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BioGeoBEARS Workshop Preparation
(What follows is standard advice for preparation for most workshops.)
Dear participants in the BioGeoBEARS workshop,
The workshop is scheduled for XXX.
Ideally, I like to have participants in these workshops run through example analyses with me during the workshop. This is not absolutely required — some people learn better by following along with others, or just by watching and getting the "big picture", and I am fine with that as well.
For those who do want to run through the examples, a few things will make it easier to "get off the ground running". These are:
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# Preparation for BioGeoBEARS Workshop
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1. LAPTOP WITH INTERNET: Bring a laptop, with some internet connection (I will have the necessary files on a thumb drive, but web access will make it easier)
2. INSTALL NEW-ISH R: Have a recent version of R installed. (Hopefully installed within a year or so. If you haven't installed R in a long time, it would be worth downloading a new version. All downloads are free. I like RStudio (any platform), or R.app (for Macs):
https://www.rstudio.com/products/rstudio/download/
https://cran.r-project.org/
3. TEXT EDITOR: Have or find a good plain-text code editor. This could be the code editor inside of Rstudio or R.app, or something else. Advice on plain-text editors:
http://phylo.wikidot.com/biogeobears#texteditors
(shorter version: Don't use Microsoft Word to save/edit your R scripts)
4. R PACKAGES: Install the R packages necessary to run BioGeoBEARS. Instructions are here:
http://phylo.wikidot.com/biogeobears#installation
This can be done during the workshop, but it will be faster if done beforehand.
5. INTRO TO R: If you are new to R, getting a little familiarity to the very basics will help a lot. I have written a short "Introduction to R" that you can run through:
Introduction to statistics in R
http://phylo.wikidot.com/2014-summer-research-experiences-sre-at-nimbios-for-undergra
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Also, if people have datasets they would like to run, I would be happy to help with that at the end of the workshop. The key files are (a) a time-scaled phylogeny, and (b) a geography file.
Example input files for BioGeoBEARS:
http://phylo.wikidot.com/biogeobears#links_to_files
Thanks very much! I'm looking forward to meeting everyone.
Cheers!
Nick
General BioGeoBEARS Workshop Description
Workshop Title: Free your mind: Comparing and statistical testing of multiple models in historical biogeography, using the R package 'BioGeoBEARS'
Workshop Summary: Historical biogeography methods have long been dominated by the "dispersal versus vicariance" debate, and different computer programs (e.g. DIVA, Lagrange, BayArea) have made different fixed assumptions about the importance of these processes. Researchers typically just run the different programs, and observe whether or not the inferences differ, but they have no ability to judge, statistically, which of the models best fits the data, or whether another model (for example, one including founder-event speciation) might be better than any of these.
The R package BioGeoBEARS allows users to build models that give different probability to vicariance, dispersal, and other processes, as well as build more complex models (dispersal probability as a function of distance, island emergence and submergence, inclusion of fossil data). All of the models are directly comparable in the common framework of statistical model choice. Attendees of this workshop will learn how to build and test models in BioGeoBEARS, as well as necessary basic skills in R and statistical model choice.
Previous experience with R is helpful, but NOT required. Attendees may wish to bring their own phylogenies and geography data and run it at the end of the workshop.
We will cover: Basic historical biogeography processes and models, basic likelihood-based statistical model selection, diagramming and interpretation of results, biogeographical stochastic mapping, and construction of advanced models (time-stratified, changing geography, inclusion of fossils, etc.)
Requirements: R experience helpful but not required - I have written a short "Intro to R" tutorial which those new to R may work through beforehand.
Equipment: Bring a laptop or share with someone (cross-plaform).
Setup: You will need to have R installed (free download). To install the necessary R packages, see the beginning of the example script: http://phylo.wikidot.com/biogeobears#script
Example:
This is an example of biogeographical stochastic mapping (BSM). Standard likelihood biogeography analyses produce probabilities of each possible ancestral range at each node, but this is not the same thing as an exact history. BSM provides a statistical sample of exact histories of approximately equal probability, given your data and model.
Here, possible histories of the Hawaiian shrub Psychotria are compared under time-stratified versions of the DEC and DEC+J model. Blue = Kauai (age ~5.2 my), Green= Oahu (age ~3.7 my), Yellow = Maui-Nui (age ~1.9 my), Red = Big Island (age ~0.5 my)
DEC vs. DEC+J ML models on a time-stratified ("M3") Psychotria analysis. Here, lineages cannot occupy islands before they rise above the ocean.
