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 https://cran.r-project.org/web/packages/simr/.

There is also a Github site if you want to keep up to date with the development version https://github.com/pitakakariki/simr.

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.

https://www.dropbox.com/sh/swvf1a2hua9jwkh/AACYf0WFg7l32TRtN_VZk0oqa?dl=0

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

Ian

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

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).

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 environments. Cang 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

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.

We will be reading a paper from Journal of Applied Ecology titled "Do protected areas benefit freshwater species?A broad-scale assessment for fish in Australia’sMurray–Darling Basin"

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.