<commit_before>### PyRate is a program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework. 


PyRate is licensed under a [AGPLv3 License](https://tldrlegal.com/license/gnu-affero-general-public-license-v3-(agpl-3.0)#summary).

#### The program's documentation is available here: 
* [Tutorials](https://github.com/dsilvestro/PyRate/tree/master/tutorials) (work in progress; Older [Wiki pages](https://github.com/dsilvestro/PyRate/wiki) are still available, although updated documentation is being only added to the Tutorials)
* [System requirements](https://github.com/dsilvestro/PyRate/wiki#compatibility-and-installation) to run the program and [Instructions](https://github.com/dsilvestro/PyRate/blob/master/pyrate_lib/fastPyRateC/README.md) to install the fastPyRateC library 
* For questions, suggestions or bugs [contact us](mailto:<EMAIL>)


#### The main methods are described here:

* <NAME>., <NAME>., <NAME>., <NAME>. and <NAME>. (2014) Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data. Systematic Biology, [63, 349-367](https://academic.oup.com/sysbio/article/63/3/349/1650079).

* <NAME>., <NAME>., <NAME>. (2014) PyRate: A new program to estimate speciation and extinction rates from incomplete fossil record. Methods in Ecology and Evolution, [5, 1126-1131](http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12263/abstract).
 
* See tutorials [1](https://github.com/dsilvestro/PyRate/blob/master/tutorials/pyrate_tutorial_1.md) and [2](https://github.com/dsilvestro/PyRate/blob/master/tutorials/pyrate_tutorial_2.md)

#### The RJMCMC algorithm is described here:
* <NAME>., <NAME>., <NAME>., <NAME>. (2018) Improved estimation of macroevolutionary rates from fossil data using a Bayesian framework. bioRxiv,
[doi:10.1101/316992](https://www.biorxiv.org/content/early/2018/05/09/316992)

* See tutorial [3](https://github.com/dsilvestro/PyRate/blob/master/tutorials/pyrate_tutorial_3.md)

#### The MCDD and MBD models are described here: 

* <NAME>., <NAME>., <NAME>., <NAME>. (2015) The role of clade competition in the diversification of North American canids. PNAS, [112, 8684-8689](http://www.pnas.org/content/112/28/8684).

* <NAME>., <NAME>., <NAME>., <NAME>. (2017) Bayesian estimation of multiple clade competition from fossil data. Evolutionary Ecology Research, 	[18:41-59](http://evolutionary-ecology.com/abstracts/v18/3010.html).

* <NAME>., <NAME>., <NAME>., <NAME>., <NAME>., <NAME>., <NAME>., <NAME>., <NAME>. (2017) Environmentally driven extinction and opportunistic origination explain fern diversification patterns. Scientific Reports, [7:4831](https://www.nature.com/articles/s41598-017-05263-7).

* See tutorial [4](https://github.com/dsilvestro/PyRate/blob/master/tutorials/pyrate_tutorial_4.md)


#### The DES model is described here:

* <NAME>., <NAME>., <NAME>., <NAME>. and <NAME>., <NAME>. (2016) Fossil Biogeography: A new model to infer dispersal, extinction and sampling from paleontological data. Philosophical Transactions of the Royal Society B [371:20150225](http://rstb.royalsocietypublishing.org/content/371/1691/20150225).

* See tutorial [5](https://github.com/dsilvestro/PyRate/blob/master/tutorials/pyrate_tutorial_5.md)


#### The ADE model is described here:

* <NAME>., <NAME>., <NAME>., <NAME>., <NAME>. (in press) Estimating Age-dependent Extinction: Contrasting Evidence from Fossils and Phylogenies. Systematic Biology, [doi: 10.1093/sysbio/syx082](https://academic.oup.com/sysbio/article/doi/10.1093/sysbio/syx082/4563320/Estimating-Agedependent-Extinction-Contrasting).

* See tutorial [4](https://github.com/dsilvestro/PyRate/blob/master/tutorials/pyrate_tutorial_4.md)


<commit_msg>Added ref to BDC model<commit_after>### PyRate is a program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework. 


PyRate is licensed under a [AGPLv3 License](https://tldrlegal.com/license/gnu-affero-general-public-license-v3-(agpl-3.0)#summary).