(larger versions)Caption: Stochastic mapping of approximately equiprobable alternative histories under each model. Left: DEC model. Right: DEC+J, which includes founder-event speciation. Key: Blue, K=Kauai. Green: O=Oahu. Yellow: M=Maui-Nui. Red: H=Hawaii Big Island. Kauai is the oldest high island (~5.2 Ma), the Big Island is the youngest island (~0.5 Ma).
Links and More information: Contact instructor Nick Matzke (gro.soibmin|ekztam#gro.soibmin|ekztam) for more information. See also these links:
http://phylo.wikidot.com/biogeobears
http://cran.r-project.org/web/packages/BioGeoBEARS/index.html
Papers about BioGeoBEARS:
- Matzke, Nicholas J. (2014). "Model Selection in Historical Biogeography Reveals that Founder-event Speciation is a Crucial Process in Island Clades." Systematic Biology. Early View: http://sysbio.oxfordjournals.org/content/early/2014/08/14/sysbio.syu056.abstract
- Matzke, Nicholas J. (2013). "Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing." Frontiers of Biogeography, 5(4), 242-248. http://escholarship.org/uc/item/44j7n141
- Publications using BioGeoBEARS, see also Google Scholar: http://scholar.google.com/scholar?scisbd=2&q=BioGeoBEARS&hl=en&as_sdt=0,43
India Biogeography Meeting, September 26, 2017 — New models and methods for historical biogeography in the R package 'BioGeoBEARS'
Matzke, Nicholas J. (2017). "New models and methods for historical biogeography in the R package 'BioGeoBEARS'." India Biogeography Meeting, September 26, 2017. Location: J.N. Tata Auditorium, Bengaluru, Karnataka, India 560012. https://www.biogeography.in/plenaries-workshops/
Twitter: https://twitter.com/NickJMatzke/status/902731875906498561 https://twitter.com/india_ibs/status/902513357206413312
Workshop Summary: Historical biogeography methods have long been dominated by the "dispersal versus vicariance" debate, and different computer programs (e.g. DIVA, Lagrange, BayArea) have made different fixed assumptions about the importance of these processes. Researchers typically just run the different programs, and observe whether or not the inferences differ, but they have no ability to judge, statistically, which of the models best fits the data, or whether another model (for example, one including founder-event speciation) might be better than any of these.
The R package BioGeoBEARS allows users to compare speciational models, as well as build more complex models (dispersal probability as a function of distance, island emergence and submergence, inclusion of fossil data). All of the models are directly comparable in the common framework of statistical model choice. Attendees of this workshop will learn how to build and test models in BioGeoBEARS, as well as necessary basic skills in R and statistical model choice.
Previous experience with R is helpful, but NOT required. Attendees may wish to bring their own phylogenies and geography data and run it at the end of the workshop.
We will cover:
Basics: historical biogeography processes and models, basic likelihood-based statistical model selection, diagramming and interpretation of results
Advanced: Biogeographical Stochastic Mapping (BSM), distance-dependent dispersal models, trait-dependent dispersal
Requirements: R experience helpful but not required - I have written a short "Intro to R" tutorial which those new to R may work through beforehand.
Equipment: Bring a laptop or share with someone (cross-plaform).
Setup: You will need to have R installed (free download). To install the necessary R packages, see the beginning of the example script: http://phylo.wikidot.com/biogeobears#script
Workshop: University of Conception, Chile
Model-Based Statistical Inference in Historical Biogeography, with BioGeoBEARS
Three-day short course at University of Conception, Chile, Jan. 16-18.
Workshop at Society of Systematic Biology, satellite meeting, Baton Rouge, Louisiana
Model-Based Statistical Inference in Historical Biogeography, with BioGeoBEARS
Workshop for the SSB Satellite Meeting, Baton Rogue, LA, January 8, 2016
https://github.com/ssb2017/biogeobears
Workshop: Model-Based Statistical Inference in Ecological and Evolutionary Biogeography
Workshop: "Model-Based Statistical Inference in Ecological and Evolutionary Biogeography"
Instructors: Dan Warren (Macquerie U.) and Nick Matzke (Australian National U.)
