Supplement 1. The code and sample data for state–space analysis of Argos movement data.

File List

Files
for running analyses from the WinBUGS gui (Windows or Linux)

DCRW.txt
WinBUGS code for
"DCRW" model, a first-difference correlated random walk 
2
KB

DCRWS.txt
WinBUGS code for
"DCRWS" model, a first-difference CRW with switching
2 KB

hsdata.txt
Hooded seal
movement data
12 KB

hsDCRWinits.txt
Hooded seal
initial values for DCRW model
3 KB

hsDCRWSinits.txt
Hooded seal
initial values for DCRWS model
5
KB

gs617data.txt
Grey seal 617
movement data
59 KB

gs617DCRWinits.txt
Grey seal 617
initial values for DCRW model
3
KB

gs617DCRWSinits.txt
Grey seal 617
initial values for DCRWS model
4
KB

gs2986data.txt
Grey seal 2986
movement data
71 KB

gs2986DCRWinits.txt
Grey seal 2986
initial values for DCRW model
3 KB

gs2986DCRWSinits.txt
Grey seal 2986
initial values for DCRWS model
5 KB

Files
for running analyses by calling WinBUGS from within R (Linux)

DCRW.rbugs.R

R script for
fitting DCRW model to hooded seal data

1
KB

DCRWS.rbugs.R

R script for
fitting DCRWS model to hooded seal data
1
KB

dat4bugs.R
R code required
by DCRW.rbugs.R
and DCRW.rbugs.R
4
KB

hseal.dat

Hooded seal data
for analysis from within
R (Linux)
6
KB

gs617.dat

Grey seal 617
data
for analysis from within
R (Linux)
27
KB

gs2986.dat

Grey seal 2986
data
for analysis from within
R (Linux)
35
KB

allfiles.zip
All files
together
48 KB

DescriptionWinBUGS
version 1.4.1 was used to run the code and is freely available at http://www.mrc-bsu.cam.ac.uk/bugs/winbugs/contents.shtml.
In Windows, to run the DCRW model on the hooded seal data, open DCRW.txt
in
WinBUGS and paste in the data file hsdata.txt
and hsDCRWinits.txt.
For all models
we ran 2 chains for 40 000 samples with a 20 000-sample burn-in and
retained every 5th sample to reduce autocorrelation. See the WinBUGS
manual, included with the software, for further details on running the
models. Follow the same procedure to run models on the other datasets.
Summary statistics and plots can be generated directly in WinBUGS or
from other software by exporting results as text
files. Alternatively,
one can call WinBUGS from within R,
a freely available statistical computing environment, using
the R2WinBUGS
package (see http://www.stat.columbia.edu/~gelman/bugsR/
for details). 

In Linux, WinBUGS can be run
via Wine (available at http://www.winehq.com/).
We recommend building Wine from sourcerather
than installing the binary files (see documentation included in Wine
download for details). We have found that WinBUGS works
flawlessly using the 20050524 release of Wine compiled on
Ubuntu Linux. In Linux, WinBUGS can be run via the gui (as above) or
called from within R using the rbugs
package (available on the CRAN site at http://www.r-project.org).
We provide sample R scripts and associated R code (in File
list) to illustrate this
approach for both the DCRW and DCRWS models. Note that in addition to
the rbugs package, these scripts also require the
chron package (available
on the CRAN site at http://www.r-project.org).
The following commands in
R will fit the DCRW model to the hooded seal data:

source('~/pathtofile/dat4bugs.R')

hseal.dat
<- read.csv('~/pathtofile/hseal.dat')

source('~/pathtofile/DCRW.rbugs.R')

The scripts
provided run the hooded seal
analyses with a timestep of 1 day. The scripts will need to be modified
to run analyses on the grey seal datasets with a timestep of 2
days. Note, also, that the path names in the scripts will need
to be altered to reflect your file structure. The scripts
create a data.frame object in R that contains all samples, after
burn-in and thinning, for each of the unobserved states and model
parameters. These can be summarized, for example by plotting the
posterior densities:
plot(density(hsealDCRW.out$gamma))