Monday, 24 June 2013

June 28: Anne Chao - a new class of measures of phylogenetic diversity

Last cab off the rank is Anne Chao and her 2010 Royal Society B paper with Chun-Huo Chiu and Lou Jost: "Phylogenetic diversity measures based on Hill numbers".

We will discuss this Friday (28th) at 2.

Friday, 14 June 2013

June 21: Will Cornwell - Measuring phylogenetic diversity

Next up is Will Cornwell, who I'm delighted to say will be taking up an appointment here at UNSW in just a few weeks.  He has diverse interests which include the measurement of functional and phylogenetic diversity, which will be the focus of the session he will speak in at the Symposium.  He has suggested the following introductory book chapter which we will discuss next Friday:
Vellend, Cornwell et al (2011) "Measuring phylogenetic diversity" from the book Biological diversity: frontiers in measurement and assessment, Oxford University Press.

Tuesday, 11 June 2013

No reading for Friday June 14

There's a lot going on at UNSW this week so we've decided to postpone the next reading until June 21.  So all you Will Cornwell/phylogenetic diversity fans will have to wait a week...

Monday, 3 June 2013

June 7: Noel Cressie - Bayesian Hierarchical ANOVA for Climate Change Projections

Next up is Noel Cressie, an expert in spatial statistics who was written two incredibly thorough and detailed textbooks on the subject. His recent focus is on Bayesian hierarchical approaches for modelling spatial data. He has suggested the following paper as being particularly relevant for his talk:

Bayesian Hierarchical ANOVA of Regional Climate-Change Projections from NARCCAP Phase II

There is a fair amount of equations in the paper, but please don't let this be a deterrent! Noel recently gave a talk on this work at UNSW and as an attendee, I can say that it was incredibly exciting and very approachable for non-statisticians.

Feel free to post any questions or comments here in anticipation of the study group at 2-3pm on Friday at UNSW.

Monday, 27 May 2013

May 31: Chris Daly - Guidelines for Assessing the Suitability of Spatial Climate Data Sets

The next speaker is Chris Daly, the renowned developer of the PRISM spatial climate modelling system. His work has earned him the 2004 Applied Meteorology Award from the American Meteorological Society.

We will discuss his 2006 paper: "Guidelines for assessing the suitability of spatial climate data sets", which can be found at the link below:

Feel free to post any questions or comments in advance of or during the discussion at UNSW at 2pm on Friday!

Monday, 20 May 2013

May 24: Shirley Pledger - Using Mixture Models to Model Abundance from Capture-Recapture Studies

Our next speaker is Shirley Pledger, an expert in capture-recapture analysis. She has suggested the following article explaining the use of mixture models to model abundance in the face of differing capture/re-capture probabilities:

Feel free to post any questions or comments in advance of the discussion group meeting at 2-3 on the 24th of May.

Monday, 13 May 2013

May 17: Gerry Quinn - Impact of Agriculture Land Use on Invertebrates in Intermittent Streams Using a Multivariate Approach

Our next speaker is Gerry Quinn, a marine ecologist who has contributed to many textbooks in wide use today. We’ll discuss a recent paper as a glimpse into how multivariate analysis is currently being applied to ecological problems, in particular on the impact of agricultural land use on invertebrates in intermittent streams. Here is a link to the article:

Hope to hear from you in the blogosphere in time for the meeting on Friday at 2.

Friday, 3 May 2013

Bill Shipley: trait-based community assembly and other cool T-shirts (May 10)

Next Symposium speaker is Bill Shipley on trait-based community assembly.  He has developed a fascinating approach to modelling the role that traits play in determining the relative abundance of different species in a community, based on maximum entropy.  He will be speaking at the Symposium in the same session as Trevor Hastie, given their respective insights into the MAXENT method.

We’ll read his landmark paper on the topic in the Science rag in 2006
(He has since written a whole book on the subject, complete with helpful T-shirt suggestion.)

If you are extra keen, a couple of technical comments on the paper have also been published, which might be helpful to get an alternate view on the topic – see links to related resources on the Science website.

Hope to hear from you on the blog next Friday 2-3 Sydney time...

Friday, 26 April 2013

Trevor Hastie: Statistical Models for Presence-Only Data (Friday 3rd May 2-3)

Trevor Hastie is a world-renowned statistician with major contributions to applied statistics, including two classic textbooks. His current research focuses on applied problems in biology and genomics, medicine and industry.

We have selected a paper co-authored with William Fithian that is sure to be a citation giant for ecologists and statisticians alike, addressing many key challenges in analyzing presence-only data: "Statistical models for presence-only data: Finite-sample equivalence and addressing observer bias".

This is a heavy-hitter, so we will focus mostly on Sections 1, 2, and 5.

Feel free to post any questions and/or comments.

Code for spatstat Lab

Here is some basic code to get started with spatstat using the Beilschmiedia pendula dataset.



fit.1 = ppm(bei, ~poly(elev, grad, degree = 2), covariates = bei.extra)
plot(bei, add = TRUE, cex = 0.4)

fit.2 = ppm(bei, ~poly(elev, grad, degree = 2) + poly(x, y, degree = 2), covariates = bei.extra)

plot(bei, add = TRUE, cex = 0.4)

Can you find a model which removes the main trend in residual plots?

Monday, 22 April 2013

Adrian Baddeley: spatstat Lab Friday Apr. 26

This Friday we aim to understand a bit more about the work of our next speaker, Adrian Baddeley. Adrian is an expert in spatial point patterns, and his freely-available R package spatstat has taken the world by storm!

To get a sense for what spatstat can do and how to use it, we will be taking a look at the lecture notes available at the following link: In particular, Chapters 1 and 2 offer a nice overview of what spatial point patterns are and what types of questions can be answered using spatstat. Taking a look at any other Chapters of the lecture notes is encouraged, but not essential for what we’ll discuss.

At UNSW,  the plan this week is a little different – we’ve booked a lab in Bioscience Room 640 for Friday from 2-3 to get familiar with some of the main features of spatstat by working through a real data set of 3605 Beilschmiedia pendula trees in the tropical rainforest of Barro Colorado Island. This will give us a chance to learn what point process models are all about and how to fit them and also to learn about about R, by far the most commonly used statistical software today.

Feel free to post any questions or ideas here.

Wednesday, 17 April 2013

Jane Elith et al: range-shifting species (Friday 19th at 2)

The first paper in our Eco-Stats Symposium reading group is first-authored by the first speaker to present at the Symposium – Jane Elith.  It is called “The art of modelling range-shifting species”
and was published in Methods in Ecology & Evolution in 2010, the journal's first volume.  This paper has attracted a lot of attention, and is currently the second most highly cited paper in the journal, and by my estimation is solely responsible for about 11% of the journal’s 2011 impact factor!  We'll discuss this paper at UNSW on Friday 19th, 2-3pm and would be interested to hear what you make of it... feel free to post here any questions you have about it, comments, ideas...

Feel free to post any time, but if you aim for Friday 2-3 we might be able to get a discussion happening.