Christoffer Moesgaard Albertsen, Kim Whoriskey, David Yurkowski, Anders Nielsen, and Joanna Mills Flemming. 2015. Fast fitting of non-Gaussian state-space models to animal movement data via Template Model Builder. Ecology 96:25982604. http://dx.doi.org/10.1890/14-2101.1


Supplement

R code for fitting Argos data with argosTrack.
Ecological Archives E096-229-S1.

Copyright


Authors
File list (downloads)
Description


Author(s)

Christoffer Moesgaard Albertsen
National Institute of Aquatic Resources, Technical University of Denmark
Jægersborg Alle 1
DK-2920 Charlottenlund
Denmark
Email: cmoe@aqua.dtu.dk

Kim Whoriskey
Department of Mathematics and Statistics
Dalhousie University
Halifax NS B3H 4R2
Canada

David Yurkowski
Great Lakes Institute for Environmental Research
University of Windsor
Windsor ON N9B 3P4
Canada

Anders Nielsen
National Institute of Aquatic Resources, Technical University of Denmark
Jægersborg Alle 1
DK-2920 Charlottenlund
Denmark

Joanna Mills Flemming
Department of Mathematics and Statistics
Dalhousie University
Halifax NS B3H 4R2
Canada


File list

argosTrack.tar.gz (md5: e7e7f6f0e502c42b4cd24ee8f9679e62)
argosTrack.R (md5: 7857ead3f7e13ed67ceb16655b546ac6)
bsam.R (md5: 2f4b064ef9089a90873b0049fea39b31)
crawl.R (md5: f36b3c25fd8e929a3d41cd4867cdfd92)

Description

argosTrack.tar.gz - Source code for the R package argosTrack.

argosTrack.R - Example of how to use the package argosTrack.

bsam.R - R code for analysis of the seal data using bsam.

crawl.R - R code for analysis of the seal data using crawl.

Installing argosTrack on Windows

The argosTrack package depends on the package TMB. To install TMB download and unzip the code from: https://github.com/kaskr/adcomp/archive/master.zip. Open R, change the working directory to the unzipped adcomp-master folder, and run source("install_windows.R"). The command will ask to install Rtools which should be accepted. After a successfull installation of TMB, change the working directory to the folder containing argosTrack.tar.gz and install with library(TMB);install.packages("mvtnorm");install.packages("argosTrack.tar.gz",repos=NULL,type="source").

Installing argosTrack on Linux

The argosTrack package depends on the package TMB. To install TMB download and unzip the code from: https://github.com/kaskr/adcomp/archive/master.zip. In the terminal, change directory to the unzipped adcomp-master folder, and run make install. After a successfull installation of TMB, change the directory to the folder containing argosTrack.tar.gz, open R, and run install.packages("mvtnorm");install.packages("argosTrack.tar.gz",repos=NULL,type="source").

Installing argosTrack on Mac OS X

The argosTrack package depends on the package TMB. To install TMB, install Xcode from the App Store, install gFortran from http://cran.r-project.org/bin/macosx/tools/, and download and unzip the TMB source code from: https://github.com/kaskr/adcomp/archive/master.zip. Open the terminal and change the directory to the unzipped adcomp-master folder. Run the command make install. After a successfull installation of TMB, change the directory to the folder containing argosTrack.tar.gz, open R, and run install.packages("mvtnorm");install.packages("argosTrack.tar.gz",repos=NULL,type="source").