23 July Raup, D.M. 1985. Mathematical models of cladogenesis. Paleobiology 11:42-52. Nee, S. 2007. Birth-death models in macroevolution. Annual Review of Ecology, Evolution, and Systematics 37:1-17. 25 July Foote, M. and D. M. Raup. 1996. Fossil preservation and the stratigraphic ranges of taxa. Paleobiology 22:121-140. 27 July Foote, M. 2005. Pulsed origination and extinction in the marine realm. Paleobiology 31:6-20 Foote, M. 2007. Extinction and quiescence in marine animal genera. Paleobiology 33:261-272. NOTES I. Preliminaries and general introduction to birth-death (branching) models I. Figures II. Applications of homogeneous birth-death model: examples of forward modeling II. Figures III. Introduction to inverse problems (rate estimation): non-hierarchical III. Figures IV. Inverse problems with hierarchical models IV. Figures IV.B. Introduction to Likelihood V. Introduction to homogeneous sampling models V. Figures VI. Some applications of homogeneous sampling models VI. Figures VII. Overview of time-varying sampling and branching models VII. Figures VIII. Inverse procedure: Use of time-varying models to estimate true time series of p, q,and r VIII. Figures EXERCISES 23 July Exercise 1: Branching simulations 24 July Exercise 2: Survivorship analysis 24 July Exercise 3: Estimating sampling probabilities CODE Discrete-time branching and extinction simulation Continuous-time branching and extinction simulation Code to read presences.txt file, convert to list of first and last appearances, calculate origination and extinction rates, and estimate standard errors via bootstrapping Code to read firstlast.txt file, convert to cohort survivorship table, and conduct survivorship analysis Code to read firstlast.txt file, convert to dynamic survivorship table, and conduct survivorship analysis Code to read presences.txt file and estimate sampling probabilities from gaps in ranges Code to read Sepkoski FO-LO files and jointly estimate extinction rate and sampling probability LISTS OF FIRST AND LAST APPEARANCES OF GENERA FROM SEPKOSKI'S COMPENDIUM List of corresponding stage names (Tommotian=1,...,Recent=79) Paired first and last appearances for all genera in the Compendium Paired first and last appearances for Mollusca Paired first and last appearances for Cephalopoda Paired first and last appearances for Bivalvia Paired first and last appearances for Gastropoda Paired first and last appearances for Brachiopoda Paired first and last appearances for Echinodermata Paired first and last appearances for Crinoidea Paired first and last appearances for Echinoidea Paired first and last appearances for Bryozoa Paired first and last appearances for Trilobita Paired first and last appearances for Malacostraca Paired first and last appearances for Porifera Paired first and last appearances for Anthozoa
25 July Foote, M. and D. M. Raup. 1996. Fossil preservation and the stratigraphic ranges of taxa. Paleobiology 22:121-140. 27 July Foote, M. 2005. Pulsed origination and extinction in the marine realm. Paleobiology 31:6-20 Foote, M. 2007. Extinction and quiescence in marine animal genera. Paleobiology 33:261-272. NOTES I. Preliminaries and general introduction to birth-death (branching) models I. Figures II. Applications of homogeneous birth-death model: examples of forward modeling II. Figures III. Introduction to inverse problems (rate estimation): non-hierarchical III. Figures IV. Inverse problems with hierarchical models IV. Figures IV.B. Introduction to Likelihood V. Introduction to homogeneous sampling models V. Figures VI. Some applications of homogeneous sampling models VI. Figures VII. Overview of time-varying sampling and branching models VII. Figures VIII. Inverse procedure: Use of time-varying models to estimate true time series of p, q,and r VIII. Figures EXERCISES 23 July Exercise 1: Branching simulations 24 July Exercise 2: Survivorship analysis 24 July Exercise 3: Estimating sampling probabilities CODE Discrete-time branching and extinction simulation Continuous-time branching and extinction simulation Code to read presences.txt file, convert to list of first and last appearances, calculate origination and extinction rates, and estimate standard errors via bootstrapping Code to read