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Advanced Courses in Life Sciences

3rd Edition

Geometric Morphometrics in R

January 23rd-27th, 2017, Barcelona (Spain)

Geometric Morphometrics in R

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

Centre de Restauració i Interpretació Paleontològica

C/ Mestre J. Lladós, 1
08781 Els Hostalets de Pierola, Barcelona.

How to get there

LANGUAGE

English

COURSE LENGHT & 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

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 – SpainIntroduction to Geometric Morphometrics – Canada or 3D Geometric Morphometrics (for those researchers with 3D data).

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

Program

Monday, January 23rd, 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, January 24th, 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, January 25th, 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, January 26th, 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, January 27th, 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

Fees

  • Course Fee
  • Early bird (until October 15th, 2016)
  • 545
  • Regular (after October 15th, 2016)
  • 765
  • This includes course material, coffee breaks and lunches.
  • Accommodation Package
  • Early bird (until October 15th, 2016)
  • 360
  • Regular (after October 15th, 2016)
  • 360
  • This includes local transportation, lodging, breakfasts, dinners and social (tourist) activities.
  • Course Fee + Accommodation Package
  • Early bird (until October 15th, 2016)
  • 905
  • Regular (after October 15th, 2016)
  • 1,125
  • This includes course material, coffee breaks and lunches.

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

If you take the Accommodation Package you will be hosted in the Youth Hostel Can Roviralta, in shared dormitories (common bathrooms), although you will only share rooms with other classmates. The possibility exists that the dormitories will be mixed. Therefore, if this is an inconvenience for you, and you require staying in a dormitory with only women, or only men, please indicate so in the “Comments” field of the Registration form (see below).

A supplemental charge will be added if you prefer to stay in a single room with private bathroom. The number of rooms is limited and if you prefer to have a single room, let us know it as soon as possible. If you want more information on this please contact the course coordinator.

Please be aware that from the centre of Barcelona city it takes about one hour by car and one hour and a half by public transport to arrive to Els Hostalets de Pierola. Course participants will find that staying in Els Hostalets de Pierola is more convenient.

If you do not want the Accommodation Package, accommodation is available in places other than Els Hostalets de Pierola. You may stay in Barcelona city, Martorell or Igualada. You will find information about Hotels in Martorell here, and information about Hotels in Igualada here.

How to get to Els Hostalets de Pierola from Barcelona city, Martorell and Igualada.

Youth Hostel Can Roviralta (Els Hostalets de Pierola, Barcelona, Spain)

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.

Schedule

Course ScheduleCourse + Accommodation Package Schedule
Sunday, January 22nd, 201719:00 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 Youth Hostel.
20:30 Dinner.
Monday, January 23rd through Friday, January 27th, 20179:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 19:00 Lessons.

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

8:30 to 9:00 Breakfast.
9:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 19:00 Lessons.
20:30 Dinner.

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

Saturday, January 28th, 20178:30 to 9:00 Breakfast.
9:15 Meeting point in the Youth Hostel to take the bus to visit a wine cellar.
10:00 Arrival at the wine cellar.
11:30 Bus to Barcelona city.
13:00 Arrival at 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.

Organizers

Transmitting Science Logo
Centre de Restauració i Interpretació Paleontològica (CRIP) Logo
Institut Català de Paleontologia Miquel Crusafont (ICP) Logo

Collaborators

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
Distributed European School of Taxonomy (DEST) Logo
European Association of Vertebrate Palaeontologists (EAVP) Logo
Sociedade Brasileira de Paleontologia (SBP) Logo

Registration

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