# Sitemap

A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.

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## <a href="https://eeholmes.github.io/r paste0("/posts/",sub("[.]Rmd","",knitr::current_input()),"/")" rel="permalink">Sparse Matrix Math in R</a>

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Parsimonious Pursuits

## Markdown

This is a page not in th emain menu

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## Baccalaureate Origins of Sloan Fellows, part 2: Liberal Arts Colleges Versus Research Universities

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Analysis of the baccalaureate origins of Sloan fellows in the hard sciences using SAT tiers.

## Baccalaureate Origins of Sloan Fellows, part 1

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Analysis of the baccalaureate origins of Sloan fellows in the hard sciences across the Equality of Opportunity tiers of institutions.

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## Notes on computing the Fisher Information matrix for MARSS models. Part I Background

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## adadpted from code by Felix Schonbrodt



## Portfolio item number 1

Short description of portfolio item number 1

## Portfolio item number 2

Short description of portfolio item number 2

## Paper Title Number 3

Published in Journal 1, 2015

This paper is about the number 3. The number 4 is left for future work.

Recommended citation: Your Name, You. (2015). "Paper Title Number 3." Journal 1. 1(3). http://academicpages.github.io/files/paper3.pdf

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# Selected Talks (and hopelessly out of date...)

• E Ward, EE Holmes and K Balcomb. 2009. Marine Mammal Bieenial Conference, Quebec City, Quebec. Quantifying the effects of prey limitation on killer whale reproduction.</em>
PDF of poster
• EE Holmes, Ecological Society of America Meetings, Memphis, TN. Parsimonious stochastic models for vertebrate population processes. August 2006This was a talk where I summarized the philosophy and justification for a generic statistical model to describe the extinction dynamics for large classes of stochastic population models. The talk in Miami, July 2005, is where I first tried to enunciate these ideas. This represents the progress made in a year -- or a 15 minute version at least. Nine months later, these ideas became the paper "A statistical approach to quasi-extinction forecasting".
PDF
• EE Holmes, LW Fritz, AE York, & K Sweeney. Evidence of continuing declines in fecundity of Steller sea lions. I've given various versions of this talk:
March 2006 &nbsp &nbsp April 2006 &nbsp &nbsp June 2006.
• EE Holmes, LW Fritz, AE York, & K Sweeney. Evidence of continuing declines in fecundity of Steller sea lions. Marine Mammal Society Meetings. San Diego, CA. December 2005.
PDF of poster.
• J Payne, EE Holmes(speaker), and AE Edwards, University of Idaho, Biology Dept. Ecosystem management: vision versus practice. November 2005
• EE Holmes, University of Florida at Miami, Math Dept. Patterns of first passage probabilities in population monitoring data. July 2005 This was an informal almost philosophical talk where I tried to ennunciate some of my ideas about the meaning of parsimony in population modeling.
PDF
• EE Holmes, L Fritz, AE York and K Sweeney, Society for Marine Mammalogy Meetings, San Diego, CA. poster: Evidence of continuing declines in fecundity in Steller Sea Lions. December 2005 This work is an extension of Holmes and York 2002. Here we are updating that work to look how demographics have been changing recently.
PDF
• EE Holmes and B Semmens, Institute of Theoretical and Mathematical Ecology, Univ. of Miami, Workshop on Spatial Ecology: The Interplay between Theory and Data. Diffusion approximation approaches for metapopulation viability analysis. January 2005 This was a talk mainly to theoreticians working in spatial ecology. I was expanding on the ideas in Holmes and Semmens 2004
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• EE Holmes and AE York, Cooperative Fish and Wildlife Research Unit, WA Dept. of Fish and Wildlife. Monitoring the effect of management on long-lived species. December 2004. Every so often I give a talk that actually has pictures of animals in it. This is basically a spashy remake of my ConsBio talk in 2001.
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• EE Holmes, University of Washington Fisheries Dept., SAFS Quantitative Seminar, University of Washington. State-space models for PVA. December 2004 The actual talk slides do not capture at all the nature of this talk, which was by and large philosophical in nature. I spent a good quarter of the time at the blackboard talking about the nature of the debate about variability in population processes and why Pimm's paper would have been considered important in the context of the debates about population regulation.
PDF
• EE Holmes, Ecological Society of America Meetings, Portland, OR, "From theory to application: diffusion approximations for Population Viability Analysis". This was in a session I organized titled Emerging approaches for the analysis of stochastic ecological data: dealing with multiple error sources, hidden states, complex nonlinearities, and uncertainty. August 2004 Although this talk has the same title as Holmes (2004), there are no slides or figures from that paper. This talk explores ideas that came up post Holmes and Fagan (2002) and Holmes et al. (2005). This shows a few results from the next installment of the Holmes and Fagan collab. The ideas in this talk hint at the ideas in U Florida in July 2005.
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• Adam U, EE Holmes and K Balcomb, University of Washington, SAFS. Analysis of Southern Resident fin growth rates 1977-2003. July 2004. This was talk given to a killer whale research group on a small project using measurements of photos of juveniles killer whale fins to look at fin growth rates over a 25 year period.
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• EE Holmes, Northwest Fisheries Science Center, Seattle, WA, "Cross-validations of a diffusion approximation approach to risk estimation for salmonids". This was in a workshop I organized at NWFSC titled Technical Workshop on Population Trends and Extinction Metrics which was required as part of the 2000 Snake River hydropower Biological Opinion, December 5, 2003. The talk was an overview of about 5 years of research. I also prepared a white paper discussing that research in more detail. I think my white paper, in the final report, on diffusion approximations in practice is a lot more lucid than Holmes 2004. The final report has point-counterpoint structure as the participants gave comments and critiques of diffusion approximations estimates as used in the Snake River ESU. It gives a sense of some of the behind the scenes discussions and debates.
TALK Final Report
• EE Holmes and W Fagan, Western Fisheries Society Annual Meeting, Symposium on Model validation and uncertainty. A statistical approach to validation applied to diffusion approximation models. Summer 2002. Basically a talk on Holmes and Fagan (2002). The talk had animation which makes the pdf look bad.
PDF
• EE Holmes and AE York, Society for Conservation Biology Annual Meeting, Symposium on Designing Marine Reserves for Marine Mammals. Using age-structure to monitor long-lived marine mammals. Summer 2001. This was a talk on Holmes and York (2002). See the remake of this talk given in December 2004 above.</a>

# ESA Workshops, 2008 - 2011

Co-taught Analysis of Multivariate Time-Series Data Using State-Space Models, and Introduction to MARSS at Ecological Society of America (ESA) annual meetings. Test

# UW Time Series Class, 2012 - present

Co-taught FISH 507 Time Series Analysis course with Eli Holmes and Mark Scheuerell