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| DATE | 2019-03-12 |
| FROM | Ruben Safir
|
| SUBJECT | Subject: [Hangout - NYLXS] Fwd: [dinosaur] Course Using Geiger, Phytools,
|
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Subject: [Hangout - NYLXS] Fwd: [dinosaur] Course Using Geiger, Phytools,
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Date: Tue, 12 Mar 2019 08:09:52 +0100
To: dinosaur-l-at-usc.edu
From: soledad.esteban
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Subject: [dinosaur] Course Using Geiger, Phytools, and other
Computational Tools to Study Macroevolution on Phylogenies, 16-19 July,
Greece.
Reply-To: soledad.esteban
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Dear colleagues,
Registration is open for Transmitting Science course: “USING GEIGER,
PHYTOOLS, AND OTHER COMPUTATIONAL TOOLS TO STUDY MACROEVOLUTION ON
PHYLOGENIES”
Dates and place: July 16th-19th, 2019, Crete (Greece).
Instructors: Dr Liam Revell (University of Massachusetts Boston, USA)
and Dr Luke Harmon (University of Idaho, USA).
PROGRAM
Monday
- Introduction to phylogenies and the comparative method. [Lecture]
- Introduction the basics of the R statistical computing
environment. [Exercise]
- Introduction to reading, writing, manipulating, and visualizing
phylogenies and comparative data in R. [Exercise]
- Models of phenotypic trait evolution on trees: Brownian motion. [Lecture]
- Simulating Brownian motion on trees using R. [Exercise]
- Introduction to the phylogenetic comparative method: Phylogenetic
independent contrasts. [Lecture]
- Phylogenetic independent contrasts and exploring the properties of
contrasts regression using simulation in R. [Exercise]
- Phylogenetic generalized least squares regression and phylogenetic
generalized ANOVA. [Exercise]
Tuesday
- Multivariate statistical methods with phylogenies: Phylogenetic
principal components analysis, canonical correlation analysis, and other
approaches. [Lecture]
- Phylogenetic PCA and phylogenetic CCA in R. [Exercise]
- Continuous character models of trait evolution on phylogenies. [Lecture]
- Fitting continuous character models to univariate trait data in
R. [Exercise]
- Ancestral state reconstruction I: Continuous characters. [Lecture]
- Reconstructing ancestral states for continuous traits on phylogenies
using R. [Exercise]
Wednesday
- Ancestral state reconstruction II: Discrete characters. [Lecture]
- Reconstructing ancestral states for discrete traits on phylogenies
using R. [Exercise]
- Exploring the limitations of ancestral state reconstruction for
continuous and discrete characters on phylogenies using R. [Exercise]
- Testing for the influence of one discrete character on a second using
Pagel’s (1994) method. [Lecture]
- Exploring the promise and limitations of the Pagel (1994) method using
R. [Exercise]
- Analysing discrete character coevolution, and the evolution of
discrete and continuous characters using the threshold model. [Lecture]
Thursday
- Fitting models of discrete and continuous character evolution on trees
using the threshold model. [Exercise]
- Multi-rate, multi-regime, and multivariate models of character
evolution on phylogenies. [Lecture]
- Fitting multi-regime and multivariate models for continuous character
evolution in - [Exercise]
- Visualizing trees and phylogenetic comparative data. [Lecture]
- Plotting phylogenies and comparative data using R. [Exercise]
- Wrap-up and optional additional exercise or lecture.
More information and registration
[https://urldefense.proofpoint.com/v2/url?u=https-3A__www.transmittingscience.org_courses_evolution_using-2Dgeiger-2Dphytools-2Dother-2Dcomputational-2Dtools-2Dstudy-2Dmacroevolution-2Dphylogenies_-5D-28https-3A__www.transmittingscience.org_courses_evolution_using-2Dgeiger-2Dphytools-2Dother-2Dcomputational-2Dtools-2Dstudy-2Dmacroevolution-2Dphylogenies_-29&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=-2y5rF2dUVJbUd5DKi_bnpdP1IZA6ScJC31Koh1bOWY&s=XEA_fxplrBRiSA37PNR-YFmhjX1VPixUuRJlrBoOKQs&e=
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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_______________________________________________
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Date: Tue, 12 Mar 2019 08:09:52 +0100
To: dinosaur-l-at-usc.edu
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Subject: [dinosaur] Course Using Geiger, Phytools, and other
Computational Tools to Study Macroevolution on Phylogenies, 16-19 July,
Greece.
