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Advanced Courses in Life Sciences

4th Edition

Geometric Morphometrics in R – Canada

August 14th-18th, 2017, Calgary (Canada)

Geometric Morphometrics in R - Canada

Concepts in geometric morphometrics will be taught using a series of original data sets and working in R for solving a series of tasks. The course will start with an introduction to R and will rapidly go into shape analysis with measurements, landmark data and outlines. The participants are welcome to bring their own data and problems so that we may find R solutions.

This is not an introductory course to Geometric Morphometrics, therefore basic knowledge of Multivariate StatisticsR and Geometric Morphometric is recommended in order to take this course.

LOCATION

University of Calgary

Calgary

Canada

LANGUAGE

English

COURSE LENGTH & ECTS

40 hours on-site.

This course is equivalent to 4 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.

PLACES

Places are limited to 22 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end of it.

Instructor

Julien Claude instructor for Transmitting Science

Dr. Julien Claude
Institut des Sciences de l’Évolution de Montpellier
France

Coordinators

Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain

Paula González coordinator for Transmitting Science

Dr. Paula González
Instituto de Genética Veterinaria
Argentina

Requirements

Graduate or postgraduate degree in any Life Sciences discipline. Knowledge of Multivariate Statistics, R and Geometric Morphometrics. Participants with that are not familiar with R environment are strongly recommended to read the book ‘R for beginners‘ and practice before the course. Participants who are not familiar with Geometric Morphometrics are recommended to take first the course Introduction to Geometric Morphometrics or 3D Geometric Morphometrics (for those researchers with 3D data).

All participants must bring their own personal laptop (Windows, Macintosh, Linux).

Program

Monday, August 14th, 2017.

1. An Introduction to R / Image Processing / Organizing Morphometric Data.

1.1. Some Basics in R.

1.1.1. The R Environment.

1.1.2. R objects, Assigning, Indexing.

1.1.3. Generating Data in R.

1.1.4. 2D and 3D Plots in R; Interacting with the Graphs.

1.2. Organizing Data for Morphometrics.

1.2.1. Data-frame, Array and List.

1.2.2. Converting and Coercing Objects.

1.2.3. Read and Write Morphometric Data in R.

1.3. Image Processing in R.

1.3.1. Reading Various Image Files.

1.3.2. Obtaining Image Properties.

1.3.3. Modifying Image Properties: Contrast, Channels, Saturation Directly from R or by Interfacing R with Imagemagick.

1.4. Simple Tests, Simple Linear Modelling, Alternatives to Linear Modelling, an example using traditional morphometrics.

1.4.1. Defining size and shape using PCA and log-shape ratio approaches.

1.4.2. Getting stats and test outputs.

1.4.3. Testing assumptions of linear modelling.

1.4.4. Testing for allometry and isometry.

1.4.5. Solutions when assumptions of linear modelling are not met.


Tuesday, August 15th, 2017.

2. Landmark data.

2.1. Acquiring Landmark Data in R.

2.2. Plotting Landmark Configurations in 2 and in 3D.

2.2.1. Using Different Symbols and Setting the Graphical Parameters.

2.2.2. Labeling Landmarks.

2.3. Geometric Transformation with Landmark Configurations.

2.3.1. Translation.

2.3.2. Scaling using Baseline or Centroid Size.

2.3.3. Rotation.

2.4. Superimposing and Comparing Two Shapes.

2.4.1. Baseline Superimposition.

2.4.2. Ordinary Least Squares Superimposition.

2.4.3. Resistant Fit.

2.5. Representing Shape Differences.

2.5.1. Plotting Superimposed Shape with Wireframe.

2.5.2. Lollipop Diagrams and Vector Fields.

2.5.3. Thin Plate Splines and Warped Shapes.

2.6. Superimposing More Than Two Shapes.

2.6.1. Baseline Registration.

2.6.2. Full Generalized Procrustes Analysis.

2.6.3. Partial Generalized Procrustes Analysis.

2.6.4. Dimensionality of Superimposed Coordinates.

Wednesday, August 16th, 2017.

2.7. Exploring Shape Variation and Testing Hypotheses.

2.7.1. PCA.

2.7.2. Multivariate Linear Modelling (Multivariate Regression and MANOVA).

2.7.3. Allometry free approaches (Burnaby correction).

2.7.4. Linear discriminant and Canonical Analysis.

3. Outlines.

3.1. Acquiring outline Data in R.

3.2. Fourier Analysis.

3.2.1. Principles.

3.2.2. Fourier Analysis of the Tangent Angle.

3.2.3. Radius Fourier Analysis.

3.2.4. Elliptic Fourier Analysis.

3.2.5. Reduction of Shape Variables.

3.2.6. Statistical Analysis of Shape Variation with Fourier Analysis.

3.2.6.1. Exploring Shape Variation and Testing Hypotheses.

3.2.6.2. PCA.

3.2.6.3. Multivariate Linear Modelling (Multivariate Regression and MANOVA).

3.2.6.4. Canonical Analysis.



Thursday, August 17th, 2017.

