Scripts & Programs

Below you will find code used in my published papers.


SSM_package.zip


A supplement to:


Breed, G. A., I. D. Jonsen, R. A. Myers, W. D. Bowen, and M. L. Leonard. 2009. Sex-specific, seasonal foraging tactics of adult grey seals (Halichoerus grypus) revealed by state-space analysis. Ecology 90:3209-3221 [pdf].


This .zip archive includes all the scripts and instructions for fitting the state-space models used in the analysis of Breed et al. (2009), and the models are very similar to those used in Jonsen et al. 2005. The instructions are for a Windows based machine, but installation is essentially the same for Linux with WINE running. Though I have done my best to make these scripts easy to use and install, they are released here with no support or warranty, and I cannot guarantee a response to requests for technical help.


particle_smoother_code.zip


A supplement to:


Breed, G. A., , D. P. Costa, P.W. Robinson, I. D. Jonsen J. Mills-Flemming. 2012. State-space methods for better inference of behavioral dynamics in tracked animals.  Ecological Modelling  235-236:49-58 [pdf].


This .zip archive includes all the Matlab scripts needed to implement the particle smoother state-space model described in Breed et al. (2012).  I do not yet have a set of instructions for this model that are easy to follow as the Breed et al. (2009) code.  However, if you follow through from the setup file, and you have little bit of experience coding, you should be able to figure it out.  I have recently discovered that the supplement file provided by Ecological Modelling was bungled and the code provided with the supplent is unusable.  I have contacted the publisher and they will hopefully correct it, so that the code above is also available from Ecological Modelling.  I will aslo try to produce a clear set of instructions soon.  Although I do not guarantee support, warranty, or response to requests for help,  I do *usually* respond to such requests.



Last update June 2017