4.7 Characteristic Hull Polygons (CHP)

Now we are going to get into another class of home range estimators that use polygons created by Delaunay triangulation of a set of relocations and then removing a subset of the resulting triangles. These polygons can have concave edges, be composed of disjoint regions, and contain empty portions of unused space within hull interiors. This estimator has been described in the adehabitatHR package and evaluated on black-footed albatross (Phoebastria nigripes; Downs and Horner 2009). Polygon-based estimators may be a useful method for a variety of species but research has been limited.

1. Exercise 4.7 - Download and extract zip folder into your preferred location
2. Set working directory to the extracted folder in R under File - Change dir...

3. First we need to load the packages needed for the exercise
   library(adehabitatHR)
   library(maptools)

   
   
   
4. Now open the script "CHPscript.R" and run code directly from the script
   
   
5. Now read in the locations and create a Spatial Points Data Frame for the 2 animals by ID using the code that follows:
   
   

   twocats <-read.csv("pantherjitter.csv",
   header=T)
   data.xy = twocats[c("X","Y")]

6. Creates a class of Spatial Points for all locations with projection defined
   
   data.xy = twocats[c("x","y")]
   xysp <- SpatialPoints(data.xy)
   proj4string(xysp) <- CRS("+proj=utm +zone=17N +ellps=WGS84")
   
   
7. Creates a Spatial Data Frame from Spatial points
   
   sppt<-data.frame(xysp)
   
   
8. Creates a spatial data frame of ID
   
   idsp<-data.frame(twocats[1])
   
   
9. Merges ID and Date into the same spatial data frame
   
   

   coordinates(idsp)<-sppt
   head(as.data.frame(idsp))
   #Results from the above code
   ID X Y
   1 121 494155.6 2904240
   2 121 498182.3 2905598
   3 121 498476.2 2905114
   4 121 499210.5 2905661
   5 121 499467.3 2905533
   6 121 502960.9 2904391

10. Code for estimation of home range using CharHull from adehabitatHR
    
    res <- CharHull(idsp[,1])
    class("res")
    
    
11. Code to display the home range in R (Fig. 4.14).
    
    plot(res)
    
    
    
    Figure 4.14. Example of CHP home range for 2 Florida panther
    
    
12. Code to compute the home range size for 20−100 percent
    
    MCHu2hrsize(res)
    
    

    20 10.70262 150.2998
    30 28.73158 342.9798
    40 79.15079 688.7553
    50 172.95317 1418.7588
    60 343.12024 2319.1578

    70 700.94072 3574.5525
    80 1333.94110 5910.8221
    90 2431.27046 12912.0320
    100 5538.22402 103361.1336

    OR
    
    
13. Computes the home range size for 95 percent
    
    MCHu2hrsize(res, percent=95)
    
    OR use
    
    getverticeshr(res, percent=95)
    
    Number of SpatialPolygons: 2
    

    Variables measured:
    id area
    1 121 2413.518
    2 143 12845.298

    Keep in mind that CHP estimates in Figure 4.14 are for 20−100 percent with 100% filling in the entire area traversed by each animal. If you want to visualize core area (i.e., 50%) or 95% that are commonly reported, the resulting home ranges might be more appropriate visualization of the area an animal traverses.