Reply-To: soledad.esteban
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Dear colleagues,
Registration is open for Transmitting Science course: “USING GEIGER,
PHYTOOLS, AND OTHER COMPUTATIONAL TOOLS TO STUDY MACROEVOLUTION ON
PHYLOGENIES”
Dates and place: July 16th-19th, 2019, Crete (Greece).
Instructors: Dr Liam Revell (University of Massachusetts Boston, USA)
and Dr Luke Harmon (University of Idaho, USA).
PROGRAM
Monday
- Introduction to phylogenies and the comparative method. [Lecture]
- Introduction the basics of the R statistical computing
environment. [Exercise]
- Introduction to reading, writing, manipulating, and visualizing
phylogenies and comparative data in R. [Exercise]
- Models of phenotypic trait evolution on trees: Brownian motion. [Lecture]
- Simulating Brownian motion on trees using R. [Exercise]
- Introduction to the phylogenetic comparative method: Phylogenetic
independent contrasts. [Lecture]
- Phylogenetic independent contrasts and exploring the properties of
contrasts regression using simulation in R. [Exercise]
- Phylogenetic generalized least squares regression and phylogenetic
generalized ANOVA. [Exercise]
Tuesday
- Multivariate statistical methods with phylogenies: Phylogenetic
principal components analysis, canonical correlation analysis, and other
approaches. [Lecture]
- Phylogenetic PCA and phylogenetic CCA in R. [Exercise]
- Continuous character models of trait evolution on phylogenies. [Lecture]
- Fitting continuous character models to univariate trait data in
R. [Exercise]
- Ancestral state reconstruction I: Continuous characters. [Lecture]
- Reconstructing ancestral states for continuous traits on phylogenies
using R. [Exercise]
Wednesday
- Ancestral state reconstruction II: Discrete characters. [Lecture]
- Reconstructing ancestral states for discrete traits on phylogenies
using R. [Exercise]
- Exploring the limitations of ancestral state reconstruction for
continuous and discrete characters on phylogenies using R. [Exercise]
- Testing for the influence of one discrete character on a second using
Pagel’s (1994) method. [Lecture]
- Exploring the promise and limitations of the Pagel (1994) method using
R. [Exercise]
- Analysing discrete character coevolution, and the evolution of
discrete and continuous characters using the threshold model. [Lecture]
Thursday
- Fitting models of discrete and continuous character evolution on trees
using the threshold model. [Exercise]
- Multi-rate, multi-regime, and multivariate models of character
evolution on phylogenies. [Lecture]
- Fitting multi-regime and multivariate models for continuous character
evolution in - [Exercise]
- Visualizing trees and phylogenetic comparative data. [Lecture]
- Plotting phylogenies and comparative data using R. [Exercise]
- Wrap-up and optional additional exercise or lecture.
More information and registration
[https://urldefense.proofpoint.com/v2/url?u=https-3A__www.transmittingscience.org_courses_evolution_using-2Dgeiger-2Dphytools-2Dother-2Dcomputational-2Dtools-2Dstudy-2Dmacroevolution-2Dphylogenies_-5D-28https-3A__www.transmittingscience.org_courses_evolution_using-2Dgeiger-2Dphytools-2Dother-2Dcomputational-2Dtools-2Dstudy-2Dmacroevolution-2Dphylogenies_-29&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=-2y5rF2dUVJbUd5DKi_bnpdP1IZA6ScJC31Koh1bOWY&s=XEA_fxplrBRiSA37PNR-YFmhjX1VPixUuRJlrBoOKQs&e=
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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