Dear all,I have made major changes to the package adehabitat. Indeed, the R environment has changed a lot since I began the development of adehabitat in 2002 (development of namespace, etc.), and new classes and efficient methods have been developed to deal with spatial data (package sp). In addition, the number of functions available in the package has grown to more than 250 functions, implementing methods for habitat selection analysis, home range estimation, animal movement analysis, or spatial operations.
Therefore, I decided to:(i) rewrite the package adehabitat to make it more compliant with these evolutions of the package R,
(ii) split adehabitat into four packages(iii) create a new project on R-Forge (https://r-forge.r-project.org/) to store the sources of these four packages.
The four new packages are:* adehabitatMA: functions to perform spatial operations (morphology, buffer, etc.)
* adehabitatHS: functions for the analysis of habitat selection * adehabitatHR: functions for home range estimation * adehabitatLT: functions for movement analysis The home page of the project is: http://adehabitat.r-forge.r-project.org/ The packages can be installed in R by typing: install.packages("packagename",repos="http://R-Forge.R-project.org";)I will keep these packages on R-forge for some time (at least several months), before submitting them to CRAN, to take into account users advices on these packages. After their submission to CRAN, I will continue to maintain the old adehabitat on CRAN for some time, but on the long term, this package will disappear. These four packages are expected to become the future of adehabitat.
I now describe several major changes:* the functions of the packages are documented precisely in a vignette (there is one vignette per package). Both their use and the theory underlying these functions are described there. To access it, type:
vignette("packagename")
* the home range estimation methods have been homogenized and return
classes compliant with the classes of the package sp:
- the functions kernelUD, kernelbb, and kernelkc all return objects of
class "estUDm", which are lists of objects of class "estUD". The class
extUD extends the class SpatialPixelsDataFrame.
- the function clusthr and LoCoH return objects of class "MCHu", which
are lists of SpatialPolygonsDataFrame
- the function mcp returns a SpatialPolygonsDataFrame* home range estimation methods now take objects of class SpatialPoints as arguments
* objects of class "ltraj" are now characterized by an additional attribute "infolocs", which is designed to store metadata on the trajectories (e.g. precision on the relocations). Most functions of the package adehabitatLT can be used to analyse these metadata (plotltr, etc. see the vignette).
* the method of characteristic hulls (Downs and Horner 2009), suggested by Paolo, on the list has been added to adehabitatHR, and returns an object of class MCHu
* the canonical OMI analysis, allowing exploration of habitat selection with radio-tracking data, has been added to the package adehabitatHS
* the autocorrelation functions described by Dray et al. (2010) for the analysis of movement have been added to the package adehabitatLT;
* all the packages have a namespace for management of internal functions.Note that the calculations performed by most functions of adehabitat have not changed (e.g. the algorithm implemented in kernelUD of adehabitat is the same as the algorithm implemented in the function kernelUD of the package adehabitatHR), since they have been deeply discussed with users and corrected during the last five years. Only the input and output of the functions have been changed.
Happy testing, Clément Calenge. -- Clément CALENGE Cellule d'appui à l'analyse de données Office national de la chasse et de la faune sauvage Saint Benoist - 78610 Auffargis tel. (33) 01.30.46.54.14 _______________________________________________ R-sig-Geo mailing list R-sig-Geo@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-geo
