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Advanced Courses in Life Sciences

6th Edition

Geometric Morphometrics in R

January 21st-25th, 2019, Barcelona (Spain)

Geometric Morphometrics

Geometric Morphometrics Logo

Geometric Morphometrics in R - Argentina

Course Overview

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

Can Carol

C/ Font de la Reina, 5
08786 Capellades, Barcelona (Spain)

How to get there

DATE

January 21st-25th, 2019

LANGUAGE

English

COURSE LENGTH & ECTS

40 hours on-site.

This course is equivalent to 2 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

Coordinator

Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain

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.

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

Program

Monday, January 21st, 2019.

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, January 22nd, 2019.

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, January 22nd, 2019.

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, January 23rd, 2019.

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, January 24th, 2019.

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

Fees

  • Course Fee
  • {{content-1}}
  • Early bird (until September 30th, 2018):
  • 515 *
  • Regular (after September 30th, 2018):
  • 643 *
  • This includes course material, coffee breaks and lunches (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.
  • Course Fee + Accommodation Package
  • {{content-1}}
  • Early bird (until September 30th, 2018):
  • 515 * + 330 = 845
  • Regular (after September 30th, 2018):
  • 643 * + 330 = 973
  • This includes course material, coffee breaks, transportation from and to Barcelona city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

We offer the possibility of paying in two instalments (contact the course coordinator). Discounts (see Funding below) are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Accommodation

Accommodation Package

If you take the Accommodation Package you will be hosted in the Rural House Can Carol, in single-sex shared dormitories (2 – 4 people) with bathroom en-suite.

If the number of participants exceeds the available rooms at Can Carol, some of them could be accommodated in the Hotel Tall del Conill, by registration order. The hotel is at 10 minutes walking, although transport will be provided in the morning and after dinner. Lunches and dinners will be with the whole group.

A supplemental charge will be added if you prefer to stay in a single room.

Accommodation is included from Sunday (check-in) to Friday (check-out). Breakfast, lunch and dinner are also provided during the week, starting from the dinner of Sunday to lunch of Friday (included).

Other accommodation options

If you do not want the Accommodation Package, accommodation is available in places other than Can Carol: Where to stay near the Venue.

Rural House Can Carol

Rural House Can Carol (Capellades, Barcelona, Spain)

Rural House Can Carol

Rural House Can Carol (Capellades, Barcelona, Spain)

Rural House Can Carol

Rural House Can Carol (Capellades, Barcelona, Spain)

Schedule

Course Schedule
  • Monday to Friday:
    • 9:30 to 13:30 Lessons.
    • 13:30 to 15:00 Lunch (included).
    • 15:00 to 19:00 Lessons.
Accommodation Package Schedule
  • Sunday:
    • 19:00 Meeting point in Plaza Catalunya (Barcelona) to take the bus to Els Hostalets de Pierola. If you are planning to arrive later, you can find more information in How to get there.
    • 20:00 Registration in the Hotel.
    • 20:30 Dinner.
  • Monday to Thursday:
    • 8:00 to 9:00 Breakfast.
    • 20:30 Dinner.
  • Friday:
    • 8:00 to 9:00 Breakfast.
    • 19:00 Meeting point in the Hotel to take the bus to Barcelona city.
    • 20:30 Arrival to Plaza Catalunya (Barcelona).

    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.

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).

Spanish unemployed scientists, as well as Spanish PhD students without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.

Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Testimonials

You will find below some testimonials from former participants to previous editions of this course:

“The course on Geometric Morphometry in R held in Piera, Spain was excellent. I heartily thank Dr. Julien Claude our instructor and Dr. Soledad De Esteban-Trivigno, our course coordinator. The week spent under the guidance of Dr. Julien Claude crystal cleared the concepts of using R in GM. The location and ambience of the course was ideal for such engaging studies. There were participants from diverse field of studies and the best part of the course was that there was ample time to work with our own data and deal with its problems. Dr. Claude was very helpful and he individually answered and looked after the problems each participant had. He always encouraged us to ask questions and was happy to help with our doubts. He helped us at every moment with each of our problems. His teaching is excellent. This course and especially the teaching of Dr. Julien Claude inspired me to include geometric morphometric studies for my PhD work. I also earnestly thank Dr. Soledad De Esteban-Trivigno for her immense care for each of the participants. The course was very well organised, well managed and the food was fantastic!! It is really a course worth to be taken!!!” (3rd Edition)

Sanjukta ChakravortiIndian Statistical Institute, India

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: 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.

Organizers

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Collaborators

Logo Ajuntament Capellades
Colegio Oficial de Biólogos de Castilla y León Logo
Colegio Oficial de Biólogos de Euskadi Logo
Colexio Oficial de Biólogos de Galicia Logo
Col·legi Oficial de Biòlegs de la Comunitat Valenciana Logo

Registration