[R-sig-Geo] Speed filter vmask() in argosfilter package

[Tim Clark]

Dear List,

I am trying to filter animal tracking data based on speed using the vmask() function in argosfilter.  However, when I check the filtered data against speed that I compute in the adehabitat package it shows that the filter is not working correctly.  The vmask() function requires coordinates in long/lat while adehabitat requires it in UTM.  I would greatly appreciate it if someone could check my work and let me know what I am doing wrong.  I have included an example below using data from adehabitat.

Thanks,

Tim


library(argosfilter)
library(adehabitat)

#Data
data(puechabon)
locs <- puechabon$locs   #Dataframe with location and date for individual animal over time

#Adehabitat package
  #Variables
    xy <- locs[,c("X","Y")]  #Locations in UTM
    id<- as.character(locs$Name)
    da <- as.character(locs$Date)
    da <- as.POSIXct(strptime(as.character(locs$Date),"%y%m%d"))
  #Create ltraj
    tr1 <- as.ltraj(xy,date = da, id = id)

  #Calculate speed
      sp1<-lapply(ltr,function (l){l$dist/l$dt})            #Compute speed in m/sec
  #Unlist
    sp2<-round(unlist(sp1,recursive = TRUE),2)


#Argosfilter package
    #Transform coordinates to long/lat
      library(rgdal)
      SP.utm<-data.frame(locs[,c("X")],locs[,c("Y")])
      SP.utm<-SpatialPoints(SP.utm,proj4string=CRS("+proj=utm +zone=31 +ellps=WGS84"))
      SP.ll<-spTransform(SP.utm, CRS("+proj=longlat +ellps=WGS84"))
      SP.ll<-data.frame(SP.ll)
      names(SP.ll)<-c("lon","lat")

      lon<- SP.ll$lon
      lat<- SP.ll$lat

    #filter by speed
      mfilter<-vmask(lat,lon,dtime=da,vmax=1)
      filtered<- locs[mfilter!=c("removed"),]

#Adehabitat package
    #Create ltraj
    xy <- filtered[,c("X","Y")]
    id<- as.character(filtered$Name)
    da <- as.character(filtered$Date)
    da <- as.POSIXct(strptime(as.character(filtered$Date),"%y%m%d"))
    tr1 <- as.ltraj(xy,date = da, id = id)

    #Calculate speed
        sp3<-lapply(ltr,function (l){l$dist/l$dt})            #Compute speed in m/sec
      #Unlist
        sp4<-round(unlist(sp1,recursive = TRUE),2)

#Check data
  quantile(sp2, probs = seq(.5, 1, 0.1), na.rm = TRUE)
  quantile(sp4, probs = seq(.5, 1, 0.1), na.rm = TRUE)





Tim Clark
Department of Zoology 
University of Hawaii