ctmm - writeShapefile

[spete...@gmail.com]

Hello,

I am still new to ctmm and tackle the following problem(s):

I have 199 tracks (cat tracks) downloaded as csv file (see below) from Movebank.

Running my script (see below), I get the sKDE polygons I want, but using writeShapefile I am loosing all attributes (e.g. individual-local-identifier, individual-taxon-canonical-name).

Is there any way to include such attribute from the original Movebank csv file in the output shapefile?

Hope anyone can help

Cheers

stefan

My_ctmm_cat_tracks_script.R :

install.packages("proj4")

install.packages('bit64')

install.packages('ctmm')

library(ctmm)

tracks <- as.telemetry('PetcatsSA199.csv',timeformat="",timezone="UTC",projection=NULL,timeout=Inf,na.rm="row",drop=TRUE)

trackIDs <- names(tracks)

no_tracks <- length(trackIDs)

folder <- paste(getwd(),"/shp-output2", sep="")

for(i in 1:no_tracks) {

  track_i <- tracks[i]

  names(track_i) <- "1"

  track_h <- track_i$'1'

  GUESS <- ctmm.guess(track_h,interactive=FALSE)

  print(i)

  FIT <- ctmm.fit(track_h,GUESS)

  UD <- akde(track_h,FIT)

  assign(paste("UD", i, sep = ""), UD) 

  writeShapefile(UD,folder,file=NULL,level.UD=0.95,level=0.95)

}

PetcatsSA199.csv (extraction):

event-id	visible	timestamp	location-long	location-lat	sensor-type	individual-taxon-canonical-name	tag-local-identifier	individual-local-identifier	study-name
5555318653	TRUE	8/28/2015 11:18	138.6275	-35.0034	gps	Felis catus	117	117	PetcatsSA199
5555318654	TRUE	8/28/2015 11:21	138.6275	-35.0034	gps	Felis catus	117	117	PetcatsSA199
5555318656	TRUE	8/28/2015 11:27	138.6274	-35.0036	gps	Felis catus	117	117	PetcatsSA199
5555318669 ...	TRUE ...	8/28/2015 12:08 ...	138.6273 ...	-35.0033 ...	gps ...	Felis catus ...	117 ...	117 ...	PetcatsSA199 ...

[Christen Fleming]

Hi Stefan,

You could name the shape files according to the identity variable stored in the objects, with something like file=track_i@info$identity. Is that what you are looking for?

I'm not very familiar with the shapefile format to know what other options there are.

Best,

Chris

[spete...@gmail.com]

Hi Christen

many thanks for your reply.

I finally solved my problem by just using the looping identifier i as file name:

writeShapefile(UD,folder,file=i,level.UD=0.95,level=0.95)

Regards

Stefan

[Ingo Miller]

Hi Stefan or Chris,

I adopted the loop function for my data set. It works fine, however, I would like to assign my original anaimal IDs to the objects instead of numbering them. As I'm very new to for loop funtions, I couldn't figure out how the change the (above) code. 

Any help would be much appreciated.

Cheers

Ingo 

[Christen Fleming]

Hi Ingo,

In most cases, you could just do something like file=names(tracks)[i] instead of file=i.

Best,

Chris