New paper on analysis of stable isotope data

Ward, E.J., Semmens, B.X., and D.E. Schindler. 2010. Including source uncertainty and prior information in the analysis of stable isotope mixing models. In press, Environmental Science & Technology. doi:10.1021/es100053v

MARSS package uploaded to CRAN

The official release of 1.0 has been uploaded to CRAN (Here's the link to the CRAN page). This is an R package to fit unconstrained and constrained multivariate autoregressive state-space models via maximum-likelihood (EM algorithm). It was developed by Eli Holmes, Eric Ward and Kellie Wills. It is fully documented with a user guide/manual: Analysis of multivariate time-series using the MARSS package, by E.E. Holmes and E.J. Ward. MARSS has bootstrap AICb and CIs and simulation features. MARSS 1.0 doesn't allow you to estimate the B matrix. MARSS 2.0 will allow that, and MARSS 3.0 will provide Bayesian fitting. If you are looking for the derivation of update equations for the Kalman-EM algorithm, take a look at Derivation of the EM algorithm for constrained and unconstrained multivariate autoregressive state-space (MARSS) models.

R short course

Taught by various statisticians at NWFSC and organized by Eric Ward. Lectures and exercises are online:
NWFSC R Short Course

Two new papers: stable isotopes meet hierarchical Bayesian models

Semmens, B.X., E.J. Ward, J.W. Moore, and CT. Darimont. 2009. Quantifying inter- and intra-population niche variability using hierarchical Bayesian stable isotope mixing models. PLoS One. Open Access Paper

Semmens, B. X., J. W. Moore, and E. J. Ward. 2009. Improving Bayesian isotope mixing models: a response to Jackson et al. (2009). Ecology Letters 12:E6-E8.

Paper on killer whale menopause

Ward, E., Parsons, K., Holmes, E., K. Balcomb, and J. Ford. 2009. The role of menopause and reproductive senescence in a long-lived social mammal. Frontiers in Zoology 6:4 Open Access PDF

New paper on spatial population structure in California sea lions

Ward, E. J., Chirakkal, H., González-Suárez, M., Aurioles-Gamboa, D., Holmes, E. E. and Gerber, L. 2009. Inferring spatial structure from time-series data: using multivariate state-space models to detect metapopulation structure of California sea lions in the Gulf of California, Mexico. Journal of Applied Ecology 47:47-56. Abstract

"Red Flags" NCEAS Working Group proposal accepted

Eli is a participant on this NCEAS working group headed by Robin Waples and Jeff Hutchings

Red flags and species endangerment: Meta-analytical development of criteria for assessing extinction risk starting Spring 2010
Summary
The proposed project builds on previous work (some of it sponsored by NCEAS) to evaluate performance of criteria for identifying species at risk. Novel aspects of our approach include the following: 1) We begin with a conceptual definition of an endangered species (one that has entered a Red Zone where both extinction risk and uncertainty about biological processes increase non-linearly); 2) We will leverage large datasets that have become available over the last decade, including those for taxa (e.g., marine fishes) for which application of standard risk criteria has been very controversial; 3) We propose a rather broad interpretation of depensation and Allee effects that facilitates consideration of the importance of ecological and evolutionary processes; 4) We will explicitly consider how risks scale on the continuum populations/metapopulations/ESUs/species; 5) We will evaluate practical utility of candidate RedFlag criteria by applying them to case studies of species that have been formally considered for federal protection in the US and Canada.