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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.

Stable version

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

Manual and vignette

Package manual and vignette are available here:

Source code

The source code is available through git on the Sourceforge platform (read only access for the moment):

git clone git://git.code.sf.net/p/hsdm/code hsdm-code

Some related publications

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

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

MacKenzie D. I., Nichols J. D., Lachman G. B., Droege S., Royle J. A. and Langtimm C. A. 2002. Estimating site occupancy rates when detection probabilities are less than one. Ecology. 83: 2248-2255. pdf

Royle, J. A. 2004. N-Mixture Models for Estimating Population Size from Spatially Replicated Counts. Biometrics. 60: 108-115. pdf

Contact

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

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