Host: Transmitting Science
Location: Barcelona, Spain
Venue: Els Hostalets de Pierola
Dates: Monday, November 28-Friday, December 2, 2016
Times: 9:30 am-1:30 pm, 3-7 pm daily
Registration cost before May 15, 2016: 515 euro
Registration cost after May 15, 2016: 720 euro
Workshop website: http://www.transmittingscience.org/courses/biog/statistical-biogeography/
Matzke webpage: http://phylo.wikidot.com/model-based-statistical-inference-in-ecological-and-evolutio
Course Announcement: Nick Matzke and Dan Warren will be teaching a course entitled “Model-based Statistical Inference in Ecological and Evolutionary Biogeography” in Barcelona from November 28 to Dec 2, 2016. This course will cover the theory and practice of widely used methods in evolutionary and ecological biogeography, namely ecological niche modelling / species distribution modelling, and ancestral range estimation on phylogenies. The course will cover both the practical challenges to using these techniques (the basics of R, obtaining and processing geographical occurrence data from GBIF, setting up and using the models), and the assumptions that various models and methods make. R packages we will use include rgbif, dismo, ENMTools, and BioGeoBEARS. Finally, this course will introduce several new approaches being developed by the instructors for linking ecological and evolutionary models. For more details or to enroll, please see the Transmitting Science web site http://bit.ly/1nCHjCP moc.liamg|nerraw.l.nad#moc.liamg|nerraw.l.nad
BioGeoBEARS workshop: June 27, 2016, Oregon State University
Date: Monday, June 27, 2016. 1-5 pm
Room: Room 164 Nash Hall
Title: Free your mind: Comparing and statistical testing of multiple models in historical biogeography, using the R package 'BioGeoBEARS'
Workshop Summary: Historical biogeography methods have long been dominated by the "dispersal versus vicariance" debate, and different computer programs (e.g. DIVA, Lagrange, BayArea) have made different fixed assumptions about the importance of these processes. Researchers typically just run the different programs, and observe whether or not the inferences differ, but they have no ability to judge, statistically, which of the models best fits the data, or whether another model (for example, one including founder-event speciation) might be better than any of these.
The R package BioGeoBEARS allows users to build models that give different probability to vicariance, dispersal, and other processes, as well as build more complex models (dispersal probability as a function of distance, island emergence and submergence, inclusion of fossil data). All of the models are directly comparable in the common framework of statistical model choice. Attendees of this workshop will learn how to build and test models in BioGeoBEARS, as well as necessary basic skills in R and statistical model choice.
Previous experience with R is helpful, but NOT required. Attendees may wish to bring their own phylogenies and geography data and run it at the end of the workshop.
We will cover:
Basics: historical biogeography processes and models, basic likelihood-based statistical model selection, diagramming and interpretation of results
Advanced: Biogeographical Stochastic Mapping (BSM), distance-dependent dispersal models, trait-dependent dispersal
Requirements: R experience helpful but not required - I have written a short "Intro to R" tutorial which those new to R may work through beforehand.
Equipment: Bring a laptop or share with someone (cross-plaform).
Setup: You will need to have R installed (free download). To install the necessary R packages, see the beginning of the example script: http://phylo.wikidot.com/biogeobears#script
BioGeoBEARS workshop: October 21, 2015, Texas A&M University
Matzke, Nicholas J. (2015). Biogeographical analysis with the R package BioGeoBEARS. Wednesday, October 21, 2015, 10 am-3 pm. Texas A&M University. MSC 2507 (Memorial Student Center). Sponsored by Michelle Lawing & Open Source for Open Science (OSOS).
Advanced BioGeoBEARS workshop: Tuesday, August 25, 2015, The Australian National University, Canberra, Australia
Title: Advanced probabilistic historical biogeography, with the R package BioGeoBEARS
Date: Tuesday, August 25, 2015
Time: 1-5 pm
Building/room: Gould Meetings Room, Room 246, Building 116 (Gould Wing),
Location: The Australian National University, Canberra, Australia
Summary: Having full probabilistic likelihood models available for biogeography makes a number of other options techniques available. This workshop will cover some of these advances, including distance-based dispersal and environment-based dispersal; biogeographical stochastic mapping, changing geography through time; inclusion of fossils.
Topics: Distance-based models and other variants on models. Biogeographical Stochastic Mapping, construction of advanced models (time-stratified, changing geography, inclusion of fossils.
Attendees may wish to bring their own phylogenies and geography data and run it at the end of the workshop.
Requirements:
- Same as the previous workshop, and:
- Take the previous workshop, or have previous experience running BioGeoBEARS (at least the online tutorial at: http://phylo.wikidot.com/biogeobears#script )
Introductory BioGeoBEARS workshop: Monday, August 24, 2015, The Australian National University, Canberra, Australia
Title: Introduction to statistical model choice in historical biogeography, with the R package BioGeoBEARS
Date: Monday, August 24, 2015
Time: 1-5 pm
Building/room: Gould Meetings Room, Room 246, Building 116 (Gould Wing),
Location: The Australian National University, Canberra, Australia
Summary: Historical biogeography methods have long been dominated by the "dispersal versus vicariance" debate, and different computer programs (e.g. DIVA, Lagrange, BayArea) have made different fixed assumptions about the importance of these processes. Researchers typically just run the different programs, and observe whether or not the inferences differ, but they have no ability to judge, statistically, which of the models best fits the data, or whether another model (for example, one including founder-event speciation) might be better than any of these.
The R package BioGeoBEARS allows users to build models that give different probability to vicariance, dispersal, and other processes, as well as build more complex models (dispersal probability as a function of distance, island emergence and submergence, inclusion of fossil data). All of the models are directly comparable in the common framework of statistical model choice. Attendees of this workshop will learn how to build and test models in BioGeoBEARS, as well as necessary basic skills in R and statistical model choice.
Previous experience with R is helpful, but NOT required.
Topics: Basic historical biogeography processes and models, basic likelihood-based statistical model selection, diagramming and interpretation of results,
Requirements:
- Laptop (or share with someone)
- wireless access
- install a recent version of R (version 3 or greater): https://www.r-project.org/
- install BioGeoBEARS and dependencies: http://phylo.wikidot.com/biogeobears#installation
Model-based Biogeographical Analyses: Principles and Practice (by Jeet Sukumaran )
Model-based Biogeographical Analyses: Principles and Practice
by Jeet Sukumaran
University of Michigan, Ann Arbor, MI
May 20, 2015
12:45 pm - 5 pm (Union: Wolverine ABC, 1st floor)
This workshop will provide a synoptic review of the major approaches to biogeographical analyses, with an emphasis on current phylogeny-based computational biogeographical analytical methods. A selection of these approaches will be visited in detail in both theory and practice (e.g., Lagrange, BioGeoBears, BayArea). Students will be expected to have Python 2.7 or later and R 3.0.0 or later installed on their computers before the workshop.
Description: http://ssb2015standalone.weebly.com/workshops.html
Workshop presentation, example files: https://github.com/jeetsukumaran/2015-SSB-AnnArbor-Biogeography
BioGeoBEARS workshop: Monday, January 19, 2015, University of Helsinki, Finland
I am visiting the University of Helsinki from Jan. 13-Jan. 20. I am giving a BEASTmasteR workshop, a lecture, and then this BioGeoBEARS workshop.
Title: Free your mind: Comparing and statistical testing of multiple models in historical biogeography, using the R package 'BioGeoBEARS'
Date: January 19, 2015
Time: 10 a.m. - 4 p.m.
Building/room: TBA
Location: University of Helsinki, Finland
Requirements: R experience helpful but not required - I will give desiring participants a short "Intro to R" tutorial online before the meeting
Equipment: Bring a laptop or share with someone.
Host: Laura K Säilä, Department of Geosciences and Geography / Geosciences Graduate Program / LUOVA , University of Helsinki, Finland
Description: see BioGeoBEARS workshop description
BioGeoBEARS workshop: Thursday, January 8, 2015, International Biogeography Society Meeting, Bayreuth, Germany
I am giving the following workshop at IBS2015:
Workshop: Free your mind: Model comparison and model testing in historical biogeography with the R package 'BioGeoBEARS'
Date: January 8, 2015
Time: 1pm - 5:30 pm
Location: Bayreuth, Germany
Room (updated Jan. 8!): conference room K3 in building RW link for map
Cost: 60 euro
Requirements: R experience helpful but not required - I will give desiring participants a short "Intro to R" tutorial online before the meeting
Equipment: Bring a laptop or share with someone.
Register: During online registration for the IBS2015 meeting. Early (cheaper) registration for IBS2015 ends Tuesday, September 30, 2014.
IBS Workshop Description: http://www.bayceer.uni-bayreuth.de/ibs2015/en/prog/gru/html.php?id_obj=11077
Some previous workshops
02/28/14 - Matzke, Nicholas J. (2014). BioGeoBEARS workshop. Invited, travel expenses paid. Bioinformatics Program at the University of Texas, El Paso. February 28 2014.
01/07/14 - Matzke, Nicholas J. (2014). BioGeoBEARS workshop. Invited, travel expenses paid. International Biogeography Society Early Career Meeting. Australian National University, Canberra, Australia. January 7, 2014.
11/12/2013 - Matzke, Nicholas J. (2013). BioGeoBEARS workshop. Invited, travel expenses paid. Jetz Lab, Department of Ecology and Evolution, Yale University. 5-7 pm, Osborn Memorial Laboratories (OML) room 40, November 12, 2013.
10/10/13 - Matzke, Nicholas J. (2013). BioGeoBEARS workshop. Invited, travel expenses paid. 2013 CEBA Thematic School, Cayenne, French Guiana. CEBA is the French CEntre for the study of Biodiversity in Amazonia. October 10, 2013.