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TUNICATA  July 2018

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Subject:

Advanced course Geometric Morphometrics with R, Jan 21-25, Barcelona (Spain)

From:

"soledad.esteban" <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Mon, 16 Jul 2018 18:23:53 +0200

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (181 lines)

Dear colleagues,

The sixth edition of the course "Geometrics Morphometrics in R" has opened registration. 

Dates: January 21th-25th, 2019.

Instructor: Dr. Julien Claude (Institut des Sciences de l’Évolution de Montpellier, France), author of Morphometrics with R (http://www.springer.com/us/book/9780387777894). 

PLACE:  Capellades, Barcelona (Spain).

Registration and more info: http://www.transmittingscience.org/courses/geometric-morphometrics/geometric-morphometrics-r/

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 23rd, 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 24th, 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.

 
With best regards

Sole

Soledad De Esteban-Trivigno
Institut Català de Paleontologia Miquel Crusafont (ICP)

Campus de la Universitat Autònoma de Barcelona
Cerdanyola del Vallès (Barcelona). Spain
www.icp.cat
   

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