Title: Home range overlap indices implemented using kernel density estimators with plug-in smoothing parameters and Program R.
General Description: These files contain computer code to implement the home range overlap indices reviewed in:
Fieberg, J. and C. O. Kochanny. 2005. Quantification of home range overlap: the importance of the utilization distribution. Journal of Wildlife Management 69:1346-1359.
Details:
- The code is written in Program R (R Core Team 2013) and makes use of a function in the KenrSmooth library (Wand 2013) to implement the "plug-in" method for determining an appropriate bandwidth or smoothing parameter.
- An illustrative example is included that uses wild boar location data contained in the adehabitat package (Calenge 2006) (saved as ExampleData.csv); Each home range overlap index is calculated for two of the animal's represented in the data.
Files:
1. Indices.txt = text file containing functions for calculating each overlap index in Fieberg & Kochanny (2005)
2. CalcHR.txt = text file containing functions that calculate HR area & also outer contours for different home range isopleths (these are useful for plotting).
3. puechabon_locs.csv = data from the adehabitat package of program R (saved as a .csv file).
4. Example1.txt = uses data in the adehabitat package to illustrate the indices.
5. Example1.pdf = shows the output produced by running the code in Example1.R, created using the knitr package of program R (Yihui 2013).
Acronyms:
A number of acronyms/abbreviations appear in the R code. Here is a summary of those that are most used:
UD: utilization distribution
UDOI: utilization distribution overlap index
VI: volume of intersection
BA: Bhattacharyya's affinity
Explantions of any other acronyms/abbreviations can be found in the related publication Fieberg & Kochanny (2005).
Steps:
1. Download and install R.
2. Install adehabitat and KernSmooth packages.
3. Change the working directory to point to where the above files "sit" on your computer.
4. Copy and paste code in Example1.txt
References:
Calenge, C. (2006) The package adehabitat for the R software: a tool for the analysis of space and habitat use by animals. Ecological Modelling, 197, 516-519.
Fieberg, J. and C. O. Kochanny. 2005. Quantification of home range overlap: the importance of the utilization distribution. Journal of Wildlife Management 69:1346-1359.
Maillard, D. (1996). Occupation et utilisation de la garrigue et du vignoble mediterraneens par le Sanglier. Universite d'Aix-Marseille III: PhD thesis.
R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.
Matt Wand (2013). KernSmooth: Functions for kernel smoothing for Wand & Jones (1995). R package version 2.23-10. http://CRAN.R-project.org/package=KernSmooth.
Yihui Xie (2013). knitr: A general-purpose package for dynamic report generation in R. R package version 1.4.1.