#### The program's documentation is available here: 
* [Tutorials](https://github.com/dsilvestro/PyRate/tree/master/tutorials) (work in progress; Older [Wiki pages](https://github.com/dsilvestro/PyRate/wiki) are still available, although updated documentation is being only added to the Tutorials)
* [System requirements](https://github.com/dsilvestro/PyRate/wiki#compatibility-and-installation) to run the program and [Instructions](https://github.com/dsilvestro/PyRate/blob/master/pyrate_lib/fastPyRateC/README.md) to install the fastPyRateC library 
* For questions, suggestions or bugs [contact us](mailto:<EMAIL>)


#### The main methods are described here:

* <NAME>., <NAME>., <NAME>., <NAME>. and <NAME>. (2014) Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data. Systematic Biology, [63, 349-367](https://academic.oup.com/sysbio/article/63/3/349/1650079).

* <NAME>., <NAME>., <NAME>. (2014) PyRate: A new program to estimate speciation and extinction rates from incomplete fossil record. Methods in Ecology and Evolution, [5, 1126-1131](http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12263/abstract).
 
* See tutorials [1](https://github.com/dsilvestro/PyRate/blob/master/tutorials/pyrate_tutorial_1.md) and [2](https://github.com/dsilvestro/PyRate/blob/master/tutorials/pyrate_tutorial_2.md)

#### The RJMCMC algorithm is described here:
* <NAME>., <NAME>., <NAME>., <NAME>. (2018) Improved estimation of macroevolutionary rates from fossil data using a Bayesian framework. bioRxiv,
[doi:10.1101/316992](https://www.biorxiv.org/content/early/2018/05/09/316992)

* See tutorial [3](https://github.com/dsilvestro/PyRate/blob/master/tutorials/pyrate_tutorial_3.md)

#### The MCDD and MBD models are described here: 

* <NAME>., <NAME>., <NAME>., <NAME>. (2015) The role of clade competition in the diversification of North American canids. PNAS, [112, 8684-8689](http://www.pnas.org/content/112/28/8684).

* <NAME>., <NAME>., <NAME>., <NAME>. (2017) Bayesian estimation of multiple clade competition from fossil data. Evolutionary Ecology Research, 	[18:41-59](http://evolutionary-ecology.com/abstracts/v18/3010.html).

* <NAME>., <NAME>., <NAME>., <NAME>., <NAME>., <NAME>., <NAME>., <NAME>., <NAME>. (2017) Environmentally driven extinction and opportunistic origination explain fern diversification patterns. Scientific Reports, [7:4831](https://www.nature.com/articles/s41598-017-05263-7).

* See tutorial [4](https://github.com/dsilvestro/PyRate/blob/master/tutorials/pyrate_tutorial_4.md)


#### The DES model is described here:

* <NAME>., <NAME>., <NAME>., <NAME>. and <NAME>., <NAME>. (2016) Fossil Biogeography: A new model to infer dispersal, extinction and sampling from paleontological data. Philosophical Transactions of the Royal Society B [371:20150225](http://rstb.royalsocietypublishing.org/content/371/1691/20150225).

* See tutorial [5](https://github.com/dsilvestro/PyRate/blob/master/tutorials/pyrate_tutorial_5.md)


#### The ADE model is described here:

* <NAME>., <NAME>., <NAME>., <NAME>., <NAME>. (2017) Estimating Age-dependent Extinction: Contrasting Evidence from Fossils and Phylogenies. Systematic Biology, [doi: 10.1093/sysbio/syx082](https://academic.oup.com/sysbio/article/doi/10.1093/sysbio/syx082/4563320/Estimating-Agedependent-Extinction-Contrasting).

* See tutorial [4](https://github.com/dsilvestro/PyRate/blob/master/tutorials/pyrate_tutorial_4.md)


#### The BDC model is described here:

* <NAME>., <NAME>., <NAME>. & <NAME>. (2018) Closing the gap between palaeontological and neontological speciation and extinction rate estimates. Nature Communications, [doi: 10.1038/s41467-018-07622-y](https://www.nature.com/articles/s41467-018-07622-y).

* See tutorial [4](https://github.com/dsilvestro/PyRate/blob/master/tutorials/pyrate_tutorial_4.md)


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