Programs / Software

Make sure to have R installed on your computer as well as the MARSS package.

R-studio is a recommended interface (instructors will use) but not required.



Cowpertwait PSP, Metcalfe AV. 2009. Introductory Time Series with R. Springer, New York.

MARSS User Guide: Holmes EE, Ward EJ, Scheuerell MD. 2013. Analysis of multivariate time-series using the MARSS package, Version 3.7. DOC-NOAA-NMFS-NWC, Seattle, WA. Available Here: MARSS User Guide

Chapter 6: Shumway DH, Stoffer DS. 2006. Time Series Analysis and Its Applications: With R Examples. Springer, New York

Day 1
Holmes EE, Fagan WF. 2002. Validating population viability analysis for corrupted data sets. Ecology 83: 2379-2386

Dennis, B., Munholland, P. L., and Scott, J. M. 1991. Estimation of growth and extinction parameters for endangered species. Ecological Monographs 61:115-143

Day 2
Ward, EJ, Chirrakal H, González-Suárez M, Aurioles-Gamboa D, Holmes EE, Gerber L. 2010. Applying Multivariate-state-space Models to Detect Spatial clustering of California sea lions in the Gulf of California, Mexico.  Journal of Applied Ecology 47: 47-56

Day 3
Hampton SE, Scheuerell MD, Schindler DE. 2006. Coalescence in the Lake Washington story: interaction strengths in a planktonic food web. Limnology and Oceanography 51: 2042-2051

Hampton SE, Holmes EE, Scheef LP, Scheuerell MD, Katz SL, Pendleton DE, Ward EJ. 2013. Quantifying effects of abiotic and biotic drivers on community dynamics with multivariate autoregressive (MAR) models. Ecology 94: 2663–2669

Ives AR, Dennis B, Cottingham, KL, Carpenter SR. 2003. Estimating community stability and ecological interactions from time series data. Ecological Monographs 73: 301–330

Day 4
Lamon EC, Carpenter SR, Stow C. 1998. Forecasting PCB concentrations in Lake Michigan salmonids: a dynamic linear model approach. Ecological Applications 8: 659-668

Scheuerell MD, Williams JG. 2005. Forecasting climate-induced changes in the survival of Snake River spring/summer Chinook salmon. Fisheries Oceanography 14: 448-457

Petris G, Petrone S, Campagnoli P. 2009. Dynamic Linear Models with R. Springer.

Day 5
Stachura MM, Mnatua NJ, Scheuerell MD. 2014. Oceanographic influences on patterns in North Pacific salmon abundance. Can J Fish Aquat Sci 71: 1–10

Zuur AF, Tuck ID, Bailey N. 2003. Dynamic factor analysis to estimate common trends in fisheries time series. Can J Fish Aquat Sci 60: 542-552

Zuur, AF, Fryer RJ, Jolliffe IT, Beukema JJ. 2003. Estimating common trends in multivariate time series using dynamic factor analysis. Environmetrics 14: 665-685

Additional resources, MARSS news and updates, etc can be found on Eli Holmes’ website