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

[Tim Clark]

Michael,

Thanks!  I totally missed that. Now it works great.

Aloha,

Tim


Tim Clark
Department of Zoology 
University of Hawaii


--- On Wed, 10/28/09, Michael Sumner <mdsumner at gmail.com> wrote:

> From: Michael Sumner <mdsumner at gmail.com>
> Subject: Re: [R-sig-Geo] Speed filter vmask() in argosfilter package
> To: "Tim Clark" <mudiver1200 at yahoo.com>
> Cc: r-sig-geo at stat.math.ethz.ch
> Date: Wednesday, October 28, 2009, 3:15 PM
> I don't see "ltr"
> defined in your code. Is that meant to be "tr1"
> throughout? 
>  
> 
> 
>  
> On Thu, Oct 29, 2009 at 8:44 AM,
> Tim Clark <mudiver1200 at yahoo.com>
> wrote:
> 
> 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
> 
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