Workshop: Introduction to Shape Analysis in R

Shape Analysis (Geometric Morphometrics) is the analytical toolkit to quantify and study shape variation of a set of specimens or artefacts.

schedule Date & time
3 Jun 2015 1:00am
person Speaker
Emma Sherratt, University of New England

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Description

Shape Analysis (Geometric Morphometrics) is the analytical toolkit to quantify and study shape variation of a set of specimens or artefacts.

Geometric morphometrics is used widely in the fields of Zoology, Botany, Palaeontology, Archaeology, and Medicine. Specifically, GMM is a collection of approaches for the multivariate statistical analysis of Cartesian coordinate data, usually (but not always) limited to landmark point locations that collectively define the shape of an object.
 
In this workshop we will cover how to analyse these data in R using the package geomorph. 
 
Numbers will be capped at 20.
 
* Note: You have to know a bit about morphometrics already and you have to know how to use R.  This is not an intro R course.  
 

Schedule

  • 09:00 Lecture – Geomorph: the integrated toolkit for geometric morphometrics
  • 09:30 Break (and computer set up)
  • 10:00 Lab 1: Intro to R and geomorph; Data input, sliding semilandmarks, & GPA
  • 11:15 Break
  • 11:30 Lab 2: Ordination, Multivariate Regression & visualising shape changes
  • 12:30 Lunch
  • 13:30 Lab 3: General linear models, group differences 
  • 14:30 Break
  • 14:45 Lab 4: Phylogenetic Comparative Methods
  • 15:45 Break
  • 16:00 Individual practice on own data/example datasets
  • 17:00 End of workshop

Topics to be covered

  • Landmarks and Semilandmarks
  • Procrustes Superimposition
  • Principal component analysis 
  • Visualizing shape changes
  • Procrustes general linear models proc glm (e.g. ANOVA, MANOVA, MANCOVA)
  • Multivariate regression, visualizing allometry
  • Phylogenetic Comparative methods (Phylogenetic signal, PGLS, phylomorphospace, rates of evolution, phylogenetic PLS)

Topics that can also be covered if requested

  • Estimating missing landmarks
  • Analysis of articulated structures
  • Collecting landmark data in R (from photos and 3D models)

Requirements and Expected Preparation

  • Bring your own laptop or have arranged a computer you can use
  • Please install* the latest version of R (3.2 “Full of Ingredients”)
  • Then install* geomorph v2.1.4 plus the dependencies and make sure all are up to date
  • Read Torfs & Brauer 2014 A very short intro to R

Suggested Reading, useful websites and guides

  • Adams, Rohlf, & Slice 2013. A field comes of age: geometric morphometrics in the 21st century. Hystrix-the Italian Journal of Mammalogy.
  • Claude, J. 2008 Morphometrics in R. Springer.
  • Zelditch, Swiderski & Sheets 2012 Geometric Morphometrics for Biologists: A Primer. Second edition. Academic Press.
  • SUNY SB Morphometrics
  • QuickR - 
  • Morphmet

Installation

  • Install R and then Rstudio. This process differs between Mac and Windows – see http://www.geomorph.net/p/installing-geomorph.html for guidance. 
  • Rapp: Packages & Data >  Package Installer >  Choose CRAN (binaries) from dropdown menu, type geomorph in box and click get list. Select geomorph, select install dependancies box, and click install selected.
  • or Rstudio: Packages tab > Install: Install from CRAN repository >  type geomorph in box and select install dependancies box, and click install.
  • Mac users with OS 10.6 (Snow Leopard) should Email Emma prior to the workshop.
 

Location

ANU