.maraujolab.com; see for example: http://www.maraujolab.com/2018-species-distributions-course/

More information about the authors of the package:

Babak Naimi: http://www.biogeoinformatics.org/about-me/

Miguel Araujo: http://www.maraujolab.com/people/miguel-araujo/

There is another website of the package developer (Babak Naimi) where you can find some articles about his research: http://r-gis.net

News

Reference manual

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install.packages("sdm")

1.0-67 by Babak Naimi, 6 months ago


http://biogeoinformatics.org


Browse source code at https://github.com/cran/sdm


Authors: Babak Naimi , Miguel B. Araujo


Documentation:   PDF Manual  


GPL (>= 3) license


Imports raster

Depends on methods, sp

Suggests R.rsp, shinyBS, shiny, dismo, rmarkdown


See at CRAN