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I am fairly new to R. I would like to use the adehabitatHR package to create kernel density and isopleths from my sea turtle GPS data. I’m running into some issues…

Basically I am having trouble assigning IDs and XY fields within R to create KDs and MCPs.

Thank you in advance for any help!

Here is what I have been doing...   


   
#loading packages
`library(adehabitatHR)
library(raster) 
library(rgdal)
library(maptools)`

#read CSV with UTM xy and ids

    track<- 
read.table("T:/GIS/Data/Tracking/state_space_model/20150210_AbHabiatatHRmodel/All_prelim_model_6hr_utm_forage_10A.csv",
   header=TRUE, sep=",", na.strings="NA", dec=".", strip.white=TRUE)

# Turn track into a SpatialPointsDataFrame sby specifying that the "X" and "Y" columns are the coordinates:
coordinates(track) <- c("X", "Y")
class(track)
plot(track)
#Project into utm:
proj4string(track) <- CRS("+init=epsg:32618")
#read shore;ine file
shore <- readShapeSpatial("C:/Users/gemme001/Desktop/R_state_space/STATES_VA_COAST_UTM.shp", delete_null_obj=TRUE)
plot(shore)
proj4string(shore) <- CRS("+init=epsg:32618")
#Add to list the list with the names "map" and "relocs" 
my.homerange.data <- list(map = shore, relocs = track)
#Assign IDs and XY – the IDs work but coordinates don’t work.  I get the following error: Error in `[.data.frame`(x@data, i, j, ..., drop = FALSE) : undefined columns selected
id<-my.homerange.data$relocs$Name
xy<-(my.homerange.data$relocs["X","Y"]
#Create CP – this works
cp <- mcp(my.homerange.data$relocs[,1], percent=95)
class(cp)
plot(cp)
#Create KUD.  This doesn’t work.  I get the following:  Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' is a list, but does not have components 'x' and 'y'
kud <- kernelUD(track[,1], h="href")
gemme001
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1 Answers1

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You've likely figured out your issues by now but just in case, I've just finally figured this out with my bird data and had the same issues as you. I ended up assigning an ID for each animal in the first column of my datasheet in excel then re-importing the data. Also, if you're following along with the adehabitatHR tutorial, make sure you have your x and y columns as the 2nd and 3rd columns and are labeled as such. Once I set up my data in this format, I was able to easily convert spatial data into a dataframe and go on to calculate KDE and obtain home range polygons.

Erika
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