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Volume 4

Issue 5

SURFACE: Detecting convergence with stepwise AIC
Online 20th February 2013

Travis Ingram gives a brief introduction to the new phylogenetic comparative method SURFACE. This method uses stepwise AIC to fit a series of stabilizing selection models to a phylogenetic tree and trait data, and to quantify the extent of convergent evolution toward the same selective regimes. The tutorial explains how SURFACE works, then shows an example analysis in R.
Read the article: SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise AIC

 

Volume 4

Issue 3

Endoscopy rationale
Online 13th December 2012

In this short video, Sarah Burthe explains the rationale for developing endoscopy as a method for non-destructively measuring endoparasites in European shag hosts.
Read the article: Endoscopy as a novel method for assessing endoparasite burdens in free-ranging European shags (Phalacrocorax aristotelis)

 

Volume 3

Issue 6

Diversitree
Uploaded 29th October 2012

In this video, Mr Blueberry and Fairly-Small-Yellow-Bird disagree on how colour affects the diversification of birds. Rich FitzJohn shows them how to test their hypotheses using the comparative phylogenetic methods implemented in the R package "diversitree", recently described in the freely available Methods application paper "Diversitree: comparative phylogenetic analyses of diversification in R".
Download diversitree from [CRAN] here.
Download a tutorial and worked examples here.

 

Movebank tutorial
Made public 11th October 2012

This short video provides a useful tutorial on how to run the Douglas Argos filter (an algorithm that flags implausible locations) in Movebank, a free online infrastructure for storing, managing, sharing and analysing animal movement data.
You can read the accompanying article here: Moderating Argos location errors in animal tracking data
You can also view this video on Methods YouTube channel.
 

 

Understanding the causes and consequences of animal movement
Uploaded 9th October 2012

In this video, John Fieberg discusses some of the challenges associated with inferring causal relationships among animal movement characteristics and indicators of an animal's physiological condition. Specifically, he and co-author Mark Ditmer explore models that relate estimates of daily movement rates to average daily heart rates (collected using surgically implanted heart monitors) in conjunction with a biotelemetry study involving black bears (Ursus americanus). They show that estimates of regression parameters are sensitive to the assumed error structure, they suggest this sensitivity is due to endgoeneity of the predictor variable(s), and they use directed acyclical graphs to develop potential explanations for the observed endogeneity. The implications of this work are relevant to most studies that make use of biotelemetry data.
You can read the accompanying forum article here: Understanding the causes and consequences of animal movement: a cautionary note on fitting and interpreting regression models with time-dependent covariates
You can also view this video on Methods YouTube channel.
 

 

FlexParamCurve - A Tutorial
Uploaded 26th September 2012

In this R tutorial, Steve Oswald (Penn State) walks us through coded examples of FlexParamCurve's main functionality: selecting which curve to use, fitting/plotting, and analyzing in nlme().
Make sure you didn't miss the the preceding introductory video, where Steve and Andre Chiaradia (Phillip Island) discuss how 'FlexParamCurve' makes nonlinear curve fitting accessible for non-monotonic parametric curves, through automated curve selection and parametrisation in a mixed effects model framework.

 

FlexParamCurve - An Introduction
Uploaded 26th September 2012

Steve Oswald (Penn State) and Andre Chiaradia (Phillip Island) discuss how 'FlexParamCurve' makes nonlinear curve fitting accessible for non-monotonic parametric curves, through automated curve selection and parametrisation in a mixed effects model framework. They visit Phillip Island's Penguin Parade to introduce avian growth as one application.
Don't miss the subsequent R tutorial video, where Steve walks us through coded examples of FlexParamCurve's main functionality: selecting which curve to use, fitting/plotting, and analyzing in nlme().

Volume 3

Issue 5

Modelling dispersal-limited species
Uploaded 16th October

This video accompanies a recently published article that deals with the problems of predicting non-native species distribution. One of the authors, Martin Sullivan, runs us through the use dispersion weighting models to overcome these problems, and discusses their results and conclusions when applied to a real case study of the distribution of common waxbill Estrilda astrild in the Iberian Peninsula.

Read the article: Using dispersal information to model the species–environment relationship of spreading non-native species
Watch the video on our YouTube channel.
 

 

 

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