firstlast.txt file, convert to cohort survivorship table, and conduct survivorship analysis Code to read firstlast.txt file, convert to dynamic survivorship table, and conduct survivorship analysis Code to read presences.txt file and estimate sampling probabilities from gaps in ranges Code to read Sepkoski FO-LO files and jointly estimate extinction rate and sampling probability LISTS OF FIRST AND LAST APPEARANCES OF GENERA FROM SEPKOSKI'S COMPENDIUM List of corresponding stage names (Tommotian=1,...,Recent=79) Paired first and last appearances for all genera in the Compendium Paired first and last appearances for Mollusca Paired first and last appearances for Cephalopoda Paired first and last appearances for Bivalvia Paired first and last appearances for Gastropoda Paired first and last appearances for Brachiopoda Paired first and last appearances for Echinodermata Paired first and last appearances for Crinoidea Paired first and last appearances for Echinoidea Paired first and last appearances for Bryozoa Paired first and last appearances for Trilobita Paired first and last appearances for Malacostraca Paired first and last appearances for Porifera Paired first and last appearances for Anthozoa
27 July Foote, M. 2005. Pulsed origination and extinction in the marine realm. Paleobiology 31:6-20 Foote, M. 2007. Extinction and quiescence in marine animal genera. Paleobiology 33:261-272. NOTES I. Preliminaries and general introduction to birth-death (branching) models I. Figures II. Applications of homogeneous birth-death model: examples of forward modeling II. Figures III. Introduction to inverse problems (rate estimation): non-hierarchical III. Figures IV. Inverse problems with hierarchical models IV. Figures IV.B. Introduction to Likelihood V. Introduction to homogeneous sampling models V. Figures VI. Some applications of homogeneous sampling models VI. Figures VII. Overview of time-varying sampling and branching models VII. Figures VIII. Inverse procedure: Use of time-varying models to estimate true time series of p, q,and r VIII. Figures EXERCISES 23 July Exercise 1: Branching simulations 24 July Exercise 2: Survivorship analysis 24 July Exercise 3: Estimating sampling probabilities CODE Discrete-time branching and extinction simulation Continuous-time branching and extinction simulation Code to read presences.txt file, convert to list of first and last appearances, calculate origination and extinction rates, and estimate standard errors via bootstrapping Code to read firstlast.txt file, convert to cohort survivorship table, and conduct survivorship analysis Code to read firstlast.txt file, convert to dynamic survivorship table, and conduct survivorship analysis Code to read presences.txt file and estimate sampling probabilities from gaps in ranges Code to read Sepkoski FO-LO files and jointly estimate extinction rate and sampling probability LISTS OF FIRST AND LAST APPEARANCES OF GENERA FROM SEPKOSKI'S COMPENDIUM List of corresponding stage names (Tommotian=1,...,Recent=79) Paired first and last appearances for all genera in the Compendium Paired first and last appearances for Mollusca Paired first and last appearances for Cephalopoda Paired first and last appearances for Bivalvia Paired first and last appearances for Gastropoda Paired first and last appearances for Brachiopoda Paired first and last appearances for Echinodermata Paired first and last appearances for Crinoidea Paired first and last appearances for Echinoidea Paired first and last appearances for Bryozoa Paired first and last appearances for Trilobita Paired first and last appearances for Malacostraca Paired first and last appearances for Porifera Paired first and last appearances for Anthozoa
