hSDM R package

hSDM is an R package for estimating parameters of hierarchical Bayesian species distribution models. Such models allows interpreting the observations (occurrence and abundance of a species) as a result of several hierarchical processes including ecological processes (habitat suitability, spatial dependence and anthropogenic disturbance) and observation processes (species detectability). Hierarchical species distribution models are essential for accurately characterizing the environmental response of species, predicting their probability of occurrence, and assessing uncertainty in the model results.

Code and manual

The last stable version of the hSDM R package (hSDM_1.0) is officially available for several operating systems (Unix, Windows and Mac OSX)  on the Comprehensive R Archive Network (CRAN).

The source code and manual for the testing version is available here:

• Package source: hSDM_1.1.tar.gz
• Reference manual: hSDM_1.1.pdf

Related publications

Latimer A. M., Wu S. S., Gelfand A. E. and Silander J. A. 2006. Building statistical models to analyze species distributions. Ecological Applications. 16(1): 33-50. pdf

Gelfand A. E., Silander J. A., Wu S. S., Latimer A., Lewis P. O., Rebelo A. G. and Holder M. 2006. Explaining species distribution patterns through hierarchical modeling. Bayesian Analysis. 1(1): 41-92. pdf

Diez J. M. and Pulliam H. R. 2007. Hierarchical analysis of species distributions and abundance across environmental gradients. Ecology. 88(12): 3144-3152. pdf

Contact

Ghislain Vieilledent
Cirad, UPR BSEF
Campus de Baillarguet
TA C-105/D
34398 Montpellier cedex 5
FRANCE

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Email: ghislain(dot)vieilledent(at)cirad(dot)fr
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