Friday, 4 December 2015

Power analysis for GLMM’s with lme4 and simr - Skills Building Day tutorial at Eco-Stats '15

Peter Green (Landcare Research NZ) will present a tutorial on power analysis for GLMM's using lme4 and the simr package.  This blog post will contain information for this session as it becomes available.

A pdf copy of the workshop slides will be available here.

An R script with the commands used during the workshop will be available here.

The package is available on CRAN

There is also a Github site if you want to keep up to date with the development version

Point process modelling on R - tutorial for Skills Building Day at Eco-Stats '15

Dear workshop attendees,

Please use the link below to access the files we will be using in the workshop.

In particular, it would be fantastic if you could run the "Install Libraries" file so that you may install the libraries that we will be using: lattice, ppmlasso, and spatstat (which should install with ppmlasso). Due to its size, it also would be great if you could download the "Quad500" file ahead of time.

I will add presentation slides to this folder on Monday. I look forward to seeing you all on Tuesday!


Friday, 13 November 2015

Michael Kasumovic & Daniel Falster - A fighting framework fight: game theory vs. machine learning for strategic behaviour during animal combat

The final reading group will meet this Friday (20th November) at 1pm, We will be reading two papers on animal and plant competition, one by Michael Kasumovic and colleagues and one by Daniel Falster and colleagues.

Michael Kasumovic is an evolutionary biologist who studies the innate differences between males and females and how the environment, both social and ecological, modifies these differences. His study species include insects, spiders and humans. Daniel Falster is an evolutionary biologist and ecologist with a particular interest in using mathematical models to test fundamental ideas about the processes shaping biological communities.

Michael's paper is in Animal Behavior titled Assessment during aggressive contests between male jumping spiders, and Daniel paper can be found in bioRxiv titled Multi-trait eco-evolutionary dynamics explain niche diversity and evolved neutrality in forests

Sunday, 8 November 2015

Darryl Mackenzie & Alan Welsh - Occupancy modelling with imperfect detection

The reading group will meet this Friday (13th November) at 1pm, We will be reading two papers, the first one by Alan Welsh and colleagues, and a response by Darryl Mackenzie and colleagues.
Alan Welsh (ANU), is a methodological statistician often motivated by ecological applications. His current research interests are in model selection, linear mixed models and occupancy modelling under imperfect detection. Darryl MacKenzie (Proteus Wildlife Research Consultants) is an ecological statistician and leading expert in occupancy modelling under imperfect detection.
The papers are in PLOS ONE, titled Fitting and Interpreting Occupancy Models and Ignoring Imperfect Detection in Biological Surveys Is Dangerous: A Response to ‘Fitting and Interpreting Occupancy Models' with a short response by Welsh et al titled Adjusting for one source of bias while ignoring others can make things worse

Note that in Welsh et al's original paper, the figures are placed wrong.  See the correction note for details, but the real Figure 1 can be found at Figure 7 (!?) and the images for Figs 2-7 are all one place higher than they should be (found at Figs 1-6).

Sunday, 1 November 2015

Melodie McGeoch & Cang Hui - Estimating biodiversity turnover

The reading group will meet this Friday (6th November) at 1pm, We are reading and discussing a recent paper on biodiversity turnover by Melodie McGeoch & Cang Hui 
Melodie is an ecologists working on  the dynamics of biological invasions and the response of communities to changing environmentsCang is a mathematical ecologist interested in proposing models and theories for explaining emerging patterns in ecology. They have been working together on quantifying and estimating biodiversity turnover. 
We will read a joint paper of theirs in the American Naturalist titled Zeta Diversity as a Concept and Metric That UnifiesIncidence-Based Biodiversity Patterns

Saturday, 24 October 2015

Bruce Chessman - Do protected areas benefit freshwater species?

The reading group will meet this Friday (30th October) at 1pm. We're going to read another paper on analyzing data along stream networks, this time from an ecological perspective,  by Bruce Chessman. Bruce is interested in conservation of freshwater species and human impacts on fresh waters.

Monday, 19 October 2015

Jay ver Hoef - Analysing data along stream networks

The reading group will meet this Friday (23rd October) at 1pm. We're going to read a paper on analysing data along stream networks by Jay ver Hoef and colleagues. They have been building spatial models for stream networks which cleverly take into account the linear dependence along streams, as well as the direction of flow.  

We will be reading a paper from Environmental and Ecological Statistics titled Spatial statistical models that use flow and stream distance.

Hope you can join us.

Saturday, 10 October 2015

Rachel Fewster - Modern statistical methods for Capture-Recapture

The reading group will meet  this Friday (16th October) at 1pm. We're going to read another paper on Capture-recapture using modern technology, this time with a more statistical slant. The paper is by Rachel Fewster and colleagues at University of Auckland. Rachel focuses on how new technologies, such as DAN barcoding, acoustic profiles, impact on the assumptions on the statistical models used in capture-recapture, and developing methods to allow better use of the data collected in this way. 

We will be reading a paper submitted to Statistical Science titled Trace-Contrast Models for Capture-Recapture without Capture Histories.

Monday, 5 October 2015

Paul Sunnucks - Capture-recapture using modern technology

The reading group will meet once again this Friday (9th October) at 1pm. We're going to switch topics to Capture-recapture using modern technology with a paper by Prof Paul Sunnucks (Monash) and colleagues. Paul uses capture-recapture models together with non-invasive remotely collected samples to estimate population size and dynamics.

We will read a paper in Animal Conservation from his group titled Demographic monitoring of an entire species (the northernhairy-nosed wombat, Lasiorhinus krefftii) by genetic analysisof non-invasively collected material

Sunday, 27 September 2015

Otso Ovaskainen - Studying species interactions

The second paper in our reading group, for Friday (2nd October) at 1pm, is by Otso Ovaskainen from the University of Helsinki.  Otso studies population dynamics and species co-occurrence in ecology with an interest in modelling metagenomics data.

We will read a 2010 paper in Ecology from his group titled Modeling species co-occurrence by multivariate logistic regression generates new hypotheses on fungal interactions

Monday, 21 September 2015

Doug Yu - Studying communities using metagenomics data

The first paper in our reading group, for Friday (25th September) at 1, is by Doug Yu from the University of East Anglia.  Doug is at the forefront when it comes to biodiversity sampling using genetic techniques such as "barcoding" as a shortcut to species identification (and potentially as a way to sample cryptic species).

We will read a 2013 paper in Ecology Letters from his group titled Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding