# Difference between revisions of "Tracy Heath"

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Assistant Professor<br/> | Assistant Professor<br/> | ||

Dept. Ecology, Evolution, & Organismal Biology<br/> | Dept. Ecology, Evolution, & Organismal Biology<br/> | ||

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== Contact Information == | == Contact Information == | ||

− | * | + | *Web page: http://phyloworks.org/ |

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*Twitter: [https://twitter.com/trayc7 @trayc7] | *Twitter: [https://twitter.com/trayc7 @trayc7] | ||

− | *Email: | + | *Email: phylo "at" iastate "dot" edu |

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== Research == | == Research == | ||

+ | [[File:heath.jpg|thumb|right]] | ||

I develop statistical models for use as priors in Bayesian methods for phylogenetic inference. In particular, I'm interested in divergence-time estimation -- e.g. modeling rate variation across the tree of life, diversification processes, and methods for incorporating information from the fossil record. | I develop statistical models for use as priors in Bayesian methods for phylogenetic inference. In particular, I'm interested in divergence-time estimation -- e.g. modeling rate variation across the tree of life, diversification processes, and methods for incorporating information from the fossil record. | ||

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== Time at MBL == | == Time at MBL == | ||

− | Sunday | + | Thursday August 1 - Sunday August 11 |

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+ | == 2019 Course == | ||

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+ | Divergence Time Estimation in RevBayes - August 4 & 5 | ||

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+ | All workshop materials will be made available on the RevBayes website: https://revbayes.github.io/workshops/woodshole2019.html | ||

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+ | == Suggested Reading == | ||

+ | |||

+ | Graphical Models | ||

+ | * Höhna, Heath, Boussau, Landis, Ronquist, Huelsenbeck. 2014. Probabilistic graphical model representation in phylogenetics. Systematic Biology, 63:753–771. ([http://sysbio.oxfordjournals.org/content/63/5/753 doi: 10.1093/sysbio/syu039]). | ||

+ | |||

+ | Divergence-Time Estimation | ||

+ | * Thorne and Kishino. 2005. Estimation of divergence times from molecular sequence data. In: Nielsen R, editor, Statistical Methods in Molecular Evolution. New York: Springer, pp. 235–256. ([ftp://statgen.ncsu.edu/pub/thorne/mypapers/clockreview1215wfigs.pdf PDF]) | ||

+ | * Heath and Moore. 2014. Bayesian inference of species divergence times. In: Bayesian Phylogenetics: Methods, Algorithms, and Applications. Chen, M.-H., L. Kuo, and P.O. Lewis (editors). Chapman & Hall/CRC. (book chapter email me for PDF) | ||

+ | * BEAST2 Book: Drummond AJ, Bouckaert RR. 2014. Bayesian evolutionary analysis with BEAST 2. Cambridge University Press. (http://www.beast2.org/book.html) | ||

+ | * Lartillot: blog post on diversification: http://bayesiancook.blogspot.com/2013/12/two-sides-of-same-coin.html | ||

+ | * also see references in [http://treethinkers.org/wp-content/uploads/2014/08/DivTime_BEAST2_tutorial_2014.pdf divergence-time tutorial] | ||

+ | |||

+ | == Additional Tutorials == | ||

+ | |||

+ | * More tutorials on divergence time estimation in RevBayes and BEAST2 ([http://phyloworks.org/workshops/divtime.html link]) | ||

+ | * Materials (tutorials and lectures) from the Taming the BEAST workshop, including some tutorials on infectious disease dynamics ([https://www.bsse.ethz.ch/cevo/taming-the-beast/materials.html link]) | ||

+ | |||

+ | == 2016 Course == | ||

+ | |||

+ | * Phylogenetic Inference using [[RevBayes]] (with [[Michael Landis]]) | ||

+ | * [http://phyloworks.org/workshops/divtime.html Bayesian Divergence Time Estimation in BEAST2] ([http://phyloworks.org/workshops/WH_2015_divtime_lec_d.pdf slides]) | ||

+ | |||

+ | == 2017 Course == | ||

− | + | Morning lecture slides and example scripts | |

+ | * Hierarchical models and integrative Bayesian analysis ([https://www.slideshare.net/trayc7/integrative-bayesian-analysis-in-revbayes slides]) | ||

+ | ** RevBayes archery model demo ([[:File:Archery_model.zip|files]]) | ||

+ | ** RevBayes GTR demo ([https://github.com/revbayes/revbayes_tutorial/tree/master/RB_CTMC_Tutorial files]) | ||

+ | * Bayesian divergence-time estimation ([https://www.slideshare.net/trayc7/bayesian-divergence-time-estimation-lecture-at-bodega-2014-workshop slides]) | ||

− | + | Afternoon tutorial | |

− | * [[ | + | * [[Total-evidence analysis in RevBayes]] |

## Latest revision as of 14:31, 3 August 2019

Assistant Professor

Dept. Ecology, Evolution, & Organismal Biology

Iowa State University

## Contact Information

- Web page: http://phyloworks.org/
- Twitter: @trayc7
- Email: phylo "at" iastate "dot" edu

## Research

I develop statistical models for use as priors in Bayesian methods for phylogenetic inference. In particular, I'm interested in divergence-time estimation -- e.g. modeling rate variation across the tree of life, diversification processes, and methods for incorporating information from the fossil record.

## Time at MBL

Thursday August 1 - Sunday August 11

## 2019 Course

Divergence Time Estimation in RevBayes - August 4 & 5

All workshop materials will be made available on the RevBayes website: https://revbayes.github.io/workshops/woodshole2019.html

## Suggested Reading

Graphical Models

- Höhna, Heath, Boussau, Landis, Ronquist, Huelsenbeck. 2014. Probabilistic graphical model representation in phylogenetics. Systematic Biology, 63:753–771. (doi: 10.1093/sysbio/syu039).

Divergence-Time Estimation

- Thorne and Kishino. 2005. Estimation of divergence times from molecular sequence data. In: Nielsen R, editor, Statistical Methods in Molecular Evolution. New York: Springer, pp. 235–256. (PDF)
- Heath and Moore. 2014. Bayesian inference of species divergence times. In: Bayesian Phylogenetics: Methods, Algorithms, and Applications. Chen, M.-H., L. Kuo, and P.O. Lewis (editors). Chapman & Hall/CRC. (book chapter email me for PDF)
- BEAST2 Book: Drummond AJ, Bouckaert RR. 2014. Bayesian evolutionary analysis with BEAST 2. Cambridge University Press. (http://www.beast2.org/book.html)
- Lartillot: blog post on diversification: http://bayesiancook.blogspot.com/2013/12/two-sides-of-same-coin.html
- also see references in divergence-time tutorial

## Additional Tutorials

- More tutorials on divergence time estimation in RevBayes and BEAST2 (link)
- Materials (tutorials and lectures) from the Taming the BEAST workshop, including some tutorials on infectious disease dynamics (link)

## 2016 Course

- Phylogenetic Inference using RevBayes (with Michael Landis)
- Bayesian Divergence Time Estimation in BEAST2 (slides)

## 2017 Course

Morning lecture slides and example scripts

- Hierarchical models and integrative Bayesian analysis (slides)
- Bayesian divergence-time estimation (slides)

Afternoon tutorial