[R-sig-Geo] Counting kernelUD home range polygons

[Angelika Gummert]

Hi,

I am sending my question again since there was a problem with my email,
making my message unreadable in the archive.

 

-------

 

Hi,

I wanted to count the number of polygons (home ranges of my species) inside
a grid in order to estimate the number of species in a given area.  I
followed the example on this website, but it doesn't work properly:
<https://3c.gmx.net/mail/client/dereferrer?redirectUrl=http%3A%2F%2Fgis.stac
kexchange.com%2Fquestions%2F116388%2Fcount-overlapping-polygons-in-single-sh
ape-file-with-r>
http://gis.stackexchange.com/questions/116388/count-overlapping-polygons-in-
single-shape-file-with-r

 

Here is what I did:

 

#Data

You can download a part of my data here:
<https://3c.gmx.net/mail/client/dereferrer?redirectUrl=http%3A%2F%2Fwww.link
file.de%2Fdownload-136449c43d7939ea2de29accbc9cc981.php>
http://www.linkfile.de/download-136449c43d7939ea2de29accbc9cc981.php

 

#Calculation of the species home range

 

Fishsplit<-split(Data, f=Data$Species ) #split data

HaeVit<-Fishsplit[["Haemulon vittata"]]

HaeVit2 <- SpatialPoints(HaeVit[,2:3])

HaeVitKernel<-kernelUD(HaeVit2,  kern ="epa") #home range estimation

HomeRange1 <- getverticeshr(HaeVitKernel, 95) #create Polygon

 

Question1: I repeated the calculation for each individual species. I have in
total around 600 species, so it will take a long time if I do it like this.
The function kernelUD returns a list of elements of class estUD when the
object xy passed as argument contains the relocations of several animals
(i.e., belong to the class SpatialPointsDataFrame). But somehow I am unable
to convert my species data to  a SpatialPointsDataFrame which allows me to
calculate several home ranges.

 

Question2: I would like to define a barrier (boundary of the Ocean) that
cannot be crossed by the animals. I know that there is an argument named
boundary, but I don't know how I can used it in order to add the ocean
borders of the Caribbean sea (shapefile) as boundary.

 

# Load shapefile of the Caribbean Sea (you are able to download it at
<https://3c.gmx.net/mail/client/dereferrer?redirectUrl=http%3A%2F%2Fwww.natu
ralearthdata.com%2Fdownloads%2F10m-physical-vectors%2F10m-ocean%2F>
http://www.naturalearthdata.com/downloads/10m-physical-vectors/10m-ocean/

 

World <- readOGR(dsn = "Z:/./Oceans", layer = "LME66") 

Caribbean <- World[World at data$OBJECTID %in% c("25"),]

 

#create a grid

 

bb <- bbox(Caribbean)

cs <- c(1, 1)*0.5 # cell size

cc <- bb[, 1] + (cs/2)  # cell offset

cd <- ceiling(diff(t(bb))/cs)  # number of cells per direction

grd <- GridTopology(cellcentre.offset=cc, cellsize=cs, cells.dim=cd)

grd

 

# find the count of polygons below each grid cell

 

sp_grd <- SpatialGrid(grd)

proj4string(sp_grd) <- CRS("+proj=cea +datum=WGS84 +ellps=WGS84
+towgs84=0,0,0")   

 

Polygons<-Homerange1+ Homerange 2+ Homerange 3+ Homerange 4

 

Question3: I don't know how I should "combine" the polygons. This is not
working since I can not count the polygons (see result). I don't know if it
is even necessary if I calculate the home range for several species at once.

 

PolygonsSP<- as(Polygons, "SpatialPolygons")

crs(sp_grd)<-crs(PolygonsSP)

o <- over(sp_grd, CombinedPolyTestSP, returnList=TRUE)

ct <- sapply(o, length)

summary(ct)

SGDF <- SpatialGridDataFrame(sp_grd, data=data.frame(ct=ct))

 

# plot

 

spplot (SGDF, "ct", colorkey=TRUE,col.regions=colorRampPalette(c("white",
"red"), bias=2),

             panel = function(...) {

                  panel.gridplot(..., border="black")

                  sp.polygons(Caribbean)

                  sp.points(Data[,2:3], cex=1,pch = 20, col="black")

               })

 

Result: the plot shows, that only 1 Polygon was counted in each grid cell.
So the 4 home range polygons were counted as one.

 

I hope you can help me to fix this problem,

Best regards

 


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