23 July Exercise 1: Branching simulations 24 July Exercise 2: Survivorship analysis 24 July Exercise 3: Estimating sampling probabilities CODE Discrete-time branching and extinction simulation Continuous-time branching and extinction simulation Code to read presences.txt file, convert to list of first and last appearances, calculate origination and extinction rates, and estimate standard errors via bootstrapping Code to read firstlast.txt file, convert to cohort survivorship table, and conduct survivorship analysis Code to read firstlast.txt file, convert to dynamic survivorship table, and conduct survivorship analysis Code to read presences.txt file and estimate sampling probabilities from gaps in ranges Code to read Sepkoski FO-LO files and jointly estimate extinction rate and sampling probability LISTS OF FIRST AND LAST APPEARANCES OF GENERA FROM SEPKOSKI'S COMPENDIUM List of corresponding stage names (Tommotian=1,...,Recent=79) Paired first and last appearances for all genera in the Compendium Paired first and last appearances for Mollusca Paired first and last appearances for Cephalopoda Paired first and last appearances for Bivalvia Paired first and last appearances for Gastropoda Paired first and last appearances for Brachiopoda Paired first and last appearances for Echinodermata Paired first and last appearances for Crinoidea Paired first and last appearances for Echinoidea Paired first and last appearances for Bryozoa Paired first and last appearances for Trilobita Paired first and last appearances for Malacostraca Paired first and last appearances for Porifera Paired first and last appearances for Anthozoa
24 July Exercise 2: Survivorship analysis 24 July Exercise 3: Estimating sampling probabilities CODE Discrete-time branching and extinction simulation Continuous-time branching and extinction simulation Code to read presences.txt file, convert to list of first and last appearances, calculate origination and extinction rates, and estimate standard errors via bootstrapping Code to read firstlast.txt file, convert to cohort survivorship table, and conduct survivorship analysis Code to read firstlast.txt file, convert to dynamic survivorship table, and conduct survivorship analysis Code to read presences.txt file and estimate sampling probabilities from gaps in ranges Code to read Sepkoski FO-LO files and jointly estimate extinction rate and sampling probability LISTS OF FIRST AND LAST APPEARANCES OF GENERA FROM SEPKOSKI'S COMPENDIUM List of corresponding stage names (Tommotian=1,...,Recent=79) Paired first and last appearances for all genera in the Compendium Paired first and last appearances for Mollusca Paired first and last appearances for Cephalopoda Paired first and last appearances for Bivalvia Paired first and last appearances for Gastropoda Paired first and last appearances for Brachiopoda Paired first and last appearances for Echinodermata Paired first and last appearances for Crinoidea Paired first and last appearances for Echinoidea Paired first and last appearances for Bryozoa Paired first and last appearances for Trilobita Paired first and last appearances for Malacostraca Paired first and last appearances for Porifera Paired first and last appearances for Anthozoa
24 July Exercise 3: Estimating sampling probabilities CODE Discrete-time branching and extinction simulation Continuous-time branching and extinction simulation Code to read presences.txt file, convert to list of first and last appearances, calculate origination and extinction rates, and estimate standard errors via bootstrapping Code to read firstlast.txt file, convert to cohort survivorship table, and conduct survivorship analysis Code to read firstlast.txt file, convert to dynamic survivorship table, and conduct survivorship analysis Code to read presences.txt file and estimate sampling probabilities from gaps in ranges Code to read Sepkoski FO-LO files and jointly estimate extinction rate and sampling probability LISTS OF FIRST AND LAST APPEARANCES OF GENERA FROM SEPKOSKI'S COMPENDIUM List of corresponding stage names (Tommotian=1,...,Recent=79) Paired first and last appearances for all genera in the Compendium Paired first and last appearances for Mollusca Paired first and last appearances for Cephalopoda Paired first and last appearances for Bivalvia Paired first and last appearances for Gastropoda Paired first and last appearances for Brachiopoda Paired first and last appearances for Echinodermata Paired first and last appearances for Crinoidea Paired first and last appearances for Echinoidea Paired first and last appearances for Bryozoa Paired first and last appearances for Trilobita Paired first and last appearances for Malacostraca Paired first and last appearances for Porifera Paired first and last appearances for Anthozoa