3.3. Combining Landmarks and Curves.

3.3.1. Hybrid Methods between Fourier and Procrustes Analysis.

3.3.2. Sliding Semi Landmarks.

3.4. Solutions for Open Curves.

4. Specific Applications.

4.1. Testing Measurement Error.

4.2. Partitional Clustering.

4.2.1. K-means, Partition Around Medoids.

4.2.2. Mclust.

4.2.3. Combining Genetic, Geographic and Morphometric Data.



Friday, August 18th, 2017.

4.3. Modularity / Integration Studies.

4.3.1. Two-block Partial Least Squares.

4.3.2. Testing Among Various Sets of Modules.

4.4. Fluctuating Asymmetry and Directional Asymmetry.

4.4.1. Inter-Individual and Intra-Individual Variation.

4.4.2. Object and Matching Symmetry.

4.5. Bending Energy, Uniform and Non-uniform Shape Variation.

Literature

Previous editions of this course

3rd Edition, January 23rd-27th, 2017

Course Geometric Morphometrics in R - 3rd Edition, January 23rd-27th, 2017Four people belonging to the following countries and institutions participated in this edition:

  • Austria: University of Vienna.
  • United States of America: University of Colorado Denver.
  • India: Indian Statistical Institute.
  • Spain: Island Ecology and Evolution Research Group – Instituto de Productos Naturales y Agrobiología – CSIC.

2nd Edition, January 18th-22nd, 2016

Course Geometric Morphometrics in R - 2nd Edition, January 18th-22nd, 2016Twenty-four people belonging to the following countries and institutions participated in this edition:

  • People’s Republic of China: Institute of Zoology – Chinese Academy of Sciences.
  • Austria: University of Vienna.
  • Belgium: Katholieke Universiteit Leuven.
  • Canada: University of Calgary, University of Toronto.
  • Croatia: Institute of Oceanography and Fisheries.
  • France: Sorbonne Universités, Muséum national d’Histoire naturelle.
  • Germany: Max Planck Insitute for Evolutionary Anthropology – Max Planck Society.
  • Italy: University of Bologna.
  • Mexico: Universidad Michoacana de San Nicolás de Hidalgo.
  • Russia: Zoological Museum of M. V. Lomonosov Moscow State University.
  • Spain: Autonomous University of Madrid, Centre for Genomic Regulation, Universidad de Murcia.
  • United Kingdom: University of Cambridge.
  • United States of America: Cornell University, Louisiana State University, Dartmouth College.

1st Edition, January 26th-30th, 2015

Course Geometric Morphometrics in R - 1st Edition, January 26th-30th, 2015Twenty-five people belonging to the following countries and institutions participated in this edition:

  • Australia: Australian National University.
  • United States of America: Cornell University, Texas State University.
  • Spain: Institut Català de Paleontologia Miquel Crusafont, Universidad de Castilla-La Mancha, Museo Nacional Ciencias Naturales – CSIC, Universitat de Barcelona, University of Alicante, University of Malaga, Autonomous University of Madrid.
  • Germany: Max Planck Insitute for Evolutionary Anthropology – Max Planck Society, Staatliches Museum für Naturkunde – Stuttgart, University of Konstanz.
  • France: Muséum national d’Histoire naturelle.
  • Sweden: Swedish University of Agricultural Sciences.
  • United Kingdom: The University of Manchester, University College London.
  • Ireland: University College Dublin.
  • Canada: University of Calgary.
  • Switzerland: University of Fribourg.
  • Finland: University of Helsinki.
  • The Netherlands: Wageningen University.

Fees

  • Course Fee
  • Early bird (until April 30th, 2017):
  • 950 C$ CAD
  • Regular (after April 30th, 2017):
  • 1,500 C$ CAD
  • This includes course material, lunches and coffee breaks.
    Prices do NOT include GST (5 %).

This course will be held if at least 50 % of the places are filled.

We offer the possibility of paying in two instalments (contact the course coordinators).

Funding

Former participants will have a 5 % discount on the Course Fee.

Unfortunately there are no scholarships available for this course. However a 20 % discount on the Course Fee is offered for members of some organizations (Organizations with discount). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Discounts are not cumulative.

Schedule

Course Schedule
Monday, August 14th through Friday, August 18th, 20178:30 to 12:30 Lessons.
14:00 to 18:00 Lessons.

There will be two coffee breaks each day, halfway through each lesson session.

The schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.

Organizer

Transmitting Science Logo

Collaborator

University of Calgary Logo